LiteFold/DisProt huggingface dataset:
Protein: DP00075 (UniProt P11387)
Region: residues 1	to 214
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: Fourier-transform infrared spectroscopy evidence used in manual assertion
Supporting statements:
To monitor the secondary structure content of the condensates, we utilized Fourier transform infrared (FTIR) spectroscopy directly applied to protein condensates harvested by centrifugating samples after the pH jump (spin assay, Fig. 3E). Before the pH jump, the second derivative spectrum of hNTD showed a main component at ~1644 cm − 1 , indicative of disordered structures [42]. Additionally, low-intensity peaks at ~1677 and ~1688 cm − 1 , within the spectral re­ gions of turns and β-sheets (black line in Fig. 3E), suggested the existence of some residual secondary structure [43]. These elements of secondary structure were also observed in the far-UV CD spectrum of hNTD recorded in alkaline phosphate buffer (Fig. S4A). After the pH jump, the FTIR spectrum of the supernatant (red line in Fig. 3E) resembled that observed before the pH jump, with the main peak shifted from ~1644 to ~1652 cm − 1 , suggesting that the pH jump induced only minor changes in the secondary structure of unassembled hNTD. The FTIR spectrum of the pellet (blue line in Fig. 3E) collected after the pH jump displayed the main peak at ~1652 cm − 1 and a new component at low intensity around 1630 cm − 1 , implying the formation of intermolecular β-sheets [42]. Overall, our data suggest that pH-induced condensation of hNTD does not induce drastic conformational changes within its disordered structure, and the involvement of intermolecular β-sheet structures in stabilizing protein condensates appears to be minimal. In summary, we have observed that pH jump can initiate the liquid condensation of hNTD.
Protein: DP00075 (UniProt P11387)
Region: residues 1	to 214
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: immunofluorescence confocal microscopy evidence used in manual assertion
Supporting statements:
Since turbidimetry alone does not specifically confirm LLPS and could be ascribable to the formation of amorphous/fibrillar aggregates, confocal microscopic analyses were conducted to identify LLPS hall­ marks: spherical shape, the ability to undergo fusion events, and liquid- like behavior [41]. The morphology and material properties of pH- induced condensates were investigated via confocal fluorescence mi­croscopy and FRAP analysis on the hNTD-GFP construct.
Condensates of hNTD-GFP obtained at low salt concentration (50 mM NaCl) displayed an average area of 0.65 ± 0.35 μ m 2 (Fig. 3B) and a liquid-like behavior, coalescing readily (Fig. 3C) and recovering fluo­ rescence efficiently after photobleaching (~80 % within 1 min) (Fig. 3D). Droplet size decreased with increasing salt concentration: their areas halved from 50 to 150 mM NaCl and were reduced ten times from 50 to 300 mM NaCl (Fig. 3B).
Protein: DP00076 (UniProt P06786)
Region: residues 632	to 652
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB structure shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:1BJT
Protein: DP00076 (UniProt P06786)
Region: residues 1072	to 1106
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB structure shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:1BJT
Protein: DP00076 (UniProt P06786)
Region: residues 1179	to 1201
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB structure shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:1BJT
Protein: DP00076 (UniProt P06786)
Region: residues 1071	to 1106
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB structure shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:4GFH
Protein: DP00076 (UniProt P06786)
Region: residues 259	to 274
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB structure shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:1QZR
Protein: DP00076 (UniProt P06786)
Region: residues 409	to 418
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The disorder region is missing from the pdb but not metioned in the article.
Cross-references: PDB:1BGW
Protein: DP00076 (UniProt P06786)
Region: residues 1077	to 1106
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The disorder region is missing from the pdb but not metioned in the article.
Cross-references: PDB:1BGW
Protein: DP00076 (UniProt P06786)
Region: residues 1178	to 1201
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The disorder region is missing from the pdb but not metioned in the article.
Cross-references: PDB:1BGW
Protein: DP00076 (UniProt P06786)
Region: residues 633	to 681
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The segment of 48 amino acids between the two subfragments (residues 634-681) is disordered.
Cross-references: PDB:1BGW
Protein: DP00076 (UniProt P06786)
Region: residues 409	to 420
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB structure shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:4GFH
Protein: DP00076 (UniProt P06786)
Region: residues 259	to 275
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB structure shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:4GFH
Protein: DP00076 (UniProt P06786)
Region: residues 409	to 418
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB structure shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:1BJT
Protein: DP00077 (UniProt P07248)
Region: residues 75	to 103
Annotation: disorder (Structural state)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
In conjunction with the low hNOE values, lack of protection from exchange, low R1,H values, and random-coil chemical shift values, the results confirm that the N-terminal region displays all the hallmarks of an unstructured polypeptide, right up to S103 or F104, the first hydrogen-bonded residue of the first zinc-finger.
Protein: DP00077 (UniProt P07248)
Region: residues 75	to 103
Annotation: molecular adaptor activity (Molecular function)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
Mutation and deletion analyses of ADR1 have identified the two (Cys2,His2) zinc fingers, residues 103 to 155, plus approximately 20 residues preceding the first finger, the proximal region, as the minimal portion of ADR1 capable of sequence-specific binding to the DNA promoter sequence UAS1 (upstream activation sequence 1; Thukral et al 1991a, Thukral et al 1991b).
Protein: DP00077 (UniProt P07248)
Region: residues 75	to 103
Annotation: nucleic acid binding (Molecular function)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
We conclude that the region of ADR1-DBD essential for high-affinity binding undergoes a disorder-to-order transition upon binding to its cognate DNA and, together with the zinc fingers, forms a cohesive molecular complex with the nucleic acid.
Protein: DP00077 (UniProt P07248)
Region: residues 75	to 103
Annotation: disorder to order (Structural transition)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
ADR1-DBD undergoes a disorder-to-order transition upon binding to its cognate DNA, with the largest changes occurring in the N-terminal proximal region.
Protein: DP00077 (UniProt P07248)
Region: residues 84	to 102
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We have used a set of HN-HN NOEs derived from a perdeuterated protein–DNA complex to describe the fold of ADR1 bound to the UAS1 binding site.
Cross-references: PDB:2ADR
Protein: DP00077 (UniProt P07248)
Region: residues 84	to 102
Annotation: nucleic acid binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The region responsible for sequence-specific DNA binding by the transcription factor ADR1 contains two Cys2–His2 zinc fingers and an additional N-terminal proximal accessory region (PAR).
Protein: DP00077 (UniProt P07248)
Region: residues 84	to 102
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The N-terminal (non-finger) PAR is unstructured in the absence of DNA and undergoes a folding transition on binding the DNA transcription target site.
Protein: DP00077 (UniProt P07248)
Region: residues 86	to 102
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The dramatic chemical shift perturbations of the N-terminus upon DNA binding are remarkably consistent with mutagenesis data that previously defined the essential N-terminal region. 1H and 13C chemical shift perturbation become significant starting at residue 86.
Furthermore the residues more perturbed lie between P87 and P97, flanking the site of the affinity-enhancing suppressor mutation R91K.
Protein: DP00077 (UniProt P07248)
Region: residues 86	to 102
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The study concluded that the two zinc fingers are pre-structured and do not undergo significant conformational change upon DNA binding. In contrast, residues 86 to 102 in the N-terminal proximal region exhibit large chemical shift perturbations upon DNA binding and do not exhibit regular secondary structure in either the free or bound form [from PMID:9642072].
Protein: DP00077 (UniProt P07248)
Region: residues 86	to 102
Annotation: nucleic acid binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The severely perturbed N-terminus does not appear to interact with the exposed, unperturbed portions of the zinc finger in the protein-DNA complex.
These data taken together suggest that the region P87-P97 plays a role in contacting DNA and therby increases the binding affinity of the construct.
Protein: DP00078 (UniProt P01100)
Region: residues 216	to 380
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
We show here that the C-terminal activation domain of human c-Fos (residues 216−380; Figure 1), although functionally active, is essentially devoid of the stable helical or β-sheet structure typical of globular proteins. We conclude that c-Fos contains an intrinsically disordered yet biologically active activation domain.
Instead, the spectrum contains a negative band at 198 nm and a shoulder centered at 220 nm (above 5 °C), which are indicative of a disordered conformation ( 33).
Protein: DP00078 (UniProt P01100)
Region: residues 216	to 380
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum of FosAD at 5 °C is reminiscent of an unfolded protein (Figure 1A), in accord with previous results.
Protein: DP00078 (UniProt P01100)
Region: residues 216	to 380
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We show here that the C-terminal activation domain of human c-Fos (residues 216−380; Figure 1), although functionally active, is essentially devoid of the stable helical or β-sheet structure typical of globular proteins. We conclude that c-Fos contains an intrinsically disordered yet biologically active activation domain.
The heteronuclear 1H-15N NOE provides information on mainchain flexibility. In particular, 1H-15N NOEs are positive in folded, globular proteins and reduced or negative in unfolded and disordered proteins ( 37−41).
Protein: DP00079 (UniProt Q92731)
Region: residues 1	to 103
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The recorded CD spectra of ERα-N and ERβ-N both show this characteristic profile (Figs. 5 and 6). The CD data therefore strengthen the conclusion from NMR that the ERα-N and ERβ-N fragments are unstructured in solution.
Protein: DP00079 (UniProt Q92731)
Region: residues 1	to 103
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Similarly, the HSQC spectrum of ERβ-N (Fig. 2 B) also has a very limited amide chemical shift dispersion that corresponds well with typical random coil resonance shifts.
Protein: DP00081 (UniProt P51123)
Region: residues 11	to 77
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
On the other hand, 1H-15N HSQC and CD spectra of free dTAFII23011–77 indicate that dTAFII23011–77 by itself is largely unfolded (Figure 2C).
Cross-references: PDB:1TBA
Protein: DP00081 (UniProt P51123)
Region: residues 11	to 77
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
During a titration experiment in which 1H-15N HSQC spectra of dTAFII23011–77 were recorded with successive additions of TBP, most peaks corresponding to the unfolded state decrease in intensity and appear at new positions corresponding to the folded state, consistent with the high affinity of dTAFII23011–77 for TBP (Kd approximately 10−9 M).
Protein: DP00081 (UniProt P51123)
Region: residues 11	to 77
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
During a titration experiment in which 1H-15N HSQC spectra of dTAFII23011–77 were recorded with successive additions of TBP, most peaks corresponding to the unfolded state decrease in intensity and appear at new positions corresponding to the folded state, consistent with the high affinity of dTAFII23011–77 for TBP (Kd approximately 10−9 M).
Protein: DP00081 (UniProt P51123)
Region: residues 1840	to 1860
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)
Protein: DP00082 (UniProt P39935)
Region: residues 393	to 490
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The eukaryotic initiation factor 4G (eIF4G) is the core of a multicomponent switch controlling gene expression at the level of translation initiation. It interacts with the small ribosomal subunit interacting protein, eIF3, and the eIF4E/cap-mRNA complex in order to load the ribosome onto mRNA during cap-dependent translation. We describe the solution structure of the complex between yeast eIF4E/cap and eIF4G (393-490). Binding triggers a coupled folding transition of eIF4G (393-490) and the eIF4E N terminus resulting in a molecular bracelet whereby eIF4G (393-490) forms a right-handed helical ring that wraps around the N terminus of eIF4E.
Cross-references: PDB:1RF8
Protein: DP00082 (UniProt P39935)
Region: residues 393	to 490
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The eukaryotic initiation factor 4G (eIF4G) is the core of a multicomponent switch controlling gene expression at the level of translation initiation. It interacts with the small ribosomal subunit interacting protein, eIF3, and the eIF4E/cap-mRNA complex in order to load the ribosome onto mRNA during cap-dependent translation. We describe the solution structure of the complex between yeast eIF4E/cap and eIF4G (393-490). Binding triggers a coupled folding transition of eIF4G (393-490) and the eIF4E N terminus resulting in a molecular bracelet whereby eIF4G (393-490) forms a right-handed helical ring that wraps around the N terminus of eIF4E.
Protein: DP00082 (UniProt P39935)
Region: residues 393	to 490
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The eukaryotic initiation factor 4G (eIF4G) is the core of a multicomponent switch controlling gene expression at the level of translation initiation. It interacts with the small ribosomal subunit interacting protein, eIF3, and the eIF4E/cap-mRNA complex in order to load the ribosome onto mRNA during cap-dependent translation. We describe the solution structure of the complex between yeast eIF4E/cap and eIF4G (393-490). Binding triggers a coupled folding transition of eIF4G (393-490) and the eIF4E N terminus resulting in a molecular bracelet whereby eIF4G (393-490) forms a right-handed helical ring that wraps around the N terminus of eIF4E.
Protein: DP00082 (UniProt P39935)
Region: residues 393	to 490
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Here we report that a 98-amino acid fragment of S. cerevisiae eIF4G1 that contains this eIF4E binding peptide undergoes an unfolded to folded transition upon binding to eIF4E. The folding of the eIF4G1 domain was evidenced by the eIF4E-dependent changes in its protease sensitivity and (1)H-(15)N HSQC NMR spectrum.
Protein: DP00082 (UniProt P39935)
Region: residues 393	to 490
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Here we report that a 98-amino acid fragment of S. cerevisiae eIF4G1 that contains this eIF4E binding peptide undergoes an unfolded to folded transition upon binding to eIF4E. The folding of the eIF4G1 domain was evidenced by the eIF4E-dependent changes in its protease sensitivity and (1)H-(15)N HSQC NMR spectrum.
Protein: DP00082 (UniProt P39935)
Region: residues 393	to 490
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Here we report that a 98-amino acid fragment of S. cerevisiae eIF4G1 that contains this eIF4E binding peptide undergoes an unfolded to folded transition upon binding to eIF4E. The folding of the eIF4G1 domain was evidenced by the eIF4E-dependent changes in its protease sensitivity and (1)H-(15)N HSQC NMR spectrum.
Protein: DP00082 (UniProt P39935)
Region: residues 1	to 249
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
The 1H-15N HSQC NMR spectrum of eIF4G1 1-249 is characteristic of an intrinsically disordered protein (IDP) with low dispersion in the proton dimension and sharp signals (Figure 1B).
Protein: DP00082 (UniProt P39935)
Region: residues 187	to 239
Annotation: order (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Analysis of eIF4G1 1-249 secondary structure based on 13C chemical shifts, T1/T2 15N relaxation times and residual dipolar couplings (RDCs) revealed the presence of an α-helix within BOX3 (Figure 2A). This finding was confirmed by characteristic sequential amide-amide NOEs measured in a 3D 1H-15N-HSQC-NOESY-1H-15N HSQC spectrum (Supplementary Figure S3). We determined the NMR structure of this α-helix using a BOX3 model peptide (eIF4G1 187-234) (Supplementary Figure S3). No further standard secondary structure elements were identified in eIF4G11-249.
Protein: DP00082 (UniProt P39935)
Region: residues 1	to 239
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The SAXS curve evidenced the IDP nature of eIF4G11-249 (Figure 2C).
Protein: DP00082 (UniProt P39935)
Region: residues 39	to 45
Annotation: protein binding (Molecular function)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
Here we mapped this interaction on eIF4G11-249 by analysis of changes on the 1H-15N HSQC spectra, which indicated three putative binding sites for RRM3 in eIF4G11-249 (orange bar chart in Figure 3A): two in RNA1 (RNA1-1 and RNA1-2) and one in BOX1. Strikingly, these sites have a small consensus sequence motif (YNNxxxY), only present in this region of the eIF4G1.
We tested the ability of short peptides of eIF4G1 that corresponded to the conserved elements (Figure 3B) to bind to 15N-labelled Pub1 RRM3, by monitoring their effect on the Pub1 RRM3 1H-15N HSQC spectrum. Only BOX1 and RNA1-1 peptides caused changes in the Pub1 spectrum arising from direct contacts (Figure 3B).
Protein: DP00082 (UniProt P39935)
Region: residues 100	to 106
Annotation: protein binding (Molecular function)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
Here we mapped this interaction on eIF4G11-249 by analysis of changes on the 1H-15N HSQC spectra, which indicated three putative binding sites for RRM3 in eIF4G11-249 (orange bar chart in Figure 3A): two in RNA1 (RNA1-1 and RNA1-2) and one in BOX1. Strikingly, these sites have a small consensus sequence motif (YNNxxxY), only present in this region of the eIF4G1.
We tested the ability of short peptides of eIF4G1 that corresponded to the conserved elements (Figure 3B) to bind to 15N-labelled Pub1 RRM3, by monitoring their effect on the Pub1 RRM3 1H-15N HSQC spectrum. Only BOX1 and RNA1-1 peptides caused changes in the Pub1 spectrum arising from direct contacts (Figure 3B).