LiteFold/DisProt huggingface dataset:
Protein: DP00699 (UniProt Q9IK91)
Region: residues 1	to 35
Annotation: molecular adaptor activity (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The N-terminal chaperone region of P is stabilized upon binding to its N0 partner, but only the first 35 residues of P, corresponding to the first fluctuating helix observed in solution (helix αP1), were visible in the crystal structure of N32–3830–P50.
Cross-references: PDB:4CO6
Protein: DP00699 (UniProt Q9IK91)
Region: residues 1	to 100
Annotation: disorder to order (Structural transition)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
In addition, the poor chemical-shift dispersion of amide resonances in the HSQC NMR spectrum was typical of disordered protein, but after assigning the NMR spectrum, the secondary-structure propensity (SSP) parameter calculated from Cα and Cβ secondary chemical shifts indicated the presence of five fluctuating α-helices (Supplementary Fig. 2c).
Protein: DP00700 (UniProt O55778)
Region: residues 1	to 404
Annotation: pre-molten globule (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In further support of the absence of an ordered structure, the far-UV CD spectra of Henipavirus PNT and NTAIL at neutral pH are typical of unstructured proteins, as seen from their large negative ellipticity at 198 nm and low ellipticity at 190 nm (Fig. 7A). However, the observed ellipticity values at 200 and 222 nm of Henipavirus NTAIL and of NiV PNT are consistent with the existence of some residual secondary structure, as observed in IDPs adopting a PMG conformation (Fig. 7B).
Protein: DP00700 (UniProt O55778)
Region: residues 1	to 404
Annotation: pre-molten globule (Structural state)
Evidence: dynamic light scattering assay evidence used in manual assertion
Supporting statements:
The obtained RS values (37±2 Å for both NTAIL proteins, and either 55±2 Å or 57±2 Å for NiV and HeV PNT, respectively) highlight a significant increase in the hydrodynamic radius in the presence of urea (see Table 1). These results argue for the presence of residual intramolecular interactions within Henipavirus PNT and NTAIL proteins under native conditions, as expected for proteins adopting a PMG conformation.
Protein: DP00700 (UniProt O55778)
Region: residues 1	to 404
Annotation: pre-molten globule (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 ppm and 8.7 ppm, see frames in Fig. 6) together with the scarcity of NOEs in the amide-amide region are typical of proteins without any stable secondary structure (for examples see [6], [18]), thereby supporting lack of a packed core within Henipavirus PNT and NTAIL domains.
Protein: DP00700 (UniProt O55778)
Region: residues 1	to 404
Annotation: pre-molten globule (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
This abnormal behavior is therefore likely to be ascribed to a rather high content of acidic residues, as already been observed in the case of the intrinsically disordered MeV PNT [18] and NTAIL domains [6], [19], and, more generally, in other IDPs [46].
Protein: DP00700 (UniProt O55778)
Region: residues 1	to 404
Annotation: pre-molten globule (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
These studies suggest that Henipavirus PNT and NTAIL proteins either adopt a PMG conformation or are folded trimers.
Protein: DP00700 (UniProt O55778)
Region: residues 1	to 404
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Henipavirus PNT and NTAIL were found to be highly sensitive to proteolysis, a property that constitutes a hallmark of structural disorder (see [47] and references therein cited).
Protein: DP00700 (UniProt O55778)
Region: residues 200	to 310
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
 The CD spectrum of a freshly purified sample of PNT3 was typical of an IDP, as illustrated by the very pronounced negative peak at 200 nm and low ellipticity in the 190–200 nm region (Figure 5).
Henipavirus phosphoprotein PNT3 region is comprised within the residues 200-310.
Protein: DP00700 (UniProt O55778)
Region: residues 200	to 310
Annotation: amyloid fibril formation (Biological process)
Evidence: electron microscopy evidence used in manual assertion
Supporting statements:
Negative staining transmission electron microscopy (TEM) unequivocally confirmed the presence of amyloid-like fibrils (Figure 4D).
Protein: DP00700 (UniProt O55778)
Region: residues 200	to 310
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
At 2 mg mL−1 (132 μM), the calculated radii of gyration (Rg) obtained after 1 h (Rg = 3.34 ± 0.1 nm) and 1.5 h (Rg = 3.01 ± 0.08 nm) of incubation are consistent with the value expected for a monomeric form of PNT3 in a disordered state according to Flory’s equation (Rg = 3.26 ± 0.03 nm) [58].
The distribution of the maximum particle sizes (Dmax) of the selected ensemble ranges from ~50 to 200 Å, centered on ~100 Å (Figure S3D). The selected ensemble exhibits a high flexibility (Rflex = 88.4 %), a value similar to that of the initial pool (87.2%, Rσ = 1.04) and consistent with pure random-coil conformations.
Henipavirus phosphoprotein PNT3 region is comprised within the residues 200-310.
Protein: DP00700 (UniProt O55778)
Region: residues 200	to 310
Annotation: amyloid fibril formation (Biological process)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
After 2 h of incubation, higher order oligomers/aggregates dominated, as judged from the intensity increase in the low-angle region of the scattering curves (Figure 6A) and from the shape of the total scattered intensities plots (Figure 6B).
In conclusion, SAXS experiments show that PNT3 was monomeric and disordered in the solution, adopting a typical Gaussian chain distribution of its parameters. However, it rapidly aggregates in a concentration-dependent manner to form rod-like particles, a behavior compatible with the formation of fibrillar species.
Henipavirus phosphoprotein PNT3 region is comprised within the residues 200-310.
Protein: DP00700 (UniProt O55778)
Region: residues 200	to 310
Annotation: amyloid fibril formation (Biological process)
Evidence: cell staining evidence used in manual assertion
Supporting statements:
CR-staining experiments showed that cells transfected to express PNT3 capture CR more than cells transfected with an empty vector (Figure 11), providing clues about the formation of PNT3 fibrils also in a cellular context. 
Henipavirus phosphoprotein PNT3 region is comprised within the residues 200-310.
Protein: DP00700 (UniProt O55778)
Region: residues 200	to 310
Annotation: amyloid fibril formation (Biological process)
Evidence: fluorescence recovery after photobleaching evidence used in manual assertion
Supporting statements:
These experiments, beyond shedding light onto the nature of the PNT3 condensates, also confirmed the ability of PNT3 to phase separate in the absence of crowding agents and revealed that the process takes place even in the sub-micromolar concentration range, although a prolonged incubation period at 37 °C was required.
PNT3 was shown to phase-separate in vitro into solid-like condensates, as shown by FRAP.
Henipavirus phosphoprotein PNT3 region is comprised within the residues 200-310.
Protein: DP00700 (UniProt O55778)
Region: residues 300	to 406
Annotation: disorder (Structural state)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
Size-exclusion chromatography was employed to estimate the Rh values of the three sets of model IDPs (Table 2). Experimental Rh values of wt NTAIL and wt PNT4 (2.71 ± 0.09 and 2.34 ± 0.11 nm, respectively) are close to the theoretical ones (Table 1) and similar to the previously determined ones [9].
Experimentally determined Rh matches the theoretical Rh for IDPs [Marsh & Forman-Kay, 2010].
Rt (nm) = 2.54
Protein: DP00700 (UniProt O55778)
Region: residues 300	to 406
Annotation: disorder (Structural state)
Evidence: electrospray ionization fourier transform ion cyclotron resonance mass spectrometry evidence used in manual assertion
Supporting statements:
Native MS was employed to assess the conformational properties of the three sets of IDPs. In this approach, the CSDs resulting from the nanoESI process reflect the overall compactness and relative amounts of the main conformers in the original solution [17,18,22]. Native-MS spectra obtained under non-denaturing conditions for the three variants of NTAIL (Figure 4a), NFM, and PNT4 (Figure S3) display multimodal CSDs, highlighting the heterogeneous conformational ensemble typical of IDPs.
Protein: DP00700 (UniProt O55778)
Region: residues 300	to 406
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Figure S2. Far-UV CD spectra of model IDPs. CD spectra of NTAIL (a), NFM (b), and PNT4 (c) variants.
Typical random coil-like far-UV CD spectrum is displayed for PNT4.
Protein: DP00702 (UniProt P46937)
Region: residues 101	to 171
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
There is no electron density for residues 230–238 of TEAD and residues 101–171 of YAP, and therefore these were not built in the model.
Cross-references: PDB:3KYS
Protein: DP00702 (UniProt P46937)
Region: residues 50	to 171
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The very narrow peak dispersion in the 1H dimension of the 1H–15N HSQC spectrum shows that YAP 50–171 is intrinsically disordered.
Cross-references: BMRB:27290
Protein: DP00705 (UniProt P22943)
Region: residues 1	to 109
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
The apparent molecular mass of Hsp12 deduced from the gel was an overestimated value of 14 kDa (Fig. 2A). Hsp12 was also reported earlier to have an apparent mobility corresponding to a protein of 14.4 kDa [3]. IDPs are known to be unusually mobile on SDS-PAGE.
Protein: DP00705 (UniProt P22943)
Region: residues 1	to 109
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
For Hsp12, a large negative peak around 200 nm was found in aqueous solution (Fig. 4A). This curve was specific to the random coil structure corresponding to an unstructured protein in solution.
Protein: DP00705 (UniProt P22943)
Region: residues 1	to 109
Annotation: lipid binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
To characterize the interaction between Hsp12 and phospholipids, ITC and DSC were performed (Fig. 5, Fig. 6). The negative peaks which appeared with each addition of protein showed an exothermic reaction and therefore an interaction between Hsp12 and liposomes (Fig. 5A)
Protein: DP00705 (UniProt P22943)
Region: residues 1	to 109
Annotation: lipid binding (Molecular function)
Evidence: differential scanning calorimetry evidence used in manual assertion
Supporting statements:
Thanks to DSC, temperature phase transition was measured at 38 °C with a peak area of 1441 μV/s for the liposome alone (Fig. 6). With Hsp12, a shift of +1 °C was observed indicating that the physicochemical properties of the phospholipid vesicle were changed. An increase in Tm is indicative of membrane rigidification. Moreover, with Hsp12, the peak area was lower (920 μV/s) indicating a change in enthalpy. This reflected a modification in the fatty acid chains, probably due to a partial insertion of Hsp12 in the hydrocarbon moiety. Hsp12 might therefore play a role in the stress‐induced remodeling of membrane lipids.
Protein: DP00705 (UniProt P22943)
Region: residues 1	to 109
Annotation: protein folding chaperone (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
NMR analysis indicated that Hsp12 is monomeric and intrinsically unfolded in solution, but switches to a 4-helical conformation upon binding to membrane-mimetic SDS micelles. The structure of micelle-bound Hsp12 reported here is consistent with its recently proposed function as a membrane-stabilising 'lipid chaperone'. Taken together, our data suggest that DR-induced Hsp12 expression contributes to lifespan extension, possibly via membrane alterations
Protein: DP00705 (UniProt P22943)
Region: residues 1	to 109
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 15N-1H HSQC spectrum showed poor resonance dispersion in the proton dimension, which suggested that Hsp12 is intrinsically disordered in aqueous buffer (Fig. 3A).
Cross-references: BMRB:18523
Protein: DP00705 (UniProt P22943)
Region: residues 1	to 109
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 15N-1H HSQC spectra of Hsp12 showed a dose-dependent increase in dispersion in response to SDS, indicating that Hsp12 adopts a folded conformation upon micelle binding (Fig. 3B).
Consistent with this, analysis of the assigned chemical shifts in Hsp12 using CSI [25] suggested that micelle binding induces the formation of four α-helices (Fig. 4G). These α-helices cover the majority of the polypeptide and comprise residues F9-A16 (Helix I), Q22-A41 (Helix II), V52-G63 (Helix III) and L74-E94 (Helix IV).
Protein: DP00705 (UniProt P22943)
Region: residues 1	to 109
Annotation: cellular heat acclimation (Biological process)
Evidence: genetic transformation evidence used in manual assertion
Supporting statements:
We found that the deletion of HSP12 does not significantly affect growth at elevated temperatures (30°C or 37°C) and that it may cause a slight inhibition of growth at lower temperatures (8°C). However, a strong growth defect was observed when the cells were exposed to a short sublethal heat shock for 20 min at 58°C. The heat-shocked WT cells produced the same number of colony-forming units (cfu) as cultures maintained at 30°C. In contrast, the ΔHSP12 strain showed a drastic loss of viability after exposure to 58°C. This suggests that Hsp12 exhibits an important protective function under heat shock conditions.
Protein: DP00705 (UniProt P22943)
Region: residues 1	to 109
Annotation: response to oxidative stress (Biological process)
Evidence: genetic transformation evidence used in manual assertion
Supporting statements:
WT and mutant strains were grown in the presence of 5 mM H2O2. As in the case of the heat-shocked cells, H2O2 did not affect the growth of the WT strain, but the growth of the ΔHSP12 strain was impaired (Figure 1A).
Protein: DP00705 (UniProt P22943)
Region: residues 1	to 109
Annotation: response to osmotic stress (Biological process)
Evidence: genetic transformation evidence used in manual assertion
Supporting statements:
To further analyze the influence of Hsp12 on S. cerevisiae growth under stress conditions, we also determined growth under osmotic stress. In the deletion strain, growth was reduced in the presence of 0.4 M NaCl, whereas the growth of the WT strain was not affected (Figure 1A).
Protein: DP00705 (UniProt P22943)
Region: residues 1	to 109
Annotation: membrane (Cellular component)
Evidence: qualitative western immunoblotting evidence used in manual assertion
Supporting statements:
Western blot analysis showed that Hsp12 is indeed expressed with increasing cell density. At low optical densities, during the early logarithmic growth phase, Hsp12 was exclusively detected in the cytosolic fraction. Further growth led to additional accumulation of Hsp12, first in the membrane and then in the cell wall fraction. This localization pattern suggests that the protein is present both in soluble and membrane-associated forms.
Protein: DP00705 (UniProt P22943)
Region: residues 1	to 109
Annotation: cytosol (Cellular component)
Evidence: qualitative western immunoblotting evidence used in manual assertion
Supporting statements:
Western blot analysis showed that Hsp12 is indeed expressed with increasing cell density. At low optical densities, during the early logarithmic growth phase, Hsp12 was exclusively detected in the cytosolic fraction. Further growth led to additional accumulation of Hsp12, first in the membrane and then in the cell wall fraction. This localization pattern suggests that the protein is present both in soluble and membrane-associated forms.
Protein: DP00705 (UniProt P22943)
Region: residues 1	to 109
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
When we analyzed the structure by circular dichroism (CD) spectroscopy in the far ultraviolet (UV) region, we found, much to our surprise, that the protein did not exhibit any detectable secondary structure, suggesting that the protein is completely unfolded in solution (Figure 2A). Because of its colocalization with membranes, we investigated the effects of lipids or lipid-like molecules on the structure of Hsp12. Strikingly, the presence of either dimyristoylphosphatidylglycerol (DMPG) or SDS resulted in a Far-UV CD spectrum resembling that of an α-helical protein (Figure 2A).
The highest α-helical content is reached at medium lengths of the fatty acid tail of the phospholipids (10.0 PG, 14.0 PG, or 16.0 PG) (Figure 2B inset); longer fatty acids resulted in a decrease in α-helical content of Hsp12 (18.0 PG).
Protein: DP00705 (UniProt P22943)
Region: residues 1	to 109
Annotation: lipid binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
When we analyzed the structure by circular dichroism (CD) spectroscopy in the far ultraviolet (UV) region, we found, much to our surprise, that the protein did not exhibit any detectable secondary structure, suggesting that the protein is completely unfolded in solution (Figure 2A). Because of its colocalization with membranes, we investigated the effects of lipids or lipid-like molecules on the structure of Hsp12. Strikingly, the presence of either dimyristoylphosphatidylglycerol (DMPG) or SDS resulted in a Far-UV CD spectrum resembling that of an α-helical protein (Figure 2A).
The highest α-helical content is reached at medium lengths of the fatty acid tail of the phospholipids (10.0 PG, 14.0 PG, or 16.0 PG) (Figure 2B inset); longer fatty acids resulted in a decrease in α-helical content of Hsp12 (18.0 PG).
Protein: DP00706 (UniProt Q15517)
Region: residues 60	to 171
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Soluble GST-GS was mainly helical, and freeGS was unstructured in solution as determined by CD measurements (Fig. 8E, F).
Protein: DP00706 (UniProt Q15517)
Region: residues 60	to 171
Annotation: amyloid fibril formation (Biological process)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
In the presence of increasing concentrations of GST-GS, ThT exhibited a dose-dependent enhanced fluorescence emission at 482 nm, consistent with an amyloid-like nature of the fibrillar assemblies (Fig. 7A).
Moreover, fibrillar GST-GS binds CR, as shown by the spectral red shift observed in the CR absorption peak, and CR-stained GST-GS aggregates exhibited green yellow birefringence under polarized light, features considered characteristic of amyloid structures (Supplemental Fig. 1 A, B).
Protein: DP00706 (UniProt Q15517)
Region: residues 60	to 171
Annotation: amyloid fibril formation (Biological process)
Evidence: Fourier-transform infrared spectroscopy evidence used in manual assertion
Supporting statements:
The recorded FTIR spectrum of fibrillar GST-GS obtained after incubation of the polypeptide at 4°C for 30 d (Fig. 8A) was centered at 1637 cm−1 (Fig. 8D).
Protein: DP00707 (UniProt Q9UER7)
Region: residues 347	to 420
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In contrast, DAXX161-243 and DAXX347-420 appeared partially aggregated or mostly unfolded, respectively.
Protein: DP00707 (UniProt Q9UER7)
Region: residues 495	to 740
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We assigned the NMR resonances of 15N,13C cDAXX (Figures S3A and S3B), which have the limited chemical shift dispersion and sharp line widths of a typical intrinsically disordered region (IDR) (Figure 3A
These spectral properties indicate that many cDAXX conformations are in fast exchange and that the IDR exhibits little structure.
Protein: DP00707 (UniProt Q9UER7)
Region: residues 495	to 740
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
A titration of unlabeled SPOPMATH into 15N,13C cDAXX and monitored by CON spectra resulted in a dose-dependent loss of signal intensity along several cDAXX regions
Protein: DP00707 (UniProt Q9UER7)
Region: residues 495	to 740
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
SPOP and DAXX localize to SPOP/DAXX bodies.
SPOP and DAXX form nuclear bodies with liquid properties.
DAXX and SPOP therefore both re-localized from their original subcellular location when expressed together. The SPOP/DAXX bodies possess liquid properties as evidenced by their ability to undergo fusion events within minutes (Fig. 1C, D, Supplemental Videos S1, S2). These properties place them into the category of liquid membraneless organelles.
 It is clear from these observations that SPOP and DAXX not only bind to each other, but binding shifts them to a different liquid organelle.
This observation suggests that weak multivalent interactions between SPOP and DAXX result in a sol-gel transition coupled to phase separation, as defined by Harmon et al (Harmon et al., 2017).
Protein: DP00707 (UniProt Q9UER7)
Region: residues 566	to 739
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The C-terminal fragment mDAXX566-739 had random coil 1HN shifts, indicating that indeed, as predicted, it is predominantly disordered.
Protein: DP00707 (UniProt Q9UER7)
Region: residues 161	to 243
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In contrast, DAXX161-243 and DAXX347-420 appeared partially aggregated or mostly unfolded, respectively.
Protein: DP00707 (UniProt Q9UER7)
Region: residues 435	to 486
Annotation: disorder (Structural state)
Evidence: curator inference from database used in manual assertion
Supporting statements:
This poly-E region is inferred by the curator to be disordered, based on MobiDB-Lite and according to experimental evidence demonstrating that poly-E repeats display random-coil-like conformation (PMID:16949547)