LiteFold/DisProt huggingface dataset:
Protein: DP01538 (UniProt P04147)
Region: residues 419	to 502
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: fluorescence microscopy evidence used in manual assertion
Supporting statements:
Because the Pab1ΔP lacks an LCR yet retains the ability to phase-separate, we examined its assembly morphology by microscopy. Pab1ΔP assemblies largely retained the droplet-cluster morphology of full-length Pab1 quinary assemblies (Fig. 3G, H). Together, these results point to an electrostatically driven phase-separation dependent on molecular determinants in the RRM regions, which is enhanced, but not solely caused, by the P domain.
Protein: DP01538 (UniProt P04147)
Region: residues 1	to 577
Annotation: intracellular non-membrane-bounded organelle (Cellular component)
Evidence: fluorescence microscopy evidence used in manual assertion
Supporting statements:
Pab1 shows diffuse localization under favorable growth conditions (near 30°C), and localizes to stress granules—large cytosolic foci—within minutes of a shift to 46°C (Fig. 1A). At 42°C, Pab1 is not recruited to stress granules detectable by standard fluorescence microscopy (Fig. 1A, (Cherkasov et al., 2013; Wallace et al., 2015)).
After a more severe shock at 46°C, a greater proportion of Pab1 is recruited into small and large sedimentable assemblies (Fig. 1) coincident with stress-granule formation.
We found that 15μM Pab1 (physiological ~20 μM, see Methods) was soluble at 30°C, but demixed to form large particles after a 46°C, 30-minute treatment (Fig. 2A,B).
Protein: DP01539 (UniProt O57173)
Region: residues 1	to 50
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
In the model, both F1L N termini protrude away from the Bcl-2 fold in an extended configuration spanning residues 1–50 in addition to the N-terminal hexahistidine tag (Fig. 2). The shape of both F1L N termini in the model suggests an absence of ordered secondary structure, thus rendering F1L residues 1–50 unfolded.
Cross-references: SASBDB:SASDBV4
Protein: DP01541 (UniProt Q9DBZ9)
Region: residues 1	to 267
Annotation: disorder (Structural state)
Evidence: temperature-induced protein unfolding evidence used in manual assertion
Supporting statements:
The murine SYD1A N-terminal domain was resistant to thermal denaturation. Thus, mSYD1A contains an intrinsically disordered domain (IDD) at the N terminus.
Protein: DP01541 (UniProt Q9DBZ9)
Region: residues 1	to 267
Annotation: self-inhibition (Disorder function)
Evidence: temperature-induced protein unfolding evidence used in manual assertion
Supporting statements:
Deletion of the intrinsically disordered domain (IDD) and C2 domain resulted in a doubling of mSYD1A GAP activity. The IDD alone as well as the IDD-C2 domain supplied in cis where able to repress activity of the isolated mSYD1A GAP domain. Thus, the mSYD1A GAP activity is regulated through protein-protein interactions with the intrinsically disordered N-terminal domain.
Protein: DP01541 (UniProt Q9DBZ9)
Region: residues 1	to 267
Annotation: protein binding (Molecular function)
Evidence: temperature-induced protein unfolding evidence used in manual assertion
Supporting statements:
The N-terminal intrinsically disordered domain of mSYD1A is a critical functional module that binds at least three different ligands: the mSYD1A GAP domain, nsec1/munc18-1, and liprin-α2.
Protein: DP01542 (UniProt P06401)
Region: residues 1	to 545
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
As shown by Coomassie stained SDS gels, the PR-NTD was highly susceptible to proteolysis resulting in nearly complete degradation with little intact NTD remaining (Fig. 6a, compare lanes 2 and 6).
Protein: DP01542 (UniProt P06401)
Region: residues 1	to 566
Annotation: disorder (Structural state)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
The hinge region and N terminal domain are represented by schematics due to lack of atomic structure. Representative peptide deuterium build up curves from each domain are indicated at top.
Protein: DP01542 (UniProt P06401)
Region: residues 632	to 641
Annotation: protein binding (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
However, substitution of two other residues in the CTE (R637A/K638A), which undergo chemical shift changes, abolished JDP2 binding (Fig. 4B). Truncation mutations of the CTE constructs were also examined for their effects on binding to JDP2 (Fig. 5A). JDP2 bound with equal efficiency to CTE constructs deleted from aa 650 to 648 and to 641, whereas no binding was detected with further deletion of the CTE to aa 632 (Fig. 5B). These data collectively indicate that residues in the CTE closest to the core DBD (aa 632–641) are most important for binding JDP2 and that residues in the core are dispensable.
Protein: DP01542 (UniProt P06401)
Region: residues 165	to 545
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Far UV CD spectroscopy was used to examine secondary structure of the PR NTD. The CD spectrum exhibited little or no negative ellipticity at 222 nm and has a large negative maximum below 210 nm that is typical of protein without a stable α-helix and random coil conformation (Fig. 1D).
Protein: DP01542 (UniProt P06401)
Region: residues 165	to 545
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
An increase in negative ellipticity at 222 nm and a decrease <210 nm was observed in the presence of TMAO indicative of a gain in α-helical content and a reduction in random coil (Fig. 1D).
Protein: DP01542 (UniProt P06401)
Region: residues 165	to 545
Annotation: disorder (Structural state)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
The overlay shows that NTD and hinge exhibit the highest rate of hydrogen-deuterium exchange, whereas structurally stable helices in the LBD and DBD exhibit dramatically less exchange. These results demonstrate the highly dynamic unstructured properties of the NTD in the context of the intact receptor.
Protein: DP01542 (UniProt P06401)
Region: residues 165	to 545
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
The PR NTD was highly susceptible to proteolytic degradation resulting in nearly complete degradation with little or no intact NTD remaining (Fig. 6A, compare lane 1 with lane 3).
Protein: DP01542 (UniProt P06401)
Region: residues 350	to 428
Annotation: disorder to order (Structural transition)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
). When PR NTD and TBPC were mixed together, protected PR NTD fragments were detected, and the patterns were distinct with each mAb indicating that multiple sites within the NTD change their accessibility to trypsin in the presence of TBPC (Fig. 6B). Protection against partial proteolysis indicates that the NTD folds into a more compact conformation when complexed with TBPC in addition to the increased secondary structure detected by CD analysis.
CD experiments show the region that changes to a more ordered state upon TBOC binding is the 350-428.
Protein: DP01542 (UniProt P06401)
Region: residues 165	to 535
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The AnDBD fragment of PR absorbs with a small negative peak at 222 nm but exhibits much more absorbance below 210 nm (Fig.3A). A similar spectrum was obtained with the single-domain AN polypeptide (Fig. ​3B), indicating that both PR polypeptides contain a large amount of random coil with some underlying helical content.
Protein: DP01542 (UniProt P06401)
Region: residues 165	to 545
Annotation: disorder to order (Structural transition)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
A more compact structure was also shown by the increased intensity of fluorescence signal and blue shift of maximal wavelength. The apparent thermodynamic parameters of TMAO-induced folding are ΔG = −3.6 ± 0.7; m = 2.2 ± 0.4 (Fig. 1B).
Both the increase in quantum yield and the blue shift in fluorescence maximum indicate the formation of a compact structure in the presence of TMAO. The conformational transition in the PR NTD occurs in a cooperative manner, as shown by monitoring the level of fluorescence at 329 nm (upon excitation at 278) and the shift in emission maximum as a function of TMAO concentration (Fig. 1C).
Protein: DP01542 (UniProt P06401)
Region: residues 1	to 545
Annotation: disorder (Structural state)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Both FE and CD analysis demonstrated that the NTD is largely unstructured under native conditions and acquires a substantial increase in α-helical content and a more compact tertiary structure in the presence of the natural osmolyte TMAO. 
 Similar results were obtained with NTD of PR-B (data not shown).
Protein: DP01542 (UniProt P06401)
Region: residues 1	to 545
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Both FE and CD analysis demonstrated that the NTD is largely unstructured under native conditions and acquires a substantial increase in α-helical content and a more compact tertiary structure in the presence of the natural osmolyte TMAO. 
 Similar results were obtained with NTD of PR-B (data not shown).
Protein: DP01542 (UniProt P06401)
Region: residues 165	to 559
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The overlay shows that NTD and hinge exhibit the highest rate of hydrogen-deuterium exchange, whereas structurally stable helices in the LBD and DBD exhibit dramatically less exchange. These results demonstrate the highly dynamic unstructured properties of the NTD in the context of the intact receptor.
Protein: DP01542 (UniProt P06401)
Region: residues 632	to 682
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence used in manual assertion
Supporting statements:
The overlay shows that NTD and hinge exhibit the highest rate of hydrogen-deuterium exchange, whereas structurally stable helices in the LBD and DBD exhibit dramatically less exchange. These results demonstrate the highly dynamic unstructured properties of the NTD in the context of the intact receptor.
Protein: DP01542 (UniProt P06401)
Region: residues 1	to 545
Annotation: protein binding (Molecular function)
Evidence: glutathione S-transferase pull-down assay evidence used in manual assertion
Supporting statements:
Full-length PR-B also bound specifically with TBPC by GST-pulldown assay with similar efficiency as the isolated PR-B NTD (Fig. 3C).
Protein: DP01542 (UniProt P06401)
Region: residues 165	to 545
Annotation: protein binding (Molecular function)
Evidence: glutathione S-transferase pull-down assay evidence used in manual assertion
Supporting statements:
The NTD of PR-A exhibited specific binding with immobilized TBPC-GST over that of free GST, and the binding increased with varying amounts of input PR-A NTD (Fig. 3, A and B). Full-length PR-B also bound specifically with TBPC by GST-pulldown assay with similar efficiency as the isolated PR-B NTD (Fig. 3C).
Protein: DP01542 (UniProt P06401)
Region: residues 165	to 545
Annotation: protein binding (Molecular function)
Evidence: surface plasmon resonance evidence used in manual assertion
Supporting statements:
The overall binding showed a moderate rate of association and a slow dissociation pattern with a calculated binding affinity (KD) of 0.17 μm (Fig. 4D). TBPC binding by SPR with isolated PR domains was only detected with NTD (Fig. 4E) but not with LBD as analyte (data not shown).
Protein: DP01542 (UniProt P06401)
Region: residues 350	to 428
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The experimental summation of CD spectra of the protein mixtures was only different from the theoretical with the aa 350–428 fragment. No differential was detected with the other NTD fragments indicating that TBP interaction and associated structural changes require a region of the PR NTD between aa 350 and 428 (Fig. 7B).
Protein: DP01542 (UniProt P06401)
Region: residues 350	to 428
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The experimental summation of CD spectra of the protein mixtures was only different from the theoretical with the aa 350–428 fragment. No differential was detected with the other NTD fragments indicating that TBP interaction and associated structural changes require a region of the PR NTD between aa 350 and 428 (Fig. 7B).
Protein: DP01542 (UniProt P06401)
Region: residues 636	to 654
Annotation: protein binding (Molecular function)
Evidence: glutathione S-transferase pull-down assay evidence used in manual assertion
Supporting statements:
To further explore the role of the CTE in binding JDP2, a synthetic peptide corresponding to CTE sequence aa 636–654 (Fig. 6A) was tested for its ability to compete for JDP2 binding to PR. The CTE peptide inhibited the interaction between JDP2 bZIP and DBD-CTE650 in a GST pulldown assay, whereas a scrambled control peptide with the same amino acid composition had little effect (Fig. 6B). This result indicates that the CTE alone is sufficient for binding JDP2 and that a specific sequence is required.
Protein: DP01542 (UniProt P06401)
Region: residues 637	to 641
Annotation: acetylation display site (Disorder function)
Evidence: qualitative western immunoblotting evidence used in manual assertion
Supporting statements:
Again, KK6 displayed decreased levels of acetylation, suggestive that some K638 is acetylated in this mutant receptor. However, K-A PR-B, containing all three Lys to Ala mutations, appeared unmodified relative to R5020-treated wt PR-B. These data indicate that PR-B is acetylated at two or more Lys residues within the KXKK motif in the hinge region and disruption of all three Lys residues is necessary to abolish PR acetylation.
Protein: DP01542 (UniProt P06401)
Region: residues 188	to 192
Annotation: phosphorylation display site (Disorder function)
Evidence: qualitative western immunoblotting evidence used in manual assertion
Supporting statements:
We first tested K-A PR-B phosphorylation relative to wt using Western blotting and the available antibodies to CDK2 phosphorylation sites Ser190 and Ser400 and to the MAPK sites Ser294 and Ser345 (29, 31).
Protein: DP01542 (UniProt P06401)
Region: residues 398	to 402
Annotation: phosphorylation display site (Disorder function)
Evidence: qualitative western immunoblotting evidence used in manual assertion
Supporting statements:
We first tested K-A PR-B phosphorylation relative to wt using Western blotting and the available antibodies to CDK2 phosphorylation sites Ser190 and Ser400 and to the MAPK sites Ser294 and Ser345 (29, 31).
Protein: DP01542 (UniProt P06401)
Region: residues 292	to 296
Annotation: phosphorylation display site (Disorder function)
Evidence: qualitative western immunoblotting evidence used in manual assertion
Supporting statements:
We first tested K-A PR-B phosphorylation relative to wt using Western blotting and the available antibodies to CDK2 phosphorylation sites Ser190 and Ser400 and to the MAPK sites Ser294 and Ser345 (29, 31).
Protein: DP01542 (UniProt P06401)
Region: residues 342	to 347
Annotation: phosphorylation display site (Disorder function)
Evidence: qualitative western immunoblotting evidence used in manual assertion
Supporting statements:
We first tested K-A PR-B phosphorylation relative to wt using Western blotting and the available antibodies to CDK2 phosphorylation sites Ser190 and Ser400 and to the MAPK sites Ser294 and Ser345 (29, 31).
Protein: DP01542 (UniProt P06401)
Region: residues 637	to 641
Annotation: negative regulation of phosphorylation (Biological process)
Evidence: qualitative western immunoblotting evidence used in manual assertion
Supporting statements:
We first tested K-A PR-B phosphorylation relative to wt using Western blotting and the available antibodies to CDK2 phosphorylation sites Ser190 and Ser400 and to the MAPK sites Ser294 and Ser345 (29, 31).
Wt PR underwent a ligand-dependent upshift at 30 min of treatment. However, acetylation-deficient mutant PR exhibited a delay for at least 3 h of progestin exposure. Basally phosphorylated Ser190, however, is comparatively well phosphorylated between wt and K-A PR-B. Wt PR displayed heightened Ser294, Ser345, and Ser400 phosphorylation after 30 min of progestin, whereas K-A phosphorylation at these sites was not robust until at least 3 h.
Protein: DP01542 (UniProt P06401)
Region: residues 637	to 641
Annotation: maintenance of protein location in nucleus (Biological process)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
To test this possibility we transiently transfected HeLa cells with wt or K-A PR-B, serum starved, and then treated cells with R5020 (1 h) before subcellular fractionation and Western blotting (Fig. 4A). WCL were run next to cytoplasmic and nuclear fractions as controls for total PR levels among the cells. Wt PR-B was present in both the cytoplasm and the nucleus in the absence of progestin. Upon treatment, a robust band appeared in the nuclear fraction. Acetylation-deficient PR-B, however, was not detectable in the nucleus in both the absence and presence of ligand.
Taken together, these data indicate that rapid nuclear localization precedes efficient PR-B phosphorylation events; nuclear retention may facilitate persistent PR phosphorylation.
Acetylation motif mutant PR displays defective nuclear retention
Protein: DP01542 (UniProt P06401)
Region: residues 637	to 641
Annotation: regulation of transcription, DNA-templated (Biological process)
Evidence: quantitative reverse transcription polymerase chain reaction evidence used in manual assertion
Supporting statements:
In response to progestin, wt PR-B robustly induced SGK expression, whereas both K-Q and K-T PR-B exhibited a weak transcriptional response to ligand. In similar experiments, TF gene regulation was assessed for wt, K-Q, and K-T PR-B at 18 h of progestin treatment. Again, regulation of TF mRNA in response to progestins was not altered by PR acetylation (data not shown). These data indicate that PR acetylation selectively inhibits hormone-dependent PR transcriptional responses on specific promoter contexts (SGK), whereas other promoters (c-myc and TF) remain insensitive to this modification (Fig. 8).
Protein: DP01543 (UniProt P84634)
Region: residues 735	to 752
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Interestingly, it appears that the C-terminal ∼18 residues (residues: 735–752) are relatively unstructured and poorly defined, having distinct conformations in different structures. This observation is in good agreement with the small chemical shift deviations and lack of the interresidual NOE connectivites over the region
Cross-references: PDB:2KOU
Protein: DP01544 (UniProt Q8WV28)
Region: residues 5	to 50
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The chemical shift dispersion of the backbone amides is about 1 part per million (ppm), which is compatible with the intrinsically disordered conformation of the N terminus in aqueous solution.
This result was further corroborated by nuclear magnetic resonance (NMR) spectroscopy, which demonstrated that the isolated SLP-65 N terminus was intrinsically disordered in solution (Fig. 1D and fig. S5) as inferred from calculations based on the chemical shifts of backbone amides, Cα and Cβ resonances (14).
Protein: DP01544 (UniProt Q8WV28)
Region: residues 5	to 50
Annotation: lipid binding (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
We therefore prepared small unilamellar vesicles (SUVs) composed of 75% phosphatidylcholine and 25% phosphatidylethanolamine and incubated them with recombinant wild-type SLP-65 protein or its N-terminal mutants, ΔN-SLP-65 and L18K-SLP-65.
Wild-type SLP-65 was concentrated in the SUV fractions and was almost absent in the soluble fractions. Conversely, none of the two signaling-incompetent SLP-65 mutants floated with the SUVs, but remained soluble (Fig. 1C). Hence, these data suggest that the N terminus of SLP-65 is capable of directly binding to general components of cellular membranes.
Protein: DP01544 (UniProt Q8WV28)
Region: residues 1	to 330
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
The sharp peaks observed in the 15N-HSQC (heteronuclear single quantum coherence) spectrum of SLP65 are typical for IDPs, implying fast reorientation motion of protein segments.
Protein: DP01544 (UniProt Q8WV28)
Region: residues 1	to 40
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
Thus, phase separation of SLP65 and CIN85 occurs in vitro at protein concentrations found in vivo, but only in the presence of vesicles. This finding was confirmed further by the increased phase transition threshold of 10 µM for the N-terminal SLP65 deletion mutant, SLP65ΔN (Fig. 1f), which is unable to attach to vesicles13 and that does neither support granule formation nor BCR-activated Ca2+ mobilization when expressed in live B cells (see Fig. 1a and Supplementary Fig. 1). Importantly, no phase separation was observed when SLP65 was mixed with SUVs in the absence of CIN85Δ57 (Fig. 1g) demonstrating again the concerted action of all three components that is needed for droplet formation in vitro.
The vesicular attachment of SLP65 appears to provide a local seeding point that concentrates SLP65 to facilitate the recruitment of CIN85 and to initiate phase separation.
Protein: DP01544 (UniProt Q8WV28)
Region: residues 1	to 40
Annotation: lipid binding (Molecular function)
Evidence: flow cytometry evidence used in manual assertion
Supporting statements:
Collectively, these data showed that the N-terminal lipid binding domain preferentially attaches at small vesicles with curved membranes and that this feature allows for tripartite phase separation at physiological concentrations, i.e. in vitro as well as in vivo.
Protein: DP01546 (UniProt P84051)
Region: residues 1	to 11
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Unstructured residues are indicated in lower case.
Cross-references: PDB:2PYO
Protein: DP01546 (UniProt P84051)
Region: residues 2	to 25
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Chemical shift indices obtained from the experimental Cα and Cβ chemical shifts confirm the presence of the histone fold core secondary structure elements with disordered tails for both histones, similar to the human dimer (Fig. 1a).
Cross-references: PDB:7PJ1