LiteFold/DisProt huggingface dataset:
Protein: DP00003 (UniProt P03265)
Region: residues 294	to 334
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Five sections of the polypeptidechain are either invisible, or poorly defined in the electron density map. For the first molecule of the dimer in the asymmetric unit they are A174 to A179 (the N terminus of the C-terminal domain), A294 to A334, A401 to A405, A427 to A432 and A454 to A464 whilst for the second molecule they are B174 to B179, B293 to B334, B344 to B349, B401 to B405 and B454 to B464.
Cross-references: PDB:1ADV
PDB:1ADU
Protein: DP00003 (UniProt P03265)
Region: residues 454	to 464
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Five sections of the polypeptidechain are either invisible, or poorly defined in the electron density map. For the first molecule of the dimer in the asymmetric unit they are A174 to A179 (the N terminus of the C-terminal domain), A294 to A334, A401 to A405, A427 to A432 and A454 to A464 whilst for the second molecule they are B174 to B179, B293 to B334, B344 to B349, B401 to B405 and B454 to B464.
Cross-references: PDB:1ADV
PDB:1ADU
Protein: DP00004 (UniProt P49913)
Region: residues 134	to 170
Annotation: disorder (Structural state)
Evidence: near-UV circular dichroism evidence used in manual assertion
Supporting statements:
the CD spectrum of LL-37 in water exhibits a minimum around 200 nm, which is indicative of a highly disordered conformation
Protein: DP00004 (UniProt P49913)
Region: residues 134	to 170
Annotation: disorder to order (Structural transition)
Evidence: near-UV circular dichroism evidence used in manual assertion
Supporting statements:
Taken together, this highly cooperative concentration-dependent helix-coil equilibrium is highly reminiscent of the monomer-oligomer transitions common to peptide sequences capable of forming amphipathic α-helices (e.g. melittin; Ref. 27).
15 mmNaCl affects the structure of LL-37 to a very limited extent (Fig. 2 B), and replacement of Na+ with Mg2+ does not have any effect on the structural transitions observed, which shows that the structural changes are predominantly caused by the SO42−, HCO3−, and CF3CO2−anions.
Protein: DP00004 (UniProt P49913)
Region: residues 134	to 170
Annotation: cytolysis (Biological process)
Evidence: experimental phenotypic evidence used in manual assertion
Supporting statements:
The helical, oligomeric conformation of LL-37 is apparently a requirement for activity, since the highest antibacterial activity correlates to maximal helical content, while intermediate and low activities correspond to less helical content and disordered secondary structure (Fig. 5).
The minimal inhibitory concentration of LL-37 againstE. coli is 5 μm, and at 13–25 μm the peptide is cytotoxic against several eukaryotic cells.
The cytotoxic effect of LL-37 was determined by the ability of intracellular eukaryotic esterases to hydrolyze fluorescein diacetate (FDA) to free fluorescein, followed by flow cytometric analysis (23).
Our data show that the active helical conformation of LL-37 is cytotoxic to eukaryotic cells in the ion compositions and at pH values that are encountered under physiological conditions.
Protein: DP00004 (UniProt P49913)
Region: residues 150	to 162
Annotation: amyloid fibril formation (Biological process)
Evidence: electron microscopy evidence used in manual assertion
Supporting statements:
We found that hLL-3717–29 formed long (several micrometers and longer), ribbon-like, fibrils, visualized using transmission electron microscopy (TEM) (Fig. 2).
Cryogenic electron microscopy (CryoEM) showed that the wide (few hundred nanometers) fibrils are composed of lateral association of thinner fibrils (Supplementary Fig. 4).
Protein: DP00004 (UniProt P49913)
Region: residues 150	to 162
Annotation: amyloid fibril formation (Biological process)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Our determination of the crystal structure of hLL-3717–29 at 1.35 Å resolution, revealed self-assembly of amphipathic helices into a densely packed and elongated hexameric structure forming a central pore (Table 1, Fig. 3 and Supplementary Movie 1). 
Cross-references: PDB:6S6M
Protein: DP00005 (UniProt P03045)
Region: residues 1	to 107
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Using NMR spectroscopy, we also show that N is disordered in solution.
Heteronuclear magnetic resonance experiments demonstrate that N is a disordered protein.
 It can be concluded, therefore, that the full-length N protein and its smaller fragments are disordered in solution.
Protein: DP00005 (UniProt P03045)
Region: residues 1	to 107
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
Small-angle X-ray scattering (SAXS) was used to characterize the bacteriophage  λ N protein, a 107 residue intrinsically disordered protein (IDP) that functions as a transcriptional antitermination factor.
The average radius of gyration from these measurements was 38 ± 3.5 Å, significantly larger than the value predicted for a denaturant-unfolded protein of 107 residues (31 ± 0.1 Å from Eq. (1) and the experimental data compiled by Kohn et al.13).
Protein: DP00005 (UniProt P03045)
Region: residues 1	to 107
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
This suggests that N exists in solution as an unfolded protein.
This conclusion is also supported by circular dichroism (CD) measurements of the uncomplexed N protein. Figure 3B shows that free N protein at 20 °C manifests only a weak CD signal at 223 nm, corresponding to a calculated (from CD) α-helix content of approximately 18%. However, further CD measurements showed that this level of apparent secondary structure is not significantly altered by changing the temperature, and CD melting curves showed that no cooperative melting occurs between 20 and 95 °C (M.R.V.G., unpublished results).
These observations are consistent with the existence of N in solution as an essentially unstructured molecule containing some (fluctuating and transient) secondary structure (Psitsyn, 1987; Kim & Baldwin, 1990).
We have shown above that N protein exists in solution as an unfolded (essentially random coil) molecule.
Protein: DP00005 (UniProt P03045)
Region: residues 1	to 107
Annotation: single-stranded RNA binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Binding of Nonspecific RNA Does Not Induce α-Helical Structure in N Protein. In principle, the change in secondary structure that occurs when N binds to boxB RNA could be a requirement for (or the result of) specific binding. However, it could also be a trivial consequence of the binding of N to any RNA or DNA oligonucleotide. To test the latter hypothesis, we measured the CD spectrum of N protein bound to the nonspecific (scrambled) single-stranded RNA oligomer used in the binding studies (above). Based on the measured nonspecific Kd of ∼1 × 10-6 M for this oligomer (Figure 2C and Table 1), the RNA oligomer concentration that was used in this experiment should have formed a complex with ∼70% of the total N protein present. Figure 5A shows no observable change in ellipticity for either the N protein or the RNA component on nonspecific complex formation. We conclude that the N protein binds nonspecific RNA in essentially its unstructured solution form.
Binding of nonspecific RNA is assessed using CD, and authors specify that ∼70% of N should be complexed with the RNAs used, therefore it is not possible to determine which part of the protein is specifically involved in the binding.
Protein: DP00005 (UniProt P03045)
Region: residues 1	to 107
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We have shown above that N protein exists in solution as an unfolded (essentially random coil) molecule.
These observations are consistent with the existence of N in solution as an essentially unstructured molecule containing some (fluctuating and transient) secondary structure (Psitsyn, 1987; Kim & Baldwin, 1990).
A two-dimensional HSMQC NMR analysis was performed on the uncomplexed 15N-labeled N protein at 20 °C (Figure 3A). Peaks corresponding to 100 of the 107 residues of N can be resolved, but the amide resonances are sharp and clustered in the center where they have chemical shifts consistent with those of a random coil structure. This suggests that N exists in solution as an unfolded protein.
Furthermore, on the NMR time-scale we find no significant secondary or tertiary structure interactions.
Protein: DP00005 (UniProt P03045)
Region: residues 1	to 107
Annotation: regulation of transcription by RNA polymerase II (Biological process)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
We have shown that the N protein is also unfolded when free in solution and that it is capable of activating RNA polymerase in this form, though we have no information on its structural state after binding to the transcription complex.
The N proteins of the lambdoid family and the Tat protein of HIV are all RNA binding transcriptional activators.
Protein: DP00005 (UniProt P03045)
Region: residues 1	to 107
Annotation: regulation of transcription by RNA polymerase II (Biological process)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We have shown that the N protein is also unfolded when free in solution and that it is capable of activating RNA polymerase in this form, though we have no information on its structural state after binding to the transcription complex.
The N proteins of the lambdoid family and the Tat protein of HIV are all RNA binding transcriptional activators.
Protein: DP00005 (UniProt P03045)
Region: residues 1	to 107
Annotation: regulation of transcription by RNA polymerase II (Biological process)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
Intrinsic Disorder Allows λN to Implement a Multi-pronged Anti-pausing and Anti-termination Strategy
Our results suggest that λN can bestow pause and termination resistance on the transcriptional apparatus by three main mechanisms.
First, λN globally repositions NusA.
Second, λN locally remodels RNAP elements.
Third, λN seems to stabilize RNAP and nucleic acids to promote processive elongation.
C-terminal parts of λN that traverse the hybrid cavity may avert pause-related conformational changes of RNAP, stabilize the hybrid, functionally insulate the exit tunnel from the active site, and possibly enhance the catalytic activity of RNAP via contacts to the connector.
Thus, λN resembles a molecular "Swiss army knife" with numerous tools that counteract essentially all modes of pausing and termination.
Remarkably, λN can comprehensively reprogram RNAP and elongation factors, although it is a very small protein (107 residues). Our results show that, due to its intrinsic disorder (VanGilst and von Hippel, 1997), it can adopt a highly elongated conformation that results in a large exposed interaction surface.
Cross-references: PDB:6GOV
Protein: DP00005 (UniProt P03045)
Region: residues 1	to 107
Annotation: RNA polymerase binding (Molecular function)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
A 3.7-Å-resolution cryo-electron microscopy structure and structure-informed functional analyses reveal a multi-pronged strategy by which the intrinsically unstructured λN directly modifies RNA polymerase interactions with the nucleic acids and subverts essential functions of NusA, NusE, and NusG to reprogram the transcriptional apparatus. λN repositions NusA and remodels the β subunit flap tip, which likely precludes folding of pause or termination RNA hairpins in the exit tunnel and disrupts termination-supporting interactions of the α subunit C-terminal domains. λN invades and traverses the RNA polymerase hybrid cavity, likely stabilizing the hybrid and impeding pause- or termination-related conformational changes of polymerase. λN also lines upstream DNA, seemingly reinforcing anti-backtracking and anti-swiveling by NusG. Moreover, λN-repositioned NusA and NusE sequester the NusG C-terminal domain, counteracting ρ-dependent termination. Other anti-terminators likely utilize similar mechanisms to enable processive transcription.
Cross-references: PDB:6GOV
Protein: DP00005 (UniProt P03045)
Region: residues 1	to 22
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We have determined the structure of this complex by heteronuclear NMR spectroscopy (P. L. et al., unpublished data) and concluded that changes in N1–22 chemical shifts caused by the addition of boxB RNA reflect both the folding of the arginine-rich domain and extensive interactions with its RNA target.
Interaction with boxB RNA induces only the RNA-binding domain of N to adopt a folded conformation, while the activating regions of the protein remain disordered in the absence of their target proteins.
Protein: DP00005 (UniProt P03045)
Region: residues 34	to 47
Annotation: protein binding (Molecular function)
Evidence: bait-prey hybrid interaction evidence used in manual assertion
Supporting statements:
When amino-terminal deletions of N1–47 fused to GST were used in these experiments, the smallest fragment that bound NusA was N34–47 (Figure 4B, lane 5).
Protein: DP00005 (UniProt P03045)
Region: residues 34	to 47
Annotation: protein binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
To confirm the location of the NusA-binding region in amino acids 34–47 using an independent method (see Figure 4C), gel mobility shift assays were performed using 32P-labeled nut site RNA, purified NusA, and purified N (full-length N and various carboxy-terminal deletion mutants), as described previously (Mogridge et al. 1995). NusA did not form a complex with nut site RNA and N1–22, which contains only the boxB-binding region of N (lanes 3–5). NusA also did not supershift an N1–39/nut site complex (lanes 7–9), but did supershift the nut site RNA complexed with N1–47 (lanes 10–13), the longer N fragments, and full-length N (lanes 14–30). Thus, the results of the gel mobility shift assays were in accord with those of the affinity chromatography experiments.
Protein: DP00005 (UniProt P03045)
Region: residues 1	to 22
Annotation: RNA binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We have determined the structure of this complex by heteronuclear NMR spectroscopy (P. L. et al., unpublished data) and concluded that changes in N1–22 chemical shifts caused by the addition of boxB RNA reflect both the folding of the arginine-rich domain and extensive interactions with its RNA target.
Protein: DP00005 (UniProt P03045)
Region: residues 1	to 22
Annotation: regulation of transcription by RNA polymerase II (Biological process)
Evidence: enzymatic activity assay evidence used in manual assertion
Supporting statements:
No appreciable effect was observed upon addition of N1–22, N1–39, N1–47, N1–58, N1–73, or N1–89 (lanes 2–7), but 69% read-through occurred in the presence of full-length N (lane 8). Thus, the carboxyl terminus of N is essential for its ability to support factor-independent antitermination.
Protein: DP00005 (UniProt P03045)
Region: residues 1	to 107
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The minimum near 200 nm in the far UV-CD spectra of free N protein and N36 peptide is characteristic for a random coil conformation (Fig. 2), consistent with the result of NMR spectroscopic studies.
Protein: DP00005 (UniProt P03045)
Region: residues 1	to 36
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Thus, the structural changes in the N protein which occur upon binding to boxB RNA are mainly localized within the 36 N-terminal amino acids of the N protein, as indicated previously [[12]].
Protein: DP00006 (UniProt P00004)
Region: residues 1	to 104
Annotation: order to disorder (Structural transition)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
A predominantly peripheral binding mechanism, rather than deep protein insertion into the membrane, provides a rationale for the general denaturing effect of the CL surface and the large-scale protein unfolding. These findings closely relate to cyt c folding dynamics and suggest a general strategy for extending the time window in monitoring the kinetics of folding.
Protein: DP00006 (UniProt P00004)
Region: residues 1	to 104
Annotation: lipid binding (Molecular function)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Interactions of cytochrome c (cyt c) with cardiolipin (CL) partially unfold the protein activating its peroxidase function, a critical event in the execution of apoptosis.
Protein: DP00006 (UniProt P00004)
Region: residues 2	to 105
Annotation: disorder (Structural state)
Evidence: viscosity measurement evidence used in manual assertion
Supporting statements:
A least squares analysis of the data gives an intrinsic viscosity of 15.5 ml per g. This value is nearly identical with an intrinsic viscosity of 15.2 ml per g calculated for the apoprotein in a randomly coiled conformation, using the equation of Tanford et al. (12).
Protein: DP00006 (UniProt P00004)
Region: residues 2	to 105
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
As seen in Fig. 2B, the fractionated apoprotein preparation exhibits negative
ellipticities between 195 and 235 nm with a minimum at 199 nm. A minimum at this wave length is characteristic of a randomly coiled conformation (15).
Protein: DP00007 (UniProt P27695)
Region: residues 1	to 42
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal 42 residues were not visible in the electron density map.
Cross-references: PDB:1E9N
Protein: DP00007 (UniProt P27695)
Region: residues 1	to 36
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Native AP Endo Contains a Flexible Amino-terminal Portion and a Tight Globular Domain
Because the first 36 residues of the amino terminus are readily accessible to proteolysis by all the proteases examined, they are flexible and only loosely associated with the remainder of the molecule.
Because the first 36 residues of the amino terminus are readily accessible to proteolysis by all the proteases examined, they are flexible and only loosely associated with the remainder of the molecule.
Protein: DP00007 (UniProt P27695)
Region: residues 32	to 43
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This electron density map allowed the interpretation of the majority of residues, although no electron density was visible for 12 N-terminal amino acids (including four vector-derived residues).
Cross-references: PDB:1BIX
Protein: DP00007 (UniProt P27695)
Region: residues 2	to 40
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N terminus (residues 1–40) was evidently flexible because it lacked unambiguous electron density.
Cross-references: PDB:4IEM
Protein: DP00008 (UniProt Q64693)
Region: residues 1	to 256
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The SAXS profiles of OctΔC1 and Bob1 indicated that both proteins do not have a folded, globular structure, and a Gaussian chainlike behavior was most appropriate to describe these experimental findings (Figure 4a).
As the polymer dimensions do not reflect the respective protein masses (OctΔC1 is nearly twice as large as Bob1), these results suggest that OctΔC1 retains some structured peptide segments, presumably from the POU domain, while Bob1 exists entirely as a random chain.
Protein: DP00008 (UniProt Q64693)
Region: residues 1	to 256
Annotation: disorder (Structural state)
Evidence: differential scanning calorimetry evidence used in manual assertion
Supporting statements:
Differential scanning calorimetry (DSC) of Bob1 shows an apparent lack of, or a very broad, melting transition, indicating that Bob1 does not adopt a stable globular fold (data not shown).
Protein: DP00008 (UniProt Q64693)
Region: residues 1	to 256
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The circular dichroism (CD) spectra of Bob1(1–65) and Bob1 are consistent with a poorly ordered fold, but there are additional features characteristic of polyproline II helix (Figure 6(b); Siligardi and Drake 1995, Sreerama and Woody 1994).
Protein: DP00008 (UniProt Q64693)
Region: residues 1	to 65
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectra of the ternary complex indicate that the helical composition is greater then the expected value calculated from free Bob1(1–65) and the Oct-1 POU/DNA complex (Figure 6(c); Table 3).
Protein: DP00008 (UniProt Q64693)
Region: residues 1	to 256
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
The integrated heat release for titrations of Bob1 into the pre-formed Oct-1 POU/DNA complex (Figure 2(c)) shows that both Bob1(1–65) and Bob1 have an exothermic reaction with the stable, pre-formed POU/DNA complex.
Electrophoretic DNA mobility experiments showed that the protein is binding Oct-1 POU, not the DNA
Protein: DP00009 (UniProt P32774)
Region: residues 89	to 103
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In addition, the non-conserved region cover-ing TOA2 amino acids 89-103 is unobserved.
Cross-references: PDB:1YTF
Protein: DP00009 (UniProt P32774)
Region: residues 89	to 103
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The 15 amino acids of hydrophilic sequence between strands 4 and 5 of TOA2 are unobserved in the structure. They correspond closely to the 14 extra and non-essential residues of the yeast small subunit compared to the human and Drosophila small subunits27. We suggest that this region forms a  flexible and disordered loop between the two B-strands.
Protein: DP00009 (UniProt P32774)
Region: residues 90	to 102
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The non-conserved 17 residue loop between TOA2 β-strands S4 and S5 is not observed, and it is shortened to a three residue turn in TFIIAγ.
Cross-references: PDB:1NH2