LiteFold/DisProt huggingface dataset:
Protein: DP01762 (UniProt P03714)
Region: residues 53	to 61
Annotation: virion assembly (Biological process)
Evidence: functional complementation evidence used in manual assertion
Supporting statements:
Fig. S3. Overlays of gpFII used to build gpFII oligomeric models. (A) Overlay of gpFII to an Hcp1 monomer. (B) Overlay of gpFII to residues 167–326 of Mu gp44. The structural overlay of gpFII and Hcp1 and gp44 is displayed in the center and the individual monomers are displayed on either side. (C ) Summary of all structural alignments discussed in this work. Initial alignments were made using DaliLite (1) or FATCAT (2) and then refined in Swiss-PDBViewer (3). 1. Holm L, Park J (2000) DaliLite workbench for protein structure comparison. Bioinformatics 16:566–567. 2. Ye Y, Godzik A (2003) Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics 19 (suppl 2):ii246–ii255. 3. Guex N, Peitsch MC (1997) SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis 18:2714–2723. Fig. S4. In vitro titration of the Δ53–61 gpFII protein. Equal volumes of purified WT and Δ53–61 gpFII protein were mixed in vitro before testing for com- plementation of an FIIam extract. WT protein was kept at a concentration of 1 μM and Δ53–61 gpFII protein concentration was varied from 0.1 to 50 μM. Even at very low ratios, e.g., 1:1, the Δ53–61 gpFII protein was able to exert a dominant negative effect on WT protein.
Protein: DP01762 (UniProt P03714)
Region: residues 1	to 24
Annotation: virion assembly (Biological process)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
Deletions of the N-terminal unstructured region, which is predicted to lie on the top surface, caused no dominant-negative behavior. Furthermore, combining an N-terminal deletion with the Δ46–61 deletion resulted in no dominant-negative phenotype, implying that activity of the putative head-binding gpFII N terminus is required for imparting a dominant negative phenotype.
Taken together, the behavior of the gpFII mutants supports our model of the oligomeric structure of gpFII within phage particles. Mutants bearing amino acid substitutions or deletions on the putative bottom surface displayed dominant-negative phenotypes because they could still bind heads and thereby inhibit the assembly of phage even in the presence of WT gpFII. By contrast, deletion of the N-terminal region, which is expected to be involved in head-binding, caused loss of activity without a dominant-negative effect.
Protein: DP01762 (UniProt P03714)
Region: residues 1	to 24
Annotation: virion assembly (Biological process)
Evidence: transmission electron microscopy evidence used in manual assertion
Supporting statements:
Deletions of the N-terminal unstructured region, which is predicted to lie on the top surface, caused no dominant-negative behavior. Furthermore, combining an N-terminal deletion with the Δ46–61 deletion resulted in no dominant-negative phenotype, implying that activity of the putative head-binding gpFII N terminus is required for imparting a dominant negative phenotype.
Taken together, the behavior of the gpFII mutants supports our model of the oligomeric structure of gpFII within phage particles. Mutants bearing amino acid substitutions or deletions on the putative bottom surface displayed dominant-negative phenotypes because they could still bind heads and thereby inhibit the assembly of phage even in the presence of WT gpFII. By contrast, deletion of the N-terminal region, which is expected to be involved in head-binding, caused loss of activity without a dominant-negative effect.
Protein: DP01763 (UniProt E6Y5X0)
Region: residues 232	to 321
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Indeed, while the CD spectrum of Jbtx in the absence of SDS presented a minimum centred at ca. 200 nm, characteristic of a random coil conformation, in the presence of 3–15 mM SDS this feature shifted to ∼205–210 nm, with the insurgence of a minimum at around 207 nm, typical of the presence of α-helices and β-sheets; consistently, the ellipticity increase around 195 nm suggests the acquisition of secondary structure by Jbtx in the presence of SDS micelles.
Protein: DP01763 (UniProt E6Y5X0)
Region: residues 232	to 321
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Superimposition of the NMR spectra of Jbtx in the absence and presence of bicelles revealed some changes in the chemical shift of a number of amino acids, even though the characteristic profile of an intrinsically disordered protein was maintained (Fig. 7B and D).
Protein: DP01763 (UniProt E6Y5X0)
Region: residues 232	to 321
Annotation: lipid binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Superimposition of the NMR spectra of Jbtx in the absence and presence of bicelles revealed some changes in the chemical shift of a number of amino acids, even though the characteristic profile of an intrinsically disordered protein was maintained (Fig. 7B and D).
Protein: DP01763 (UniProt E6Y5X0)
Region: residues 232	to 321
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Indeed, while the CD spectrum of Jbtx in the absence of SDS presented a minimum centred at ca. 200 nm, characteristic of a random coil conformation, in the presence of 3–15 mM SDS this feature shifted to ∼205–210 nm, with the insurgence of a minimum at around 207 nm, typical of the presence of α-helices and β-sheets; consistently, the ellipticity increase around 195 nm suggests the acquisition of secondary structure by Jbtx in the presence of SDS micelles.
Compared to the CD spectrum of free Jbtx, which showed a pronounced negative peak around 200 nm typical of random coil structures, the CD spectrum of Jbtx in the presence of negatively charged bicelles shows a reduced intensity in the random coil region, indicative of an increase in the polypeptide secondary structure content (Fig. 7A).
Protein: DP01763 (UniProt E6Y5X0)
Region: residues 232	to 321
Annotation: lipid binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Indeed, while the CD spectrum of Jbtx in the absence of SDS presented a minimum centred at ca. 200 nm, characteristic of a random coil conformation, in the presence of 3–15 mM SDS this feature shifted to ∼205–210 nm, with the insurgence of a minimum at around 207 nm, typical of the presence of α-helices and β-sheets; consistently, the ellipticity increase around 195 nm suggests the acquisition of secondary structure by Jbtx in the presence of SDS micelles.
Compared to the CD spectrum of free Jbtx, which showed a pronounced negative peak around 200 nm typical of random coil structures, the CD spectrum of Jbtx in the presence of negatively charged bicelles shows a reduced intensity in the random coil region, indicative of an increase in the polypeptide secondary structure content (Fig. 7A).
Protein: DP01763 (UniProt E6Y5X0)
Region: residues 232	to 321
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H,15N-HSQC NMR spectrum of Jbtx, recorded in the absence and presence of SDS below and above its CMC (0.25 and 10–15 mM, respectively, Fig. 3C) reveals that the protein does not change its structure in the presence of SDS below its CMC, while large chemical shifts modifications are observed in solutions containing SDS above the CMC, indicative of structural conformational changes.
Protein: DP01763 (UniProt E6Y5X0)
Region: residues 232	to 321
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
The SDS/PAGE profile of the final purified protein is shown in Fig. 1C. Notably, although the predicted molecular mass determined from the amino acid sequence of Jaburetox with the six-histidine extension is 11 kDa, the protein exhibited a 2 kDa shift in the SDS/PAGE and migrated as a 13 kDa polypeptide.
Protein: DP01763 (UniProt E6Y5X0)
Region: residues 232	to 321
Annotation: disorder (Structural state)
Evidence: particle scattering evidence used in manual assertion
Supporting statements:
The hydrodynamic radius measured by QELS is 2.7 ± 0.1 nm. This value is larger than the expected value of 1.74 nm for a well-folded protein of the same molecular mass [31], and is very close to that predicted for intrinsically disordered pre-molten globular proteins (2.46 nm) or random coil proteins (2.77 nm) of the same molecular mass [31].
Protein: DP01763 (UniProt E6Y5X0)
Region: residues 232	to 321
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum of the protein under native conditions (Fig. 2A) presents features typical of a random coil conformation, with a minimum centered at 200 nm.
Protein: DP01763 (UniProt E6Y5X0)
Region: residues 232	to 321
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Figure 4 shows the 1H-15N heteronuclear single quantum coherence (HSQC) spectrum of Jaburetox. The spectrum is characterized by low signal dispersion in the proton dimension, indicative of a disordered state of the protein.
The NMR-derived solution structural ensemble of Jaburetox, featuring large values of rmsd, confirms its disordered fold, as predicted by earlier [23] and the present bioinformatics studies (Fig. 3).
Cross-references: BMRB:19830
PDB:2mm8
Protein: DP01763 (UniProt E6Y5X0)
Region: residues 232	to 321
Annotation: molecular function inhibitor activity (Molecular function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
As shown in Fig. 4, the lethal effect of Jaburetox-2Ec was time dependent, with a lag phase of 3–4 days and 100% mortality being reached after 11 days. Mortality of canatoxin-fed insects showed a slower rate with 20% insects still alive at the end of the experiments.
A lag phase of 2 days was observed before lethality of the insects and on sixth day, after ingesting a total of 47 μg jaburetox-2Ec, all larvae were dead (Fig. 5B).
In this context it is noteworthy to mention that neurotoxic symptoms (such as paralysis and uncoordinated movements of limbs and antenna) are seen in R. prolixus intoxicated by Jaburetox-2Ec.
Protein: DP01764 (UniProt O95718)
Region: residues 169	to 194
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Resonances for 15 of the 20 residues C-terminal of Arg-174 could not be assigned since sequential and medium-range NOEs are either weak or absent.
Furthermore, the analysis establishes that the CTE does not adopt a regular secondary structure, but has chemical shifts characteristic of a random coil. The absence of long-range NOEs and most sequential NOEs for residues C-terminal of Arg-174 also provides strong evidence that the CTE is unstructured.
The region after helix-2 shows no sign of secondary structure and may be disordered (see below).
Protein: DP01765 (UniProt Q9NQA5)
Region: residues 587	to 725
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
As often observed for intrinsically unstructured proteins, all expressed fragments migrated in the SDS gel slower than expected based on amino acid sequence, including V5c20.
Protein: DP01765 (UniProt Q9NQA5)
Region: residues 587	to 725
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Spectra of V5c20 (residues 587-725) with and without GB1-tag display a characteristic dip around 200 nm for proteins classified as intrinsically disordered.
Protein: DP01765 (UniProt Q9NQA5)
Region: residues 587	to 725
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Several auxiliary calcium-binding proteins, such as 80K-H protein, calbindin-D28K and calmodulin, were shown to bind in vivo to the C-terminus of TRPV5 and dramatically affect calcium reabsorption in kidney.
Protein: DP01767 (UniProt Q9H1D0)
Region: residues 655	to 725
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The remainder of the peaks belongs to TRPV6 and the linker region (thrombin cleavage site LVPRGS). Lower intensity or absence of the peaks may be indicative of flexibility of the protein. Dispersion of the chemical shifts is quite low as most of the peaks are located in the region of the spectrum characteristic for random coil and alpha-helical proteins (1H chemical shift 7.6–8.2).
Protein: DP01767 (UniProt Q9H1D0)
Region: residues 655	to 725
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Upon addition of calmodulin to V6c7 at 1:1 molar ratio the followings changes were observed: approximately 20 new peaks appeared in the spectrum, several peaks became more intense and spectral dispersion generally increased.
Protein: DP01767 (UniProt Q9H1D0)
Region: residues 655	to 725
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
As often observed for intrinsically unstructured proteins, all expressed fragments migrated in the SDS gel slower than expected based on amino acid sequence, including V6c7 (residues 655-725).
Protein: DP01768 (UniProt P58753)
Region: residues 15	to 35
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
TIRAP PBM transitions from a disordered to a helical conformation in the presence of either zwitterionic micelles or monodispersed PIs.
Protein: DP01769 (UniProt Q8WUG5)
Region: residues 112	to 216
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H,15N HSQC spectrum of hLCN2-R-NTD exhibits the distinctive narrow 1HN dispersion of IDPs. Surprisingly, the spectrum also exhibits unusually broad resonances for an IDP, which would indicate that hLCN2-R-NTD, although devoid of any stable secondary or tertiary structures, experiences significant conformational exchange on the micro-to-millisecond timescale.
Protein: DP01769 (UniProt Q8WUG5)
Region: residues 112	to 216
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
When performing a 1H,15N HSQC-based titration of 15N-labeled hLCN2-R-NTD with unlabeled NGAL many resonances disappear upon the addition of unlabeled NGAL whereas only very limited chemical shift changes can be observed. This type of signal decrease is often observed in complexes involving one or more disordered partners, hampering the direct characterization of the bound state.
Protein: DP01769 (UniProt Q8WUG5)
Region: residues 112	to 216
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
After refolding, the protein is pure, soluble, and appears on the size exclusion chromatography profile to have an hydrodynamic radius consistent with a monomeric intrinsically disordered protein (IDP) of this molecular weight.
Protein: DP01769 (UniProt Q8WUG5)
Region: residues 112	to 216
Annotation: protein binding (Molecular function)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
To determine whether hLCN2-R-NTD can interact with NGAL, we first used ITC. hLCN2-R-NTD binds to NGAL with an affinity (KD) of 10 μm and a stoichiometry of 1 to 1. Noteworthy, after being loaded with ferric-enterobactin, NGAL is no longer able to interact with hLCN2-R-NTD, suggesting that enterobactin and hLCN2-R-NTD bind to the same site on NGAL.
Protein: DP01770 (UniProt P50402)
Region: residues 46	to 187
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Analysis of the NMR 1H–15N HSQC spectrum of refolded EmN showed that this emerin fragment is only partially structured. Indeed, about 50 HSQC signals show a nonrandom coil 1H chemical shift and/or correspond to positive 1H → 15N NOE values (Figure 1D). Most of these signals can be assigned to the emerin LEM domain based on previous 1H chemical shift assignments (BMRB entry 5074). The remaining HSQC signals have a 1H chemical shift comprised between 7.8 and 8.4 ppm (Figure 1D).
The authors refers as LEM domain to the 1-45 region.
Protein: DP01770 (UniProt P50402)
Region: residues 67	to 170
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Here we report 1H, 15N, 13CO, 13Cα and 13Cβ NMR chemical shift assignments of the emerin fragment from residue 67 to residue 170, which is sufficient for nuclear localization and involved in lamin A binding. Chemical shift analysis confirms that this fragment is intrinsically disordered in 0 and 8 M urea.
The limited chemical shift dispersion of the 1H–15N HSQC signals, particularly in the 1H dimension (between 7.6 and 8.7 ppm), indicates that the emerin fragment is not folded in the NMR experimental conditions (20 mM phosphate, 30 mM NaCl, pH 6.5).
Cross-references: BMRB:26654
Protein: DP01770 (UniProt P50402)
Region: residues 95	to 99
Annotation: amyloid fibril formation (Biological process)
Evidence: natural variation mutant evidence used in manual assertion
Supporting statements:
EmN Variants del95–99 and Q133H Occurring in EDMD Are Impaired in Their Capacity to Self-assemble
Observation by negative staining EM of the different variants after incubation at a concentration higher than 300 µM and a temperature of 65 °C for 1 h confirmed that, if del95–99 was unable to form filaments under these conditions (data not shown), Q133H and P183T self-assembled into filaments (Figure 6). Filaments obtained from variant P183T were indistinguishable from wild-type filaments, whereas filaments formed by Q133H at a similar time point were systematically shorter and less regular.
Altogether, these experiments suggest that P183H has the strongest capacity to self-assemble or aggregate, whereas Q133H and then del95–99 have the lowest capacities to form filament-like structures.
Protein: DP01770 (UniProt P50402)
Region: residues 131	to 135
Annotation: amyloid fibril formation (Biological process)
Evidence: natural variation mutant evidence used in manual assertion
Supporting statements:
EmN Variants del95–99 and Q133H Occurring in EDMD Are Impaired in Their Capacity to Self-assemble
Observation by negative staining EM of the different variants after incubation at a concentration higher than 300 µM and a temperature of 65 °C for 1 h confirmed that, if del95–99 was unable to form filaments under these conditions (data not shown), Q133H and P183T self-assembled into filaments (Figure 6). Filaments obtained from variant P183T were indistinguishable from wild-type filaments, whereas filaments formed by Q133H at a similar time point were systematically shorter and less regular.
Altogether, these experiments suggest that P183H has the strongest capacity to self-assemble or aggregate, whereas Q133H and then del95–99 have the lowest capacities to form filament-like structures.
Protein: DP01771 (UniProt P78560)
Region: residues 95	to 136
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
 The terminal residues 1–3 and 95–136 could not be assigned at all, as they appear unstructured and their amide protons exchange rapidly with the solvent.
Protein: DP01773 (UniProt P98170)
Region: residues 241	to 254
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The N terminus (residues 241–254) and C terminus (residues 345–356) corresponding to the amino acids outside of the Bir3 domain are disordered.
Cross-references: PDB:1F9X
Protein: DP01773 (UniProt P98170)
Region: residues 345	to 356
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The N terminus (residues 241–254) and C terminus (residues 345–356) corresponding to the amino acids outside of the Bir3 domain are disordered.
Cross-references: PDB:1F9X
Protein: DP01774 (UniProt O54928)
Region: residues 175	to 244
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H-15N HSQC spectrum of mSOCS5 175-244 is characteristic of a largely disordered protein, with the amide proton shifts confined to 6.9–8.9 ppm. While IDPs usually have uniformly sharp resonances, these spectra displayed a diversity of peak intensities and peak shapes, indicating conformational heterogeneity. Residues Asp225–Ile233 are helical, while the N-terminal region shows random coil Cα chemical shifts.
Protein: DP01774 (UniProt O54928)
Region: residues 175	to 244
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The conserved N-terminal region in SOCS5 (SOCS5175-244) facilitates a direct interaction with the kinase domain of JAK and has therefore been designated the JAK interaction region (JIR).The KD for the interaction of SOCS5 JIR with the kinase domain of JAK1 was found to be 0.5 μM.
Protein: DP01774 (UniProt O54928)
Region: residues 175	to 244
Annotation: phosphorylation display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Using mass spectrometry, we identified Ser211 within the JAK interaction region (JIR) of SOCS5, as a candidate phosphorylation site. A high confidence peptide corresponding to phosphorylated Ser211 was identified with a MaxQuant score of 143.25.
Protein: DP01775 (UniProt P53632)
Region: residues 128	to 160
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Missing electron density
Cross-references: PDB:4U4C
Protein: DP01775 (UniProt P53632)
Region: residues 1	to 160
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Due to significant sample degradation during purification (Fig. S1), we were not able to isolate a complex consisting of full-length forms of Trf4p and Air2p. We therefore worked with Trf4p/Air2p subcomplexes, where the proteolytically sensitive N and C termini of both proteins were removed.
Protein: DP01775 (UniProt P53632)
Region: residues 1	to 160
Annotation: localization (Biological process)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Colocalization by tethering for increasing the local effective concentrations of Trf4 and Air2, promoting   synergistic binding to Mtr4 (ref. PubMedID: 25175027).
Protein: DP01775 (UniProt P53632)
Region: residues 1	to 160
Annotation: protein binding (Molecular function)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Residues 121–127 interact with Mtr4 DExH-helicase core (ref. PubMed ID: 25175027)
Cross-references: imex : IM-15808-1