LiteFold/DisProt huggingface dataset:
Protein: DP00082 (UniProt P39935)
Region: residues 35	to 49
Annotation: protein binding (Molecular function)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
The NMR spectrum of the eIF4G1 peptide fused to the C-terminus of Pub1 was similar to that of Pub1 RRM3 alone (Figure 4A right), whereas that of the N-terminally fused chimera differed significantly (Figure 4A, left), suggesting that the peptide can effectively fold-back into the binding site only in the latter case. Using this latter construct, we obtained enough experimental restraints to calculate the structure of the eIF4G135-49-Pub1 RRM3 chimera (PDB: 6Z29), which shed light on the key elements required for molecular recognition (Figure 4B and Supplementary Figure S8).
Cross-references: PDB:6Z29
Protein: DP00082 (UniProt P39935)
Region: residues 35	to 49
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The NMR spectrum of the eIF4G1 peptide fused to the C-terminus of Pub1 was similar to that of Pub1 RRM3 alone (Figure 4A right), whereas that of the N-terminally fused chimera differed significantly (Figure 4A, left), suggesting that the peptide can effectively fold-back into the binding site only in the latter case. Using this latter construct, we obtained enough experimental restraints to calculate the structure of the eIF4G135-49-Pub1 RRM3 chimera (PDB: 6Z29), which shed light on the key elements required for molecular recognition (Figure 4B and Supplementary Figure S8).
Cross-references: PDB:6Z29
Protein: DP00082 (UniProt P39935)
Region: residues 35	to 49
Annotation: order (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The NMR spectrum of the eIF4G1 peptide fused to the C-terminus of Pub1 was similar to that of Pub1 RRM3 alone (Figure 4A right), whereas that of the N-terminally fused chimera differed significantly (Figure 4A, left), suggesting that the peptide can effectively fold-back into the binding site only in the latter case. Using this latter construct, we obtained enough experimental restraints to calculate the structure of the eIF4G135-49-Pub1 RRM3 chimera (PDB: 6Z29), which shed light on the key elements required for molecular recognition (Figure 4B and Supplementary Figure S8).
Cross-references: PDB:6Z29
Protein: DP00082 (UniProt P39935)
Region: residues 135	to 160
Annotation: protein binding (Molecular function)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
We next studied the interaction between eIF4G1 and Pab1 using similar approaches. NMR titrations of unlabeled Pab1 RRM12 over 15N-eIF4G11-249 (blue bar chart in Figure 3A) caused similar pattern of perturbations and signal disappearance than Pub1 RRM3 but with additional changes in BOX2 (aa 135–160) and BOX3 (aa 200–234).
The BOX2 peptide also interacted with RRM2 through a similar interface; but probably weakly because it causes fewer changes than the BOX3 peptide.
Protein: DP00082 (UniProt P39935)
Region: residues 200	to 234
Annotation: protein binding (Molecular function)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
We next studied the interaction between eIF4G1 and Pab1 using similar approaches. NMR titrations of unlabeled Pab1 RRM12 over 15N-eIF4G11-249 (blue bar chart in Figure 3A) caused similar pattern of perturbations and signal disappearance than Pub1 RRM3 but with additional changes in BOX2 (aa 135–160) and BOX3 (aa 200–234).
As expected, the BOX3 peptide interacted with Pab1 RRM12 causing significant perturbations in the helix1-helix2 interface of RRM2 (Figure 3C right), an equivalent region to that involved in human eIF4G-PABP1 recognition (Safaee et al., 2012).
Protein: DP00082 (UniProt P39935)
Region: residues 1	to 243
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: dynamic light scattering assay evidence used in manual assertion
Supporting statements:
Dynamic light scattering (DLS) indicated that large aggregates were formed in some protein combinations (Figure 6A). In contrast, the individual proteins exhibited autocorrelation functions that did not differ from that of Ficoll-70 alone, suggesting that the individual proteins did not aggregate. Moreover, the curve profiles of the single proteins remained stable for several hours. The Pab1:Pub1 mixture (Figure 6, row 2, column 1) showed the same behavior, but other double protein mixtures and the triple one showed a second phase, evidencing the presence of micrometer-size particles.
Protein: DP00082 (UniProt P39935)
Region: residues 93	to 114
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: dynamic light scattering assay evidence used in manual assertion
Supporting statements:
Dynamic light scattering (DLS) indicated that large aggregates were formed in some protein combinations (Figure 6A). In contrast, the individual proteins exhibited autocorrelation functions that did not differ from that of Ficoll-70 alone, suggesting that the individual proteins did not aggregate. Moreover, the curve profiles of the single proteins remained stable for several hours. The Pab1:Pub1 mixture (Figure 6, row 2, column 1) showed the same behavior, but other double protein mixtures and the triple one showed a second phase, evidencing the presence of micrometer-size particles. 
Consistent with this using the eIF4G1 ΔBOX1 mutant in the triple mixture showed no aggregation (Figure 6, row 3, column 2).
Protein: DP00082 (UniProt P39935)
Region: residues 1	to 243
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: confocal laser scanning microscopy evidence used in manual assertion
Supporting statements:
Confocal fluorescence microscopy images of triple mixtures containing Pab1 RRM12, Pub1 RRM123 and Alexa 488 labelled eIF4G11-249 in Ficoll 70 (200 g/L) revealed the presence of discrete rounded particles (∼1 µm and smaller, Figure 6B upper panels). Both, Pab1 and Pub1 were observed to colocalize with eIF4G1 in these assemblies, as observed in fluorescent images in which the proteins were pairwise labelled with spectrally different dyes (Alexa 488 and Alexa 647, Figure 6B middle and lower panels).
Protein: DP00082 (UniProt P39935)
Region: residues 1	to 82
Annotation: RNA binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We titrate the eIF4G11-82 construct with three poly (A) probes and found that the strength of the interaction is higher with longer oligos (Figure 7A). The chemical shift changes almost doubled when going from A12 to A14 and a new signal appears in the spectra that corresponds to the side chain Arg guanidinium group (Nε-Hε) (Figure 7B).
The interaction with poly(A) maps three regions centered around R34, R55, and G65, peaking at R55PH57. In contrast, the canonical RGG box (R60GG), a well-known RNA binding motif (Thandapani et al., 2013; Chong et al., 2018; Chowdhury and Jin, 2022), is less affected by binding.
Protein: DP00082 (UniProt P39935)
Region: residues 1	to 82
Annotation: RNA binding (Molecular function)
Evidence: filter binding assay evidence used in manual assertion
Supporting statements:
Typical titration curves for three of the proteins are shown in Figure 1C​1C.. We cleaved the GST moiety from the fusion proteins for these experiments; however, control experiments showed that GST fusion proteins behave identically in RNA-binding experiments. Full-length eIF4G11–952 showed the highest affinity for RNA with an estimated KD (KDapprox.) of 5 × 10−8 M whereas the fragments eIF4G11–82, eIF4G1492–539, and eIF4G1883–952 show about 100-fold lower affinity.
The fragments eIF4G1160–492, eIF4G1542–883 (not shown), and eIF4G1592–862, as well as GST (used as negative control) did not bind significant amounts of RNA.
Protein: DP00082 (UniProt P39935)
Region: residues 1	to 82
Annotation: RNA binding (Molecular function)
Evidence: RNA-protein binding evidence used in manual assertion
Supporting statements:
We tested full-length eIF4G11–952 and the fragments eIF4G11–82, eIF4G1492–539, and eIF4G1883–952 carrying RNA-binding sites as determined by filter-binding assays. 
We conclude from these results that eIF4G1 contains at least three sites, amino acids 1–82, 492–539, and 883–952, able to interact with RNA.
Protein: DP00083 (UniProt P03069)
Region: residues 101	to 134
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H,15N-HSQC spectra of each individual AD (Gcn4 1–100 and 101–134) overlay almost perfectly with the spectrum of a construct containing both ADs (residues 1–134), indicating that the two regions are structurally independent (Fig S1A). In all three spectra, the dispersion of resonances is over a narrow range in the 1HN-dimension, indicating that both Gcn4 ADs are intrinsically disordered in the absence of binding partners.
Backbone resonance chemical shifts, particularly 1Hα, 13Cα, and 13Cβ shifts, depend on local backbone geometry and provide a means to identify regions of regular secondary structure (Wishart et al., 1991). No patterns could be discerned from the cAD chemical shifts, consistent with a lack of ordered secondary structure.
Protein: DP00083 (UniProt P03069)
Region: residues 117	to 127
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In all three spectra, the dispersion of resonances is over a narrow range in the 1HN-dimension, indicating that both Gcn4 ADs are intrinsically disordered in the absence of binding partners.
Comparison of Gcn4 backbone resonances (1HN, 15N, 13Cα, 13Cβ, and 13C’) in the free and bound states indicates that the cAD adopts an α-helical conformation for binding to ABD1.
13C’ and 1Hα chemical shift values also indicate stabilization of helical structure upon binding: 13C’ resonances of residues 115–122 shift downfield upon addition of Gal11 (Fig S1C) and 1Hα resonances of residues 117–127 resonate upfield when compared to random coil values (Fig S1D; the 1Hα-chemical shifts for free Gcn4-cAD were not assigned).
Cross-references: PDB:2LPB
Protein: DP00083 (UniProt P03069)
Region: residues 1	to 100
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H,15N-HSQC spectra of each individual AD (Gcn4 1–100 and 101–134) overlay almost perfectly with the spectrum of a construct containing both ADs (residues 1–134), indicating that the two regions are structurally independent (Fig S1A). In all three spectra, the dispersion of resonances is over a narrow range in the 1HN-dimension, indicating that both Gcn4 ADs are intrinsically disordered in the absence of binding partners.
Protein: DP00083 (UniProt P03069)
Region: residues 101	to 134
Annotation: mediator complex binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Several cAD backbone amide resonances are strongly perturbed upon addition of ABD1. At the endpoint of the NMR titration (three-fold molar excess of ABD1), perturbations of up to 1.0 ppm are observed for residues 121–125 (Fig 1C). Importantly, similar shifts were observed in the spectrum of the tandem Gcn4-ADs when Gcn4 1–134 was titrated with ABD1, suggesting that the mode and affinity of interaction between the cAD and ABD1 is conserved in the context of the tandem Gcn4 ADs (Fig S1B).
cAD chemical shift perturbations observed upon addition of unlabeled Taf12 or ABD3 are remarkably similar to those seen with ABD1 (Fig 1B).
ABD1 corresponds to Gal11 residues 158-238 and ADB3 corresponds to Gal11 residues 496–651.  
Cross-references: PDB:2LPB
Protein: DP00083 (UniProt P03069)
Region: residues 101	to 134
Annotation: TFIID-class transcription factor complex binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
cAD chemical shift perturbations observed upon addition of unlabeled Taf12 or ABD3 are remarkably similar to those seen with ABD1 (Fig 1B). The same Gcn4 residues undergo the largest backbone amide perturbations in each case, though the absolute magnitudes of resonance perturbations are smaller compared to Gcn4 binding to Gal11-ABD1 (compare Figs. 1C and S5).
Protein: DP00083 (UniProt P03069)
Region: residues 101	to 134
Annotation: mediator complex binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
Binding affinities were measured using isothermal titration calorimetry (Table 2, Fig S3A–E). Wild-type cAD binds ABD1 with a Kd of 10.1 µM, similar to values measured using fluorescence polarization (Herbig et al., 2010).
Protein: DP00084 (UniProt P61244)
Region: residues 1	to 14
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
This is consistent with the existence of a predominantly unfolded basic region from residues 1–14 with a persistent helical turn from 15 to 18 and contiguous with H1.
As discussed in the text, almost no NOEs were observed in the first 14 residues due to an apparent and mainly unfolded nature and fast HN exchange rate near neutral pH.
Protein: DP00084 (UniProt P61244)
Region: residues 1	to 21
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Different phosphorylation sites have been identified in the C-terminal region (residues 103–160) and in the shorter disordered N-terminus (residues 2–21), which are both enriched in acidic residues and serines.
Cross-references: BMRB:51505
Protein: DP00084 (UniProt P61244)
Region: residues 1	to 21
Annotation: protein binding (Molecular function)
Evidence: magnetic resonance evidence used in manual assertion
Supporting statements:
Based on the observed chemical shift perturbations (CSPs), we conclude that the N- and C-terminal MAX regions bind to the MYC:MAX DBD.
Intrinsically disordered MAX regions interact with the MYC:MAX DBD.
Protein: DP00084 (UniProt P61244)
Region: residues 103	to 160
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
MAX contains two highly negatively charged disordered regions in its N- and C-terminus.
Protein: DP00084 (UniProt P61244)
Region: residues 103	to 160
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Based on the observed chemical shift perturbations (CSPs), we conclude that the N- and C-terminal MAX regions bind to the MYC:MAX DBD.
Protein: DP00084 (UniProt P61244)
Region: residues 103	to 160
Annotation: Myc-Max complex (Cellular component)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Based on the observed chemical shift perturbations (CSPs), we conclude that the N- and C-terminal MAX regions bind to the MYC:MAX DBD.
Protein: DP00084 (UniProt P61244)
Region: residues 1	to 21
Annotation: Myc-Max complex (Cellular component)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Based on the observed chemical shift perturbations (CSPs), we conclude that the N- and C-terminal MAX regions bind to the MYC:MAX DBD.
Protein: DP00084 (UniProt P61244)
Region: residues 1	to 5
Annotation: phosphorylation display site (Disorder function)
Evidence: protein kinase assay evidence used in manual assertion
Supporting statements:
We were able to obtain near quantitative phosphorylation of S2 and S11 within MAX(2–103) and could separate the double phosphorylated protein from minor fractions of mono- or unphosphorylated protein with anion-exchange chromatography.
Protein: DP00084 (UniProt P61244)
Region: residues 9	to 13
Annotation: phosphorylation display site (Disorder function)
Evidence: protein kinase assay evidence used in manual assertion
Supporting statements:
We were able to obtain near quantitative phosphorylation of S2 and S11 within MAX(2–103) and could separate the double phosphorylated protein from minor fractions of mono- or unphosphorylated protein with anion-exchange chromatography.
Protein: DP00084 (UniProt P61244)
Region: residues 1	to 21
Annotation: self-regulatory activity (Disorder function)
Evidence: surface plasmon resonance evidence used in manual assertion
Supporting statements:
Firstly, the MAX N-terminus confers specificity toward high-affinity DNA binding sites, i.e. E-Box DNA. For MAX(2–160) homodimers, the difference in affinity between E-Box and non-E-Box DNA that we observe is about 50-fold (see Table 2, last column). Contrarily, MAX(22–160) homodimers lacking the N-terminus show only a small change of 3- to 4-fold.
Protein: DP00084 (UniProt P61244)
Region: residues 1	to 21
Annotation: regulation of DNA binding (Biological process)
Evidence: surface plasmon resonance evidence used in manual assertion
Supporting statements:
Firstly, the MAX N-terminus confers specificity toward high-affinity DNA binding sites, i.e. E-Box DNA. For MAX(2–160) homodimers, the difference in affinity between E-Box and non-E-Box DNA that we observe is about 50-fold (see Table 2, last column). Contrarily, MAX(22–160) homodimers lacking the N-terminus show only a small change of 3- to 4-fold.
Taken together, our data suggests that direct binding of the MAX N-terminus to the MYC:MAX or MAX:MAX DBDs modulates DNA binding behavior.
Once bound to the target E-Box sequence, the MAX N-terminus competes for binding to the DBD, which ultimately leads to dissociation of MYC:MAX from the DNA.
The MAX N-terminus confers specificity for E-Box DNA and accelerates binding kinetics
Protein: DP00084 (UniProt P61244)
Region: residues 1	to 21
Annotation: flexible N-terminal tail (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
MAX contains two highly negatively charged disordered regions in its N- and C-terminus.
Cross-references: BMRB:51505
Protein: DP00084 (UniProt P61244)
Region: residues 103	to 160
Annotation: flexible C-terminal tail (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
MAX contains two highly negatively charged disordered regions in its N- and C-terminus.
Protein: DP00084 (UniProt P61244)
Region: residues 1	to 21
Annotation: self-assembly (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Notably, the observed CSPs for MAX(1–21) in presence of MYC:MAX DBD are larger than those obtained with MAX:MAX DBD (Suppl. Figure 1A), suggesting a lower affinity for the latter interaction.
Indeed, we find that binding of the MAX:MAX DBD to MAX(1–21) is ionic strength-dependent: we observe pronounced CSPs in buffer with 150 mM NaCl, while the CSPs are even larger at 100 mM NaCl but completely abolished at 300 mM NaCl (Suppl. Figure 2). These results further support electrostatic interactions between the MAX N-terminus and the DBD as the main driving force for binding.
We were able to show that the acidic, disordered MAX N-terminus interacts with the basic, folded DNA binding domain which is formed by dimerization of the MYC and MAX bHLH-LZ motifs, and that this interaction is competitive with DNA binding.
Protein: DP00085 (UniProt Q04206)
Region: residues 428	to 551
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The NOE pattern was typical for a random conformation; furthermore, the weakness of the NOEs indicates a large inherent flexibility of the unstructured p65 C terminus.
Protein: DP00085 (UniProt Q04206)
Region: residues 428	to 551
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The results of the CD analysis are shown in Fig. 2A. The negative e value at a wavelength of 190 nm and the 0 value near 0 at wavelengths exceeding 210 nm is indicative for a random conformation of the TA, peptides in an aqueous buffer at pH 7.
Protein: DP00086 (UniProt P04637)
Region: residues 1	to 12
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We show here that an essential element in the interaction of p53 with HMGB1 is the N-terminal disordered region (Lee et al., 2000; Dawson et al., 2003; Wells et al., 2008), comprising the transactivation domain and the proline-rich region, the major interacting motif being a region of inducible structure in TAD2 (Lee et al., 2000).
Cross-references: PDB:2LY4
BMRB:18709
Protein: DP00086 (UniProt P04637)
Region: residues 1	to 93
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
RDC analysis showed that the isolated domain p53(1–93) was an IDP with two regions of nascent secondary structure.
Protein: DP00086 (UniProt P04637)
Region: residues 291	to 312
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Our final model of the quadruple mutant comprises residues 96–290 for both molecules in the asymmetric unit. As in the structure of wild type, the C-terminal residues up to Thr-312 are disordered.
Cross-references: PDB:1UOL
Protein: DP00086 (UniProt P04637)
Region: residues 1	to 93
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
SAXS data were accurately reproduced by intensity curves simulated from the ensemble of p53(1–93) conformers that reproduced the RDC data (shown in the form of a semilogarithmic and a Kratky-type plot in Fig. 2), demonstrating that the overall shape of the predicted and measured ensembles was consistent with the model of the unfolded chain described above. The SAXS profile was not consistent with a collapsed structure of the transactivation domain, reported from paramagnetic relaxation enhancement experiments (Fig. S7) (28).
Protein: DP00086 (UniProt P04637)
Region: residues 20	to 73
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
This short helix interacts with the surface of Tfb1 formed by beta strands b5, b6, and b7 and the loop connecting b5 to b6.
Cross-references: PDB:2GS0
Protein: DP00086 (UniProt P04637)
Region: residues 20	to 73
Annotation: molecular function activator activity (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The interaction between the p62/Tfb1 subunit of TFIIH and the TAD of p53 has been shown to be important for the recruitment of p53 to the TFIIH complex in both human and yeast. This interaction is directly correlated with the ability of the p53 TAD to stimulate transcriptional elongation (Blau et al., 1996).
Protein: DP00086 (UniProt P04637)
Region: residues 37	to 57
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
In contrast, the N-terminal p53 transactivation domain is largely disordered in solution, but residues 37-57 fold into two amphipathic helices, H1 and H2, upon binding with RPA70N.
Cross-references: PDB:2B3G