LiteFold/DisProt huggingface dataset:
Protein: DP04134 (UniProt O54918-2)
Region: residues 1	to 113
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
During purification, BimLΔC27 was observed to be highly protease sensitive and behaved as a larger protein, migrating in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) as an approximately 16 kDa protein and eluting from gel filtration columns with an apparent molecular weight of ∼25 kDa (see Figure 3a).
Elution as a larger protein when analyzed by size exclusion chromatography, and sensitivity to proteases, are both properties commonly observed for IUPs and suggest that BimLΔC27 may be disordered in solution.
Protein: DP04134 (UniProt O54918-2)
Region: residues 1	to 113
Annotation: disorder (Structural state)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
During purification, BimLΔC27 was observed to be highly protease sensitive and behaved as a larger protein, migrating in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) as an approximately 16 kDa protein and eluting from gel filtration columns with an apparent molecular weight of ∼25 kDa (see Figure 3a).
Elution as a larger protein when analyzed by size exclusion chromatography, and sensitivity to proteases, are both properties commonly observed for IUPs and suggest that BimLΔC27 may be disordered in solution.
Protein: DP04134 (UniProt O54918-2)
Region: residues 1	to 113
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectra obtained for BimLΔC27 over the range 5–65°C is characteristic of an unstructured protein, although the slight inflection near 222 nm may indicate some residual α-helical structure, but this is not enhanced at lower temperatures as seen for some proteins (Figure 2b).
Protein: DP04134 (UniProt O54918-2)
Region: residues 1	to 113
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In the 1H-15N-HSQC spectrum (Figure 2c), the backbone amide resonances fall between 8.0 and 8.5 p.p.m., and there is little dispersion in the aliphatic region in the 1D 1H NMR spectrum (data not shown). The sharp resonances and lack of chemical shift dispersion reflect the intrinsic mobility and lack of long-range order in BimLΔC27.
Protein: DP04134 (UniProt O54918-2)
Region: residues 76	to 113
Annotation: protein binding (Molecular function)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
When Bcl-wΔC10 and BimLΔC27 were mixed before trypsin digestion, a different proteolytic profile was obtained (Figure 3b, lanes 8 and 9). Mass spectrometry analysis of the peptide mixtures revealed changes consistent with complex formation. 
The mass of the new peptide corresponds to that expected for a peptide derived from the C-terminus of BimLΔC27 (sequence shown at the bottom of Figure 3b). This peptide includes the BH3 domain and suggests that interaction with the hydrophobic binding groove protects the BH3 domain and the hydrophobic groove of Bcl-w from proteolysis.
Together, these results suggest that Bim remains largely unstructured in the presence of prosurvival proteins and that only a limited conformational change of just the BH3 domain is associated with binding.
Protein: DP04134 (UniProt O54918-2)
Region: residues 76	to 113
Annotation: disorder to order (Structural transition)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
When Bcl-wΔC10 and BimLΔC27 were mixed before trypsin digestion, a different proteolytic profile was obtained (Figure 3b, lanes 8 and 9). Mass spectrometry analysis of the peptide mixtures revealed changes consistent with complex formation.
The mass of the new peptide corresponds to that expected for a peptide derived from the C-terminus of BimLΔC27 (sequence shown at the bottom of Figure 3b). This peptide includes the BH3 domain and suggests that interaction with the hydrophobic binding groove protects the BH3 domain and the hydrophobic groove of Bcl-w from proteolysis.
Together, these results suggest that Bim remains largely unstructured in the presence of prosurvival proteins and that only a limited conformational change of just the BH3 domain is associated with binding.
Protein: DP04134 (UniProt O54918-2)
Region: residues 83	to 108
Annotation: disorder to order (Structural transition)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
A localized conformational change is supported by comparison of the 1H-15N-HSQC spectra for 15N-labeled BimLΔC27 in the presence and absence of Bcl-w (Figure 3c).
The new peaks in the 15N-BimLΔC27/Bcl-wΔC10 complex spectra primarily arise from interaction of the BH3 domain with Bcl-w as addition of Bcl-wΔC10 to 15N-labeled BimBH3 (a peptide including residues 83–108 of mouse BimL) results in similar shifts (Figure 3d).
The few differences seen are likely due to end effects. The comparable binding constants observed for Bcl-w binding to BimLΔC27 protein (32 nM) and the BimBH3 peptide (22 nM)29 supports this conclusion.
Protein: DP04134 (UniProt O54918-2)
Region: residues 83	to 108
Annotation: protein binding (Molecular function)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
A localized conformational change is supported by comparison of the 1H-15N-HSQC spectra for 15N-labeled BimLΔC27 in the presence and absence of Bcl-w (Figure 3c).
The new peaks in the 15N-BimLΔC27/Bcl-wΔC10 complex spectra primarily arise from interaction of the BH3 domain with Bcl-w as addition of Bcl-wΔC10 to 15N-labeled BimBH3 (a peptide including residues 83–108 of mouse BimL) results in similar shifts (Figure 3d). 
The few differences seen are likely due to end effects. The comparable binding constants observed for Bcl-w binding to BimLΔC27 protein (32 nM) and the BimBH3 peptide (22 nM)29 supports this conclusion.
Protein: DP04134 (UniProt O54918-2)
Region: residues 83	to 108
Annotation: order (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
A localized conformational change is supported by comparison of the 1H-15N-HSQC spectra for 15N-labeled BimLΔC27 in the presence and absence of Bcl-w (Figure 3c).
The new peaks in the 15N-BimLΔC27/Bcl-wΔC10 complex spectra primarily arise from interaction of the BH3 domain with Bcl-w as addition of Bcl-wΔC10 to 15N-labeled BimBH3 (a peptide including residues 83–108 of mouse BimL) results in similar shifts (Figure 3d).
Protein: DP04134 (UniProt O54918-2)
Region: residues 76	to 113
Annotation: order (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
When Bcl-wΔC10 and BimLΔC27 were mixed before trypsin digestion, a different proteolytic profile was obtained (Figure 3b, lanes 8 and 9). Mass spectrometry analysis of the peptide mixtures revealed changes consistent with complex formation.
The mass of the new peptide corresponds to that expected for a peptide derived from the C-terminus of BimLΔC27 (sequence shown at the bottom of Figure 3b). This peptide includes the BH3 domain and suggests that interaction with the hydrophobic binding groove protects the BH3 domain and the hydrophobic groove of Bcl-w from proteolysis.
Together, these results suggest that Bim remains largely unstructured in the presence of prosurvival proteins and that only a limited conformational change of just the BH3 domain is associated with binding.
Protein: DP04135 (UniProt Q92800)
Region: residues 1	to 30
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region lacks electron density in the PDB structure of the Polycomb Repressive Complex 2 (PRC2:EZH1) bound to AEBP2 and JARID2, indicating it is disordered.
Cross-references: EMDB:EMD-23021
PDB:7KSO
Protein: DP04135 (UniProt Q92800)
Region: residues 728	to 747
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region lacks electron density in the PDB structure of the Polycomb Repressive Complex 2 (PRC2:EZH1) bound to AEBP2 and JARID2, indicating it is disordered.
Cross-references: EMDB:EMD-23021
PDB:7KSO
Protein: DP04135 (UniProt Q92800)
Region: residues 125	to 271
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Aside from a different build of AEBP2 (Supplementary Fig. 3f, g), the overall structure of PRC2:EZH1 is very similar to that of PRC2:EZH228. However, we did note that several loops are disordered in both PRC2:EZH1 and PRC2:EZH2, making us wonder whether any functional differences could be explained by differences contained in these loops (Supplementary Fig. 4a, b).
Supplementary Fig. 4: Regulatory domains of EZH1 are flexible.
a, Cartoon representation of domains that are visible in the cryo-EM density of EZH1. b, Depiction of the key
unstructured loops in EZH1. Labels indicate the last structured residues flanking the flexible loops in EZH1. c,
Sequence comparison of the flexible loops in EZH1 and EZH2. Underlined sequences represent regions rich in
basic (blue) or acidic residues (red), RNA-interaction domains (purple), and automethylation sites (green). Acidic
or basic regions are based on manual inspection of the EZH1/2 sequences. RNA-interaction domains and
automethylation sites are based on reports describing EZH2 features63-66.
Cross-references: EMDB:EMD-23021
PDB:7KSO
Protein: DP04135 (UniProt Q92800)
Region: residues 323	to 431
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Aside from a different build of AEBP2 (Supplementary Fig. 3f, g), the overall structure of PRC2:EZH1 is very similar to that of PRC2:EZH228. However, we did note that several loops are disordered in both PRC2:EZH1 and PRC2:EZH2, making us wonder whether any functional differences could be explained by differences contained in these loops (Supplementary Fig. 4a, b).
Supplementary Fig. 4: Regulatory domains of EZH1 are flexible.
a, Cartoon representation of domains that are visible in the cryo-EM density of EZH1. b, Depiction of the key
unstructured loops in EZH1. Labels indicate the last structured residues flanking the flexible loops in EZH1. c,
Sequence comparison of the flexible loops in EZH1 and EZH2. Underlined sequences represent regions rich in
basic (blue) or acidic residues (red), RNA-interaction domains (purple), and automethylation sites (green). Acidic
or basic regions are based on manual inspection of the EZH1/2 sequences. RNA-interaction domains and
automethylation sites are based on reports describing EZH2 features63-66.
Cross-references: EMDB:EMD-23021
PDB:7KSO
Protein: DP04135 (UniProt Q92800)
Region: residues 478	to 517
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Aside from a different build of AEBP2 (Supplementary Fig. 3f, g), the overall structure of PRC2:EZH1 is very similar to that of PRC2:EZH228. However, we did note that several loops are disordered in both PRC2:EZH1 and PRC2:EZH2, making us wonder whether any functional differences could be explained by differences contained in these loops (Supplementary Fig. 4a, b).
Supplementary Fig. 4: Regulatory domains of EZH1 are flexible.
a, Cartoon representation of domains that are visible in the cryo-EM density of EZH1. b, Depiction of the key
unstructured loops in EZH1. Labels indicate the last structured residues flanking the flexible loops in EZH1. c,
Sequence comparison of the flexible loops in EZH1 and EZH2. Underlined sequences represent regions rich in
basic (blue) or acidic residues (red), RNA-interaction domains (purple), and automethylation sites (green). Acidic
or basic regions are based on manual inspection of the EZH1/2 sequences. RNA-interaction domains and
automethylation sites are based on reports describing EZH2 features63-66.
Cross-references: EMDB:EMD-23021
PDB:7KSO
Protein: DP04135 (UniProt Q92800)
Region: residues 323	to 431
Annotation: nucleosome binding (Molecular function)
Evidence: site-directed mutagenesis phenotypic evidence used in manual assertion
Supporting statements:
Since this loop contains a patch of basic amino acids, we wondered if it plays a role in nucleosome interactions and/or the methyltransferase activity of PRC2:EZH1 (Fig. 2b). To test this possibility, we generated an EZH1 version in which we mutated the five consecutive arginines in the basic patch (green box in Fig. 2b) to alanines (5RtoA mutation).
PRC2:EZH15RtoA showed severely decreased nucleosome-binding activity and no detectable methyltransferase activity (Fig. 2c).
Protein: DP04135 (UniProt Q92800)
Region: residues 323	to 431
Annotation: histone methyltransferase activity (H3-K27 specific) (Molecular function)
Evidence: site-directed mutagenesis phenotypic evidence used in manual assertion
Supporting statements:
PRC2:EZH15RtoA showed severely decreased nucleosome-binding activity and no detectable methyltransferase activity (Fig. 2c).
Protein: DP04135 (UniProt Q92800)
Region: residues 323	to 431
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
We wondered if the MS2L basic patch contributed to the activity of PRC2:EZH1 dimers. Since the 5RtoA mutation severely inhibited the nucleosome-binding and methyltransferase activities of the PRC2:EZH1 core complex (Fig. 2), we decided to test if this mutation also impacts nucleosome-array compaction. When we tested the mutant complex, we observed no promotion of nucleosome-array compaction by the monomeric complex at the highest PRC2:EZH1 concentration tested, and we saw a fourfold reduction in the activity of the dimeric complex, consistent with the basic patch of PRC2 being involved in promoting chromatin compaction (Fig. 3d).
Protein: DP04137 (UniProt O43561-2)
Region: residues 30	to 233
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
The 1H-15N HSQC two dimensional spectrum of this LAT protein segment (Figure 6) is characteristic of a largely disordered polypeptide.
Protein: DP04137 (UniProt O43561-2)
Region: residues 30	to 233
Annotation: TCR signalosome (Cellular component)
Evidence: fluorescence microscopy evidence used in manual assertion
Supporting statements:
The addition of full-length Grb2 and the proline-rich domains of SOS leads to the networked condensation of LAT:Grb2:SOS on the membrane surface of GUVs, as shown in Fig. 2 (top row). Here, the condensates are visualized as concentrated regions of pLAT-AF555 fluorescence on GUVs by confocal microscopy. This condensate is mediated by tyrosine phosphorylation on LAT and is reversible (Fig. 2, bottom row).
Protein: DP04137 (UniProt O43561-2)
Region: residues 30	to 233
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: fluorescence microscopy evidence used in manual assertion
Supporting statements:
The addition of full-length Grb2 and the proline-rich domains of SOS leads to the networked condensation of LAT:Grb2:SOS on the membrane surface of GUVs, as shown in Fig. 2 (top row). Here, the condensates are visualized as concentrated regions of pLAT-AF555 fluorescence on GUVs by confocal microscopy. This condensate is mediated by tyrosine phosphorylation on LAT and is reversible (Fig. 2, bottom row).
Protein: DP04137 (UniProt O43561-2)
Region: residues 30	to 233
Annotation: membrane raft distribution (Biological process)
Evidence: fluorescence microscopy evidence used in manual assertion
Supporting statements:
In the imaging chamber maintained at 31°C, the pLAT-associated vesicle membranes exhibit a homogeneous distribution of fluorescent markers (TR-DHPE and OG-DHPE), as expected because this temperature is slightly above the Tmisc of 29°C. The addition of Grb2-AF647 and SOS triggers a rapid LAT:Grb2:SOS condensation on the membrane surface, which is readily visualized by the appearance of concentrated regions of 647-nm fluorescence, tracking Grb2. This is accompanied by a clear partitioning of TR-DHPE (yellow) and OG-DHPE (blue), indicating a miscibility phase transition within the lipids has also occurred, although under isothermal conditions here.
We observed that the formation of protein condensate can drive the lipid phase transition under isothermal conditions, redistributing lipids in a signal-dependent manner.
Protein: DP04138 (UniProt P19597)
Region: residues 19	to 105
Annotation: disorder (Structural state)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
AGF and DLS were employed to investigate the hydrodynamic behavior of PfCSP N . Both techniques demonstrate that the apparent molecular mass (MM app) and hydrodynamic radius (Rh,app ) are higher than the theoretical values for globular proteins of the same size (1.8 and 1.2 times, respectively; Figures 4A and 4B). This discrepancy is characteristic of an IDP and suggests that PfCSP N adopts a nonglobular conformation (Csizmók et al., 2006).
Protein: DP04138 (UniProt P19597)
Region: residues 19	to 105
Annotation: disorder (Structural state)
Evidence: dynamic light scattering assay evidence used in manual assertion
Supporting statements:
AGF and DLS were employed to investigate the hydrodynamic behavior of PfCSP N . Both techniques demonstrate that the apparent molecular mass (MM app) and hydrodynamic radius (Rh,app ) are higher than the theoretical values for globular proteins of the same size (1.8 and 1.2 times, respectively; Figures 4A and 4B). This discrepancy is characteristic of an IDP and suggests that PfCSP N adopts a nonglobular conformation (Csizmók et al., 2006).
Protein: DP04138 (UniProt P19597)
Region: residues 19	to 105
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
To further examine the structural features of PfCSP N , a far-UV CD spectrum was collected (Figure 4C). The spectrum is typical for a protein with a significant amount of intrinsic disorder with a dominant negative peak at 205 nm (Tompa, 2002). However, completely disordered proteins have a mean residue ellipticity (MRE) value close to zero around 220 nm. This is clearly not the case for PfCSP N , suggesting that the protein contains some secondary structure elements despite being mainly disordered.
Protein: DP04138 (UniProt P19597)
Region: residues 19	to 105
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The IDP nature of PfCSP N was further confirmed by investigating its in-solution structural parameters using SAXS (Figures 4E and 4F). Macromolecular flexibility in solution is readily visualized by the normalized Kratky plot (Figure 4E, inset). While a globular protein displays a bell-shaped curve with a maximum at (1.732, 1.104), the curve of a completely unfolded protein behaving like a random chain increases steeply until it reaches a plateau at ~2 (Durand et al., 2010). The normalized Kratky plot of PfCSP N undoubtedly illustrates that it behaves like a highly flexible protein.To further examine the structural features of PfCSP N , a far-UV CD spectrum was collected (Figure 4C). The spectrum is typical for a protein with a significant amount of intrinsic disorder with a dominant negative peak at 205 nm (Tompa, 2002). However, completely disordered proteins have a mean residue ellipticity (MRE) value close to zero around 220 nm. This is clearly not the case for PfCSP N , suggesting that the protein contains some secondary structure elements despite being mainly disordered.
Protein: DP04138 (UniProt P19597)
Region: residues 19	to 105
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The high degree of structural disorder is further illustrated by solution NMR spectroscopy. In particular, the 1 H- 15 N HSQC spectrum of 15 N labeled PfCSP N exhibits poor signal dispersion, with most of the peaks confined to a narrow spectral region (Figure 4D, blue). Such a cluttered 1 H- 15 N HSQC spectrum indicates that PfCSP N backbone amides sample a range of random-coil chemical shift values and is a salient feature of many IDPs (Burke et al., 2015; Conicella et al., 2016; Ryan et al., 2018).
Protein: DP04139 (UniProt O14497)
Region: residues 1	to 1016
Annotation: disorder (Structural state)
Evidence: combinatorial experimental and author inference evidence used in manual assertion
Supporting statements:
Human cBAF complex (PDBDEV_00000056) with putative ARID1A N-terminal region of unassigned cryoelectron microscopy (cryo-EM) density and C-terminal CBR highlighted.
Region corresponding to IDR1 of ARID1A.
Protein: DP04139 (UniProt O14497)
Region: residues 1124	to 1611
Annotation: disorder (Structural state)
Evidence: combinatorial experimental and author inference evidence used in manual assertion
Supporting statements:
Human cBAF complex (PDBDEV_00000056) with putative ARID1A N-terminal region of unassigned cryoelectron microscopy (cryo-EM) density and C-terminal CBR highlighted.
Region corresponding to IDR2 of ARID1A.
Protein: DP04140 (UniProt Q8R4E9)
Region: residues 420	to 451
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The mCdt1CL structure can be divided into the two parts; the first 31 residues form an N-terminal arm (residues 420 to 451), which is highly flexible [Fig. 1(A)]. The Cα and Cβ chemical shift values and the sequential and medium range NOEs of the backbone amide protons confirmed that this N-terminal region also contains a well-defined helical structure [residues 431 to 442; Fig. 1(B,C)].
The flexible linker between the N-terminal arm and the core of mCdt1CL allows significant movement of the N-terminal arm relative to the mCdt1 core and the end to end distance between the N-terminal ends of solution NMR structures could move more than 50 Å [Fig. 1(A)].
The red square marked for the residues from helix H0 in the flexible N-terminal part.
Cross-references: PDB:2KLO
Protein: DP04141 (UniProt Q96E09)
Region: residues 1	to 124
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
The 2D 1H,15N heteronuclear single quantum coherence (HSQC) spectra of unbound ARPP1921,22 and FAM122ANterm confirmed that both are IDPs with multiple regions of amino acids with preferred α-helical propensities (using chemical shift index (CSI) analysis; Extended Data Fig. 3a–f).
Cross-references: BMRB:51828
Protein: DP04141 (UniProt Q96E09)
Region: residues 30	to 115
Annotation: protein phosphatase 2A binding (Molecular function)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
Similar NMR interaction experiments with FAM122ANterm showed that the intensities of around 85 cross-peaks (residues 30–115) were reduced with PP2A:B55 (Fig. 1e and Extended Data Fig. 4e). On the basis of these data, we created FAM122AID (amino acids 29–120), which includes all PP2A:B55 interacting residues (Extended Data Figs. 3d–f and 4f,g).