LiteFold/DisProt huggingface dataset:
Protein: DP01797 (UniProt O96017)
Region: residues 66	to 70
Annotation: phosphorylation display site (Disorder function)
Evidence: immunodetection assay evidence used in manual assertion
Supporting statements:
The baculovirus expressed protein, which contains high-levels of pThr68 (as measured by phospho-specific antibody) and is therefore likely to be substantially phosphorylated on T-loop residues Thr383 and Thr387, was found to be very significantly (100-fold compared to GST-CHK2-KD, 400-fold to CHK2-KD) more active than either of the kinase domain constructs over the course of the assay period (Figure 5G).
Protein: DP01797 (UniProt O96017)
Region: residues 1	to 63
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
An N-terminal fragment of human Chk2 (residues 1–225) was expressed in E. coli BL21(DE3) cells as a GST-fusion protein, purified by glutathione-affinity chromatography, and released by digestion with viral protease 3C (Pharmacia-LKB). Limited proteolysis with chymotrypsin and endoproteinase Glu-C (Promega) was performed essentially as described previously (Durocher et al. 2000). N- and C- terminal limits were determined by Edman sequencing and electrospray mass spectrometry, and the minimal chymotryptic FHA fragment (residues 64–219) was purified by anion exchange and gel filtration chromatography prior to further use in binding and crystallization experiments.
Protein: DP01799 (UniProt P49790)
Region: residues 1313	to 1390
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The amino acid specific backbone dihedral angle distributions determined from the ensemble selections (Figure S1) show that negligible secondary structure is present.
Protein: DP01799 (UniProt P49790)
Region: residues 1313	to 1390
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
To characterize the effects of Importinβ binding on Nup153FGPxFG at atomic resolution, we titrated Importinβ into a solution of 15N labeled Nup153FGPxFG and measured 1H-15N HSQC spectra at different molar ratios. Peak intensities, as well as 1HN and 15N chemical shifts of Nup153FGPxFG, were analyzed for each titration step (Figures 3 and ​S4).
Protein: DP01799 (UniProt P49790)
Region: residues 1313	to 1390
Annotation: protein binding (Molecular function)
Evidence: fluorescence resonance energy transfer evidence used in manual assertion
Supporting statements:
We added unlabeled Importinβ to the FRET labeled Nup153FGPxFG and followed the smFRET response. While the diffusion of Nup153FGPxFG in the absence and presence of Importinβ confirmed the binding of Importinβ under single molecule conditions (Figures 2 and ​andS2),S2), we detected neither substantial changes in EFRET nor in the width of the histograms indicating absence of significant changes in the distance distribution (Figure S2 shows an all F to all A negative control).
Protein: DP01799 (UniProt P49790)
Region: residues 875	to 1475
Annotation: molten globule (Structural state)
Evidence: fluorescence resonance energy transfer evidence used in manual assertion
Supporting statements:
As shown in Fig. 3 a, our measured distances are much shorter than expected for an IDP behaving like a relaxed coil (42,50). In fact, the distances are reminiscent of molten-globule or collapsed-coil behavior (23,42,51), showing that the protein stretches are compact in their native state.
Despite the different characteristics of the N-terminal stretch, a similar phenotypic property (RE) of both the N-terminal and the C-terminal stretches was observed.
Protein: DP01799 (UniProt P49790)
Region: residues 875	to 1475
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: microscopy evidence used in manual assertion
Supporting statements:
As shown in Fig. 4 a, Nup153FG indeed formed a hydrogel.
A gel was mounted on a microscope and in Fig. 4 b, we show the results of a dual color fluorescence experiment. The large transport receptor Importin β (97 kDa) added to the surrounding buffer could easily enter the gel. The smaller dextran (70 kDa) added simultaneously did not considerably penetrate the gel. These findings demonstrate that highly concentrated human Nup153FG can also form a functional hydrogel in vitro.
Protein: DP01799 (UniProt P49790)
Region: residues 875	to 1475
Annotation: amyloid fibril formation (Biological process)
Evidence: thioflavin T based fluorescence spectroscopy evidence
Supporting statements:
The ThT assay reported dramatically fastened amyloid formation kinetics of hNup153FG in buffer containing serine. Increasing serine concentrations even led to instantaneous aggregation of the protein (Fig 1A).
Protein: DP01799 (UniProt P49790)
Region: residues 875	to 1475
Annotation: amyloid fibril formation (Biological process)
Evidence: fluorescence resonance energy transfer evidence used in manual assertion
Supporting statements:
This aggregation occurred even at the single-molecule level (pM protein concentrations, see Fig 1F; supplementary Fig S2 online) and is thus extremely high under molecular crowding conditions. As enhanced aggregation also occurred in the presence of other cosolutes such as lysine, trimethylaminoxid and the large molecule polyethylene glycol 20,000, we conclude that the aggregation accelerating effect is not owing to a specific chemical functionality but rather a general phenomenon, like space restriction or sequestering of water.
Protein: DP01799 (UniProt P49790)
Region: residues 875	to 1475
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: electron microscopy evidence used in manual assertion
Supporting statements:
Figure 3 and supplementary Movie S1 online show that hNup153FG hydrogels are formed from interlaced fibres that build up a meshwork giving rise to the supramolecular architecture of a hydrogel (see supplementary Fig S3 online; supplementary Movie S2 online for yNup49FG).
To exclude artifacts that might arise from sample preparation, we confirmed these results using alternative preparation and imaging methods, namely scanning electron microscopy of heavy metal-shaded samples (Fig 3; supplementary Fig S3 online), as well as transmission electron microscopy of frozen-hydrated cryosections (supplementary Fig S5 online). We consistently observed fibrous networks within the hydrogels.
Protein: DP01801 (UniProt P04985)
Region: residues 1	to 747
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The primary focus of these experiments was to determine the degree of spatial averaging in hydrated elastin, and all results indicate that functional elastin is highly disordered.
Protein: DP01804 (UniProt P53999)
Region: residues 1	to 60
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
However, the moderate NOE signal intensities, in combination with the chemical-shift data, indicate that these regions are predominantly unstructured in nature, which suggests either a pliable structure or exchange between the random-coil and more ordered structures. Also upon interaction with VP16ad, we did not observe significant changes in NOE contacts for PC4ntd, which suggest that PC4ntd is highly flexible and mostly unstructured both in the free form and in the complex with the activator.
Protein: DP01804 (UniProt P53999)
Region: residues 1	to 60
Annotation: regulation of DNA binding (Biological process)
Evidence: glutathione S-transferase pull-down assay evidence used in manual assertion
Supporting statements:
Remarkably, the presence of PC4ntd can either be stimulatory (VP16 interaction), neutral (dsDNA), or inhibitory (ssDNA) on the PC4ctd functions. The apparent Kd values at room temperature for the interaction with PC4 and PC4ctd, respectively, are 391 ± 80 and 991 ± 195 nM for VP16ad, 55 ± 33 and 41 ± 21 nM for dsDNA, and 25 ± 4 nM and 0.98 ± 0.23 nM for ssDNA.
Protein: DP01804 (UniProt P53999)
Region: residues 1	to 60
Annotation: protein binding (Molecular function)
Evidence: glutathione S-transferase pull-down assay evidence used in manual assertion
Supporting statements:
Remarkably, the presence of PC4ntd can either be stimulatory (VP16 interaction), neutral (dsDNA), or inhibitory (ssDNA) on the PC4ctd functions. The apparent Kd values at room temperature for the interaction with PC4 and PC4ctd, respectively, are 391 ± 80 and 991 ± 195 nM for VP16ad, 55 ± 33 and 41 ± 21 nM for dsDNA, and 25 ± 4 nM and 0.98 ± 0.23 nM for ssDNA.
Protein: DP01804 (UniProt P53999)
Region: residues 1	to 60
Annotation: self-regulatory activity (Disorder function)
Evidence: radioisotope assay evidence used in manual assertion
Supporting statements:
The modulatory role for PC4ntd, as observed for the other interactions, is underscored by the small increase in unwinding activity upon the mutation of the lysine residues within the amino-terminal domain and reflects the higher unwinding activity of PC4ctd in comparison with full-length PC4.
Protein: DP01805 (UniProt P40855)
Region: residues 1	to 165
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
We carried out limited proteolysis experiments with trypsin and V8 protease. Facts suggest that the C-terminal half of Pex19p is a relatively stable domain. On the other hand, the N-terminal half of Pex19p was susceptible to proteolytic degradation, which suggests that it has a flexible conformation.
Protein: DP01805 (UniProt P40855)
Region: residues 1	to 165
Annotation: protein binding (Molecular function)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
We performed cell-free translation assays for each half as well as the full-length protein. Pex19p(N-half) bound to Pex3p-(34–373). Binding of Pex19p to PMP22, PMP70, and Pex16p requires more than the C-terminal half-sized domain of Pex19p.
Protein: DP01805 (UniProt P40855)
Region: residues 1	to 165
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
His10-Pex19p(N-half) displayed little secondary structure; its α-helix content was estimated as 6%. The additive spectrum of His10-Pex19p(N-half) plus Pex19p(C-half) almost coincided with that of the full-length His10-Pex19p. Therefore, we conclude that both halves of Pex19p maintain their respective three-dimensional structures as in the corresponding regions of the full-length His10-Pex19p.
Protein: DP01805 (UniProt P40855)
Region: residues 1	to 165
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
We performed cell-free translation assays for each half as well as the full-length protein. Pex19p(N-half) bound to Pex3p-(34–373). Binding of Pex19p to PMP22, PMP70, and Pex16p requires more than the C-terminal half-sized domain of Pex19p.
Protein: DP01805 (UniProt P40855)
Region: residues 4	to 182
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence used in manual assertion
Supporting statements:
All PEX19 peptides from the N-terminal region A4 - L182, as well as the C-terminal end F278 - L297 were already fully deuterated after 30 seconds incubation in D2O (Figure 3A and Figure S1) indicating that these areas, consisting of two thirds of the protein, are highly solvent exposed and structurally disordered
Protein: DP01805 (UniProt P40855)
Region: residues 278	to 297
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence used in manual assertion
Supporting statements:
All PEX19 peptides from the N-terminal region A4 - L182, as well as the C-terminal end F278 - L297 were already fully deuterated after 30 seconds incubation in D2O (Figure 3A and Figure S1) indicating that these areas, consisting of two thirds of the protein, are highly solvent exposed and structurally disordered
Protein: DP01806 (UniProt Q67953)
Region: residues 1	to 108
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 13Cα chemical-shift index (Supplementary Fig. 2b), an indicator of secondary structure27, confirmed that preS1 had only short segments of partially populated α-helical or extended structure. Thus, the 108-residue preS1 domain is an IDP
Protein: DP01806 (UniProt Q67953)
Region: residues 1	to 108
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We report here atomic-resolution descriptions of the binding thermodynamics and structural biology of the interaction between preS1 and the EAR domain of g2-adaptin. NMR, protein engineering, X-ray crystallography and MS showed that preS1 contains multiple g2-EAR–binding motifs that mimic the membrane-trafficking motifs (and binding modes) of host proteins.
Protein: DP01806 (UniProt Q67953)
Region: residues 1	to 108
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD analysis showed that the purified preS1, which was largely unstructured in aqueous solution, acquired a significant (16%) alpha-helical structure when analyzed in 50% trifluoroethanol or 20 mM SDS. The results suggest that the preS1 assumes a mainly unstructured conformation and may form induced secondary structures upon binding to target proteins or under hydrophobic environment.
Protein: DP01806 (UniProt Q67953)
Region: residues 1	to 108
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The spectrum shows narrow chemical-shift dispersion in both dimensions, indicating that it is largely unstructured with no tertiary structure under a nondenaturing experimental condition.
Protein: DP01806 (UniProt Q67953)
Region: residues 66	to 92
Annotation: protein binding (Molecular function)
Evidence: cell-based assay evidence used in manual assertion
Supporting statements:
IL-6 and Not IL-6R Carries the Binding Site for the preS(21-47)
Segment of the HBV env Protein.
This search revealed that interleukin 6 contains recognition sites for the preS(21-47) sequence and mediates HBV-cell interactions. Thus, HBV belongs to a group of viruses utilizing cytokines or cytokine receptors for replication and interference with the host immune system.
Protein: DP01806 (UniProt Q67953)
Region: residues 72	to 90
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The most prominent pre-structured region encompasses
residues 27–45 and contains two helical turn motifs
(black bars in Fig. 6) composed of residues Pro 32 –Ala 36
and Pro 41 –Phe 45 , both of which are located within the
putative HBD (residues 21–47) proposed by other techniques.
Location of pre-structured regions (this work) and previously suggested functional domains in preS1. Pre-structured regions
are shown above the amino acid sequence of preS1 N-terminal 60 residues and are indicated by black, gray, or hatched bars. The most
prominently pre-structured region is formed by residues 27–45.
Protein: DP01807 (UniProt P49005)
Region: residues 42	to 53
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The crystal structure of POLD2 (p50) and N-terminal domain of POLD3 (p66N) has been solved.
"The density was not observed for the total of 56 residues, including p50 amino acid residues 42–53, 102–122, 251–253, 382–387 and 466–469."
"each molecule contained all amino acid residues of p66N and p50, except disordered regions in four loops and the C-terminal tail of p50."
Cross-references: PDB:3E0J
Protein: DP01807 (UniProt P49005)
Region: residues 102	to 122
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The crystal structure of POLD2 (p50) and N-terminal domain of POLD3 (p66N) has been solved.
"The density was not observed for the total of 56 residues, including p50 amino acid residues 42–53, 102–122, 251–253, 382–387 and 466–469."
"each molecule contained all amino acid residues of p66N and p50, except disordered regions in four loops and the C-terminal tail of p50."
Cross-references: PDB:3E0J
Protein: DP01808 (UniProt Q9I832)
Region: residues 90	to 120
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
the region encompassing residues 90–120 exhibitsincreased backbone flexibility as evidenced by both decreasedR2values and more negative heteronuclear NOEs.
Protein: DP01808 (UniProt Q9I832)
Region: residues 90	to 120
Annotation: order to disorder (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Concluding, the PRE (paramagnetic relaxation enhancement) data indicate that the central segment (residues 90–150) of OPN expands upon heparin binding, comparable to an “unfolding-upon-binding”event.
Protein: DP01808 (UniProt Q9I832)
Region: residues 1	to 264
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In contrast to the uniformity observed in ubiquitin, qOPN rates present a distinctive profile. This is particularly noticeable in the transverse rates (Fig. 6A), where three regions encompassing residues 120–132, 140–175 and 176–190 are less flexible (higher rates) [82], [88].
Protein: DP01817 (UniProt Q15910)
Region: residues 346	to 421
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Recombinant PRC2 was much less prone to aggregation when EZH2 was expressed in two parts (EZH2N 1–385 and EZH2C 421–746), removing the linker between the end of MCSS and the beginning of SANT2, thus 28 residues are missing from the middle lobe as indicated in Fig. 1d.
Cross-references: PDB:5HYN
Protein: DP01817 (UniProt Q15910)
Region: residues 480	to 514
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region are missing in two different x-ray experiments
Cross-references: PDB:5HYN
Protein: DP01817 (UniProt Q15910)
Region: residues 730	to 746
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
However, the 17 C-terminal residues including most of the post-SET domain were not observed.
Cross-references: PDB:4MI0
Protein: DP01817 (UniProt Q15910)
Region: residues 183	to 210
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region lacks electron density in the PDB structure of the Human Polycomb Repressive Complex 2 (PRC2) with oncogenic histone H3K27M peptide, indicating it is disordered.
Cross-references: PDB:5HYN
Protein: DP01817 (UniProt Q15910)
Region: residues 732	to 746
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model consisted of one EZH2-SET domain (chain A) containing a total of 209 residues, 6 zinc atoms, 159 water molecules, and 1 sulfate ion. 96.6% of residues are in the most favored region of the Ramachandran plot, and 100% are in the allowed region. The C-terminal residues 737-751 are disordered. Due to lack of representative electron density, internal residues 598-603 and the side chain atoms of residues Q559, D597, V604, K616, D625, K661, D664, K665, and M667 were omitted.
Cross-references: PDB:4MI5
Protein: DP01817 (UniProt Q15910)
Region: residues 733	to 746
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the isolated structure, residues 727–729 partially fold into the substrate-binding channel and thereafter the chain is disordered.
Cross-references: PDB:5HYN
Protein: DP01817 (UniProt Q15910)
Region: residues 386	to 420
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Recombinant PRC2 was much less prone to aggregation when EZH2 was expressed in two parts (EZH2N 1–385 and EZH2C 421–746), removing the linker between the end of MCSS and the beginning of SANT2, thus 28 residues are missing from the middle lobe as indicated in Fig. 1d.
Cross-references: PDB:5HYN
Protein: DP01817 (UniProt Q15910)
Region: residues 1	to 10
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region lacks electron density in the PDB structure of the Human Polycomb Repressive Complex 2 (PRC2) with oncogenic histone H3K27M peptide, indicating it is disordered.
Cross-references: PDB:5HYN
Protein: DP01817 (UniProt Q15910)
Region: residues 480	to 514
Annotation: disorder to order (Structural transition)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
When bound to substrate nucleosome, the amino-acids-497-to-511 segment in EZH2 forms an alpha helix that is sandwiched between the nucleosomal DNA, the EZH2 (SET) domain, and the H3 tail, which we therefore call the EZH2 bridge helix (Fig. 2A). Its tripartite interaction results in the stabilization of this EZH2 region that has otherwise been unstructured or highly flexible in previous structural studies of PRC2 lacking nucleosome substrate (22, 27, 28).
Cross-references: EMDB:EMD-21707
PDB:6WKR
Protein: DP01817 (UniProt Q15910)
Region: residues 487	to 513
Annotation: nucleosome binding (Molecular function)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
In the present structure, we have identified and modeled a region of EZH2 rich in lysines and arginines (amino acids 487 to 513) that interacts extensively with the nucleosomal DNA.
Cross-references: EMDB:EMD-21707
PDB:6WKR
Protein: DP01817 (UniProt Q15910)
Region: residues 507	to 511
Annotation: methylation display site (Disorder function)
Evidence: liquid chromatography coupled with tandem mass spectrometry evidence used in manual assertion
Supporting statements:
The region includes lysines K509 and K510 within the IQLKK motif of EZH2, which had been predicted to be disordered and had been shown to be modified during PRC2 automethylation (25, 26). Mass spectrometry analysis of our PRC2-AJ1–450 sample confirms the presence of dimethylation of both K509 and K510.
Cross-references: EMDB:EMD-21707
PDB:6WKR