LiteFold/DisProt huggingface dataset:
Protein: DP00133 (UniProt P03422)
Region: residues 1	to 230
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum o fPNT at neutral pH lacks evidence of any significant ordered secondary structure, as seen from its large negative ellipticity at 198 nm and nil ellipticity at 185 nm (Fig. 4).

On the other hand, the hypothesis of an unfolded protein is consistent with the CD  and  NMR  data,  which  show  that  PNT  lacks  stable secondary structure.
Moreover,CD studies further confirm that PNT is unfolded in aqueous solution.
Protein: DP00133 (UniProt P03422)
Region: residues 1	to 230
Annotation: disorder (Structural state)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
The very small spread of the resonance  frequencies for amide protons (between 7.8 and 8.7 ppm,see box in Fig. 3) together with the absence of NOEs in the  amide–amide  region  is  typical  of a  protein  without any  constant  secondary  structure.
NMR  data show that PNT exhibits no short-range interactions, indicating the lack of any constant secondary structure as well as the absence of any stable oligomers.
On the other hand, the hypothesis of an unfolded protein is consistent with the CD  and  NMR  data,  which  show  that  PNT  lacks  stable secondary structure.
Protein: DP00133 (UniProt P03422)
Region: residues 1	to 230
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
As shown in Fig. 2, PNT displays an abnormally  slow  migration  in  SDS–PAGE  with  an  apparentmolecular  weight  (MW)  o  f33  kDa  (expected  weight  25kDa). This abnormal behavior has been reported previously for all P proteins of Morbilliviruses and Paramyxoviruses (Lamb and Kolakofsky, 2001) and attributed to the occurrence of acidic stretches in PNT, which is consistent with our result.
Protein: DP00133 (UniProt P03422)
Region: residues 1	to 230
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
 In the absence of TFE, PNT is entirely digested in 6 h, wherea sit shows resistance to digestion in the presence of 15% TFE (compare lanes C and 4).
Protein: DP00133 (UniProt P03422)
Region: residues 1	to 50
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
 The minimal peptide required to form the complex was identified using NMR spectroscopy as P1‐50 (Figure S2), resulting in a high‐yielding, soluble, and stable N0P complex. 
P50 is bound to N so that peaks are too weak to be observed
Protein: DP00133 (UniProt P03422)
Region: residues 1	to 300
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The coiled coil is too large to be observed by standard solution NMR analysis because of the effective rotational correlation time, and only the flexible residues give rise to sharp signals. By this method, all amino acids up to residue 300 could be identified, proving the absence of the additional helices that were observed in the Sendai virus domain.
Protein: DP00133 (UniProt P03422)
Region: residues 1	to 229
Annotation: disorder (Structural state)
Evidence: atomic force microscopy evidence used in manual assertion
Supporting statements:
PNT-GFP exhibited a thin and flexible tail-like structure with a temporarily appearing and disappearing small globule at the N-terminal end, together with the C-terminal GFP (Fig. 4e and Supplementary Video 7).
The R2D histogram of the IDR was best fitted to a double Gaussian with peaks at 8.9 ± 0.33 and 14.3 ± 9.26 nm (Fig. 4i). The mean height of the IDR was 0.4–0.5 nm, in both metastable shorter and longer states (Extended Data Fig. 5b), indicating that the IDR is fully disordered even on disorder-to-order transition of the small globule.
Protein: DP00133 (UniProt P03422)
Region: residues 1	to 50
Annotation: protein folding chaperone (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The minimal peptide required to form the complex was identified using NMR spectroscopy as P1‐50 (Figure S2), resulting in a high‐yielding, soluble, and stable N0P complex.
Protein: DP00133 (UniProt P03422)
Region: residues 1	to 230
Annotation: disorder (Structural state)
Evidence: dynamic light scattering assay evidence used in manual assertion
Supporting statements:
Thus, the Rso fPNT measured by DLS corresponds to the value expected for a fully unfolded protein.
Protein: DP00133 (UniProt P03422)
Region: residues 1	to 230
Annotation: disorder (Structural state)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
Therefore, the Stokes radius measured for PNT (41 Å) is not compatible with a monomeric, globular protein. Such a large value for the Stokes radius could be attributed either to a high degree of multimerization  or  to  a  monomeric,  unfolded  protein (RsU predicted: 46 Å). Multimers in the form of nonspecific aggregates would have led to a broad peak in gel filtration, which is not the case here. 
The  hydrodynamic  properties  of  PNT  inferred  from both  gel  filtration  and  dynamic  light-scattering  experiments  are  consistent  with  PNT  being  either  a  stableoligomer  or  a  monomeric,  unfolded  protein.
Protein: DP00133 (UniProt P03422)
Region: residues 1	to 304
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We used NMR spectroscopy to investigate the conformational behavior of MeV PNTD in its free state and to describe the structural, dynamic, and kinetic behavior of this highly disordered 90-kDa complex. Although unfolded, PNTD exhibits transient helical propensities in the N-terminal N binding site (α1/2), around residues 87 to 93 (α3) and 189 to 198 (α4), linked by long, highly dynamic segments (Fig. 1).
Protein: DP00133 (UniProt P03422)
Region: residues 377	to 457
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Carbon chemical shifts of P304–507 did not change significantly in comparison with PLOOP, demonstrating that PLOOP remains disordered in the context of the construct that links the tetramerization domain and XD and that is required for phase separation (see fig. S6).
Protein: DP00133 (UniProt P03422)
Region: residues 377	to 457
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: fluorescence microscopy evidence used in manual assertion
Supporting statements:
Several mixtures formed condensed phases: P50N525 + P1–507, P304N525 + P304–507, and P50N525 + P304–507 (Fig. 1B). P50N525 + P304–507 was thus identified as the minimal phase-separating system, forming spherical bimolecular condensates as measured by fluorescence microscopy (Fig. 1B) and showing increased turbidity (Fig. 1D).
Both proteins therefore remain liquid in the condensed phase, although their rotational dynamics are slowed, possibly due to increased viscosity in the droplets. In summary, these results confirm that LLPS occurs under near-physiological protein and salt concentrations upon mixing of full-length N- and the C-terminal domains of P in vitro, complementing recent in vivo observations (32).
Protein: DP00133 (UniProt P03422)
Region: residues 377	to 457
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
An additional interaction between PLOOP and N was identified using NMR spectroscopy (Fig. 4, A and B), suggesting that the role of this domain, which is present in all constructs involved in phase separation, involves a direct interaction with N rather than acting as a simple spacer (35).
Protein: DP00133 (UniProt P03422)
Region: residues 377	to 457
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Carbon chemical shifts of P304–507 did not change significantly in comparison with PLOOP, demonstrating that PLOOP remains disordered in the context of the construct that links the tetramerization domain and XD and that is required for phase separation (see fig. S6).
Protein: DP00134 (UniProt Q06787)
Region: residues 281	to 422
Annotation: disorder (Structural state)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
The one-dimensional 1 H spectrum is typical of an unfolded and monomeric peptide with very little resonance dispersion (Fig. 4B).
Protein: DP00134 (UniProt Q06787)
Region: residues 516	to 632
Annotation: poly(A) binding (Molecular function)
Evidence: qualitative western immunoblotting evidence used in manual assertion
Supporting statements:
The binding of the FCT domain is so strong that it shows comparable affinity for poly-(rA), (rG) and (rU).
Protein: DP00134 (UniProt Q06787)
Region: residues 444	to 632
Annotation: intracellular non-membrane-bounded organelle (Cellular component)
Evidence: fluorescence microscopy evidence used in manual assertion
Supporting statements:
(C) DIC and fluorescent images of FMRP, FMRPΔLCR, and FMRPLCR protein (50 μM) mixed with Cy3-labeled sc1 RNA (5 μM) in 25 mM Na2PO4, pH 7.4, 30 mM NaCl, 2 mM DTT. Images show that only FMRP and FMRPLCR form droplets with sc1 RNA. (Scale bar, 10 μm.)
Upon addition of Cy3-labeled sc1 RNA, droplets were formed with FMRP and FMRPLCR, but not with FMRPΔLCR (Fig. 1C). Our results show that FMRPLCR alone is necessary and sufficient to drive phase separation with sc1 RNA in vitro.
Protein: DP00134 (UniProt Q06787)
Region: residues 444	to 632
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Overlay of 1H-15N heteronuclear single-quantum coherence spectra of the protein-depleted (i.e., monomeric) and condensed phases shows almost identical chemical shifts with narrow amide proton dispersion (∼8.0–8.7 ppm), reflecting similar global disordered character (SI Appendix, Fig. S3B).
In contrast, our solution NMR data show FMRPLCR to be primarily structurally disordered in the condensed phase.
Protein: DP00134 (UniProt Q06787)
Region: residues 445	to 632
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
To address these questions, we first reconstituted a model biomolecular condensate containing the intrinsically disordered C-terminal regions of FMRP (445–632, hereafter referred to as FMRP) and CAPRIN1 (607–709, hereafter referred to as CAPRIN1) for biophysical studies (Fig. 1A). 
Using isothermal titration calorimetry (ITC), we detected no FMRP-CAPRIN1 interaction; however, after in vitro phosphorylation of FMRP (pFMRP; fig. S3, A and B) by casein kinase II (CK2), a known kinase that Ser/Thr-phosphorylates FMRP in vivo (22, 23), we observed an effective 1 μM CAPRIN1-pFMRP binding affinity (fig. S4, A and B).
Protein: DP00134 (UniProt Q06787)
Region: residues 445	to 632
Annotation: protein binding (Molecular function)
Evidence: fluorescence resonance energy transfer evidence used in manual assertion
Supporting statements:
To address these questions, we first reconstituted a model biomolecular condensate containing the intrinsically disordered C-terminal regions of FMRP (445–632, hereafter referred to as FMRP) and CAPRIN1 (607–709, hereafter referred to as CAPRIN1) for biophysical studies (Fig. 1A). 
Fluorescence resonance energy transfer (FRET) experiments between highly phosphorylated Cy3-labeled pFMRP and Cy5-labeled CAPRIN1 yielded an apparent 6 μM binding affinity, with decreasing affinities corresponding to lower numbers of phosphate groups on pFMRP (Fig. 1B and fig. S3).
Protein: DP00134 (UniProt Q06787)
Region: residues 445	to 632
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: fluorescence resonance energy transfer evidence used in manual assertion
Supporting statements:
To address these questions, we first reconstituted a model biomolecular condensate containing the intrinsically disordered C-terminal regions of FMRP (445–632, hereafter referred to as FMRP) and CAPRIN1 (607–709, hereafter referred to as CAPRIN1) for biophysical studies (Fig. 1A). 
Using fluorescence microscopy, we observed that CAPRIN1 does not co–phase-separate with FMRP (fig. S4, C to E) even at protein concentrations of 1 mM, but does so with pFMRP over a wide range of concentrations (Fig. 1, C and D, and fig. S4D).
Protein: DP00134 (UniProt Q06787)
Region: residues 445	to 632
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
To identify residues mediating pFMRP-CAPRIN1 interactions, we used nuclear magnetic resonance (NMR) spectroscopy and assigned the CAPRIN1 resonances (fig. S5). Titrating pFMRP into [15N]CAPRIN1 resulted in co–phase separation, forming a turbid mixture containing many small droplets. Our results show global decreases in [15N]CAPRIN1 amide peak intensities with no sizable chemical shift perturbations (CSPs) (fig. S6).
Protein: DP00134 (UniProt Q06787)
Region: residues 527	to 541
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
RNA-bound peptide (Fig. 1c) revealed a transition from a ‘random coil’ to a well-ordered conformation of the peptide upon RNA binding. 
Cross-references: PDB:2LA5
Protein: DP00134 (UniProt Q06787)
Region: residues 527	to 541
Annotation: G-quadruplex RNA binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The N-terminal amino acids of the peptide are poorly defined in both crystal and NMR structures in agreement with the observation that only 10 residues in the middle of the peptide facilitate the G-quadruplex formation (37). 
These data suggest that the most important intermolecular interactions between RGG motif and sc1 RNA involve residues 6–18 of the peptide.
Cross-references: PDB:2LA5
Protein: DP00134 (UniProt Q06787)
Region: residues 529	to 542
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Although a solid evidence for the formation of β-turns in the unbound RGG box is missing, our structural data clearly shows feasibility of the turn formation in the RGG motif.
The structure contained two RNA-peptide complexes in the asymmetric unit, with all nucleotides and 13 amino acids of peptide chain present in the electron density map.
Cross-references: PDB:5DE5
PDB:5DEA
PDB:5DE8
Protein: DP00134 (UniProt Q06787)
Region: residues 529	to 542
Annotation: G-quadruplex RNA binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The structure contained two RNA-peptide complexes in the asymmetric unit, with all nucleotides and 13 amino acids of peptide chain present in the electron density map.
Our crystal structure provides the molecular basis for previous biochemical (21) and NMR (37) observations that formation of the sc1 RNA structure and RGG peptide binding critically depend on K+ cations.
Cross-references: PDB:5DE8
PDB:5DEA
PDB:5DE5
Protein: DP00134 (UniProt Q06787)
Region: residues 281	to 422
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In the far-UV CD spectrum, the two expected helical peaks at 208 and 222 nm collapse into a single minimum shifted at 200 nm (Fig. 4A).
Protein: DP00134 (UniProt Q06787)
Region: residues 516	to 632
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Its CD spectrum consists of a single minimum around 200 nm (Fig+ 5), characteristic
of an unfolded state.
Protein: DP00134 (UniProt Q06787)
Region: residues 516	to 632
Annotation: poly(G) binding (Molecular function)
Evidence: qualitative western immunoblotting evidence used in manual assertion
Supporting statements:
The binding of the FCT domain is so strong that it shows comparable affinity for poly-(rA), (rG) and (rU).
Protein: DP00134 (UniProt Q06787)
Region: residues 516	to 632
Annotation: poly(U) RNA binding (Molecular function)
Evidence: qualitative western immunoblotting evidence used in manual assertion
Supporting statements:
The binding of the FCT domain is so strong that it shows comparable affinity for poly-(rA), (rG) and (rU).
Protein: DP00135 (UniProt P10961)
Region: residues 1	to 167
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Yeast heat shock transcription factor N-terminal activation domains are unstructured as probed by heteronuclear NMR spectroscopy.
Using the DNA-binding domain as a structural reference, we show that the protein backbone of the N-terminal activation domain undergoes rapid, large-amplitude motions and is therefore unstructured. Difference CD data also show that the N-terminal activation domain remains random-coil, even in the presence of DNA.
In addition, we used two-dimensional heteronuclear 15N{1h} NOE NMR and measurements of 15N relaxation parameters to show that the N-terminal activation domains from both yeast strains have a high degree of flexibility, which is consistent with an unstructured state in solution. The results are particularly compelling because they offer the first positive evidence for a dynamically disordered transcriptional activation domain.
N-terminal activation domain of yeast HSF is unstructured
The remaining signals, attributable to the N-terminal activation domain, all had negative NOEs indicative of rapid, large-amplitude motions. This shows that the N-terminal activation domain of S. cerevisiae also behaves as an unstructured protein.
To confirm that the N-terminal activation domains were not unstructured because of denaturation at low pH, further NMR spectroscopic studies were performed at pH 5.75 (data not shown). Comparison of the chemical shift distribution in spectra acquired at higher pH with those at lower pH indicated no change in the structural state of the constructs. The DNA- binding domains remained folded, whereas the activation do- mains persisted in an unstructured state.
Protein: DP00135 (UniProt P10961)
Region: residues 260	to 332
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Yeast heat shock transcription factor contains a flexible linker between the DNA-binding and trimerization domains
The Proposed Linker Region Has No Ordered Secondary Structure-To look directly at the secondary structure of the linker, the CD spectra of the DNA-binding domain (S. cerevisiae residues 171-259) and the trimerization domain (S. cerevisiae residues 333-424) were subtracted from each of the CD spectra of the HSF derivatives. As shown in Fig. 4 B , it is apparent that the difference CD spectrum representing the linker region of Sc-DT(21L) is characteristic of random coil with a minimum at 230 nm and maximum at 220 nm (27).
The molar ellipticity (qprot) of the Sc-DT series of protein were each subtracted by the molar ellipticity of the isolated DNA-binding domain and the molar ellipticity of the isolated trimerization domain. The resulting difference spectra should approximate the spectra of the linker region alone. The difference circular dichroism spectra of Sc-DT(21L) and Sc-D(21L) show that the linker has no ordered secondary structure.
Protein: DP00135 (UniProt P10961)
Region: residues 260	to 332
Annotation: flexible linker (Disorder function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Yeast heat shock transcription factor contains a flexible linker between the DNA-binding and trimerization domains
The Proposed Linker Region Has No Ordered Secondary Structure-To look directly at the secondary structure of the linker, the CD spectra of the DNA-binding domain (S. cerevisiae residues 171-259) and the trimerization domain (S. cerevisiae residues 333-424) were subtracted from each of the CD spectra of the HSF derivatives. As shown in Fig. 4 B , it is apparent that the difference CD spectrum representing the linker region of Sc-DT(21L) is characteristic of random coil with a minimum at 230 nm and maximum at 220 nm (27).
The molar ellipticity (qprot) of the Sc-DT series of protein were each subtracted by the molar ellipticity of the isolated DNA-binding domain and the molar ellipticity of the isolated trimerization domain. The resulting difference spectra should approximate the spectra of the linker region alone. The difference circular dichroism spectra of Sc-DT(21L) and Sc-D(21L) show that the linker has no ordered secondary structure.
Protein: DP00135 (UniProt P10961)
Region: residues 1	to 167
Annotation: molecular function activator activity (Molecular function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
Yeast heat shock transcription factor N-terminal activation domains are unstructured as probed by heteronuclear NMR spectroscopy.
Using the DNA-binding domain as a structural reference, we show that the protein backbone of the N-terminal activation domain undergoes rapid, large-amplitude motions and is therefore unstructured. Difference CD data also show that the N-terminal activation domain remains random-coil, even in the presence of DNA.
Deletions of the entire C-terminal region result in a functional HSF at physiological temperatures (Nieto-Sotelo et al., 1990; Sorger, 1990); this implies that the N-terminal activation domain is sufficient for the required constitutive level of transcriptional activity.
In addition, we used two-dimensional heteronuclear 15N{1H} NOE NMR and measurements of 15N relaxation parameters to show that the N-terminal activation domains from both yeast strains have a high degree of flexibility, which is consistent with an unstructured state in solution. The results are particularly compelling because they offer the first positive evidence for a dynamically disordered transcriptional activation domain.
Protein: DP00135 (UniProt P10961)
Region: residues 1	to 167
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Far-UV CD spectroscopy, performed at pH 7.0, also indicate that the N-terminal activation domains of yeast HSF are unstructured. Figure 5A shows CD spectra for the DNA-binding domain, and for the N-terminal activation domain plus the DNA-binding domain, as well as the difference between the two. The difference spectrum is characteristic of a random coil. We also examined the possibility that the N-terminal activation do- main might behave differently when the DNA-binding domain is bound to a DNA-binding site (Fig. 5B). An examination of this CD difference spectrum indicates that binding of the DNA- binding domain to the DNA does not induce any structural changes in the N-terminal activation domain.
Protein: DP00136 (UniProt P15865)
Region: residues 1	to 219
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
 Without Pi in the solution, only 4.5±0.7% of the protein appeared folded into α-helix and an increase up to 10.5% was observed when the Pi concentration was increased to 50 mM (Fig. 1B).