LiteFold/DisProt huggingface dataset:
Protein: DP01620 (UniProt P20823)
Region: residues 181	to 200
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The linker between POUS and POUH domains (residues 182–200) is disordered. Nevertheless, connectivity between domains was established based on crystal packing and distance considerations (Figure 2A). The presence of neighboring molecules in the crystal lattice precludes the alternative configuration.
Cross-references: PDB:1IC8
Protein: DP01621 (UniProt E5LC01)
Region: residues 1065	to 1117
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Our observation of very narrow 1H chemical shift dispersion of merely 0.9 ppm (7.7–8.6 ppm) in the 15N-HSQC spectrum of LANA C-terminal fragment (residues 1110–1162) indicates that this region is unstructured (Figure S1A).
The LANA gene fragment used in this publication was derived from the Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). IDR is 100% identical and corresponds to 1065-1117 region.
Cross-references: DisProt:DP02334r001
Protein: DP01621 (UniProt E5LC01)
Region: residues 1086	to 1104
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We thus constructed a BRD4 ET domain fused at its N-terminus to LANA comprising residues 1110–1162 via a flexible linker (GSGSGS), and determined by NMR analysis that the minimal ET binding site in LANA is confined to residues 1131–1149 (NLQSSIVKFKKPLPLTQPG) (data not shown). Notably, the 15N-HSQC spectra of the ET domain displayed nearly identical protein backbone resonance perturbation patterns induced by adding a LANA segment consisting of residues 1110–1162 or 1131–1149 (Figure S1A), or a LANA peptide of residues 1133–1144 (Figure 1B, red vs. blue signals), thereby defining the ET domain binding site in LANA to residues 1133–1144. We further determined binding affinity of the ET domain to the LANA peptide by NMR titration to be approximately Kd = 635 μM (Figure S1A).
The LANA gene fragment used in this publication was derived from the Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). IDR is 100% identical and corresponds to 1086-1104 region.
Cross-references: PDB:2ND0
BMRB:26042
DisProt:DP02334r004
Protein: DP01621 (UniProt E5LC01)
Region: residues 1086	to 1104
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We next solved the three-dimensional structure of the BRD4 ET domain bound to the LANA peptide (residues 1133–1144) using heteronuclear multidimensional NMR spectroscopy (Clore and Gronenborn, 1994) (Figure 1C and Table 1). The structure reveals that the viral peptide establishes a two-strand inter-molecular antiparallel β-sheet with the protein.
The LANA gene fragment used in this publication was derived from the Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). IDR is 100% identical and corresponds to 1086-1104 region.
Cross-references: PDB:2ND0
BMRB:26042
DisProt:DP02334r003
Protein: DP01621 (UniProt E5LC01)
Region: residues 640	to 880
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: DP01621 (UniProt E5LC01)
Region: residues 325	to 423
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: DP01621 (UniProt E5LC01)
Region: residues 586	to 625
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: DP01621 (UniProt E5LC01)
Region: residues 1086	to 1104
Annotation: viral life cycle (Biological process)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We thus constructed a BRD4 ET domain fused at its N-terminus to LANA comprising residues 1110–1162 via a flexible linker (GSGSGS), and determined by NMR analysis that the minimal ET binding site in LANA is confined to residues 1131–1149 (NLQSSIVKFKKPLPLTQPG) (data not shown). Notably, the 15N-HSQC spectra of the ET domain displayed nearly identical protein backbone resonance perturbation patterns induced by adding a LANA segment consisting of residues 1110–1162 or 1131–1149 (Figure S1A), or a LANA peptide of residues 1133–1144 (Figure 1B, red vs. blue signals), thereby defining the ET domain binding site in LANA to residues 1133–1144. We further determined binding affinity of the ET domain to the LANA peptide by NMR titration to be approximately Kd = 635 μM (Figure S1A).
The LANA gene fragment used in this publication was derived from the Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). IDR is 100% identical and corresponds to 1086-1104 region.
Cross-references: PDB:2ND0
BMRB:26042
DisProt:DP02334r015
Protein: DP01622 (UniProt Q06609)
Region: residues 1	to 15
Annotation: disorder (Structural state)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
Residues 1 to 15 and 86 to 114 are disordered as judged by narrower 1H NMR linewidths compared with that of the structured region of the polypeptide, presence of strong HN-H2O crosspeaks in the 15N-separated NOESY spectrum (Marion et al., 1989), and the absence of long range nuclear Overhauser enhancement (NOE) signals.
Cross-references: PDB:1B22
Protein: DP01622 (UniProt Q06609)
Region: residues 86	to 114
Annotation: disorder (Structural state)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
Residues 1 to 15 and 86 to 114 are disordered as judged by narrower 1H NMR linewidths compared with that of the structured region of the polypeptide, presence of strong HN-H2O crosspeaks in the 15N-separated NOESY spectrum (Marion et al., 1989), and the absence of long range nuclear Overhauser enhancement (NOE) signals.
Cross-references: PDB:1B22
Protein: DP01622 (UniProt Q06609)
Region: residues 1	to 21
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The atomic models include DNA and most of the residues of RAD51 except for the N-terminal 1-21 residues and a few residues in flexible loop regions.
Cross-references: EMDB:EMD-9567
PDB:5H1B
PDB:5H1C
EMDB:EMD-9566
Protein: DP01623 (UniProt Q03834)
Region: residues 1	to 304
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The Msh6 NTR Is an Unstructured Peptide that Can
Interact with PCNA Trimers at a 3:1 Ratio
Protein: DP01624 (UniProt Q06433)
Region: residues 328	to 361
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Overall, the electron density for the protein was well ordered except for two short loop regions (Asp-245 to Gly-248 and Asp-309 to Ser-316 in Subunit I and Asn-247 to Arg-250 and Gly-311 to Ser-316 in Subunit II) and two larger regions that are located on the same side of the molecule (Gly-328 to Glu-362 and Leu-394 to Lys-413 in Subunit I and Gly-328 to Glu-361 and Gly-395 to Lys-413 in Subunit II).
Cross-references: PDB:2NVW
Protein: DP01624 (UniProt Q06433)
Region: residues 395	to 413
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Overall, the electron density for the protein was well ordered except for two short loop regions (Asp-245 to Gly-248 and Asp-309 to Ser-316 in Subunit I and Asn-247 to Arg-250 and Gly-311 to Ser-316 in Subunit II) and two larger regions that are located on the same side of the molecule (Gly-328 to Glu-362 and Leu-394 to Lys-413 in Subunit I and Gly-328 to Glu-361 and Gly-395 to Lys-413 in Subunit II).
Cross-references: PDB:2NVW
Protein: DP01625 (UniProt P07567)
Region: residues 546	to 605
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
As found in previous studies of retroviral nucleocapsid proteins studied by NMR, there was no evidence of stable, easily identifiable secondary structural regions in the molecule. Comparison of the experimentally determined Ca and Ha chemical shifts with random coil values are largely consistent with this picture, with no systematic deviation toward a-helical or /3-strand values among contiguous residues. 
Cross-references: BMRB:4498
PDB:1CL4
BMRB:4600
Protein: DP01625 (UniProt P07567)
Region: residues 546	to 605
Annotation: metal ion binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The zinc was covalently attached to the SY atom of each of the Cys and Ne2 of each His. Zn(l1)-ligand bonds were assigned distances of 2.10 8, (Zn-SY) and 2.00 A (Zn-Ne2) and a force constant of 200 kcal/(mol A2).
Cross-references: PDB:1CL4
Protein: DP01626 (UniProt Q01831)
Region: residues 815	to 940
Annotation: disorder (Structural state)
Evidence: temperature-induced protein unfolding evidence used in manual assertion
Supporting statements:
Thermal denaturation monitored by the ellipticity at 222 nm (Figure 2B) shows that the protein loses progressively (noncooperative unfolding) its helical structure between 5 °C and 40 °C, suggesting a low degree of tertiary structural organization ( 34).
Protein: DP01626 (UniProt Q01831)
Region: residues 815	to 940
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
 The Rg value is 2-fold larger than the value expected for a compact, globular protein with the same number (n) of residues which is Rg ∼ 3n1/3 = 15 Å ( 40). It can also be compared with the expected value for a completely unfolded protein.
Protein: DP01626 (UniProt Q01831)
Region: residues 815	to 940
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Moreover, in the (15N)NOESY-HSQC spectrum no medium or long-range NOE cross-peaks were observed, suggesting a lack of
persistent secondary or tertiary structure, in agreement with the SAXS results.
Protein: DP01626 (UniProt Q01831)
Region: residues 815	to 940
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Figure 6A shows the thermogram and the binding isotherm corresponding to the titration of HsCen2 (200 μM) into C-XPC (15 μM). Fitting the isotherm to a single-site binding model gives a stoichiometry of 1:1, a binding constant of 2.9 (1) × 108 M-1, and a reaction enthalpy ΔH = −30.2 (0.2) kcal/mol. Therefore, C-XPC binds HsCen2 with high affinity and thermodynamic parameters similar to that of the 17-mer peptide (Table 1).
Protein: DP01626 (UniProt Q01831)
Region: residues 815	to 940
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
A quantitative analysis of the far-UV CD spectra of C-XPC domain was made by fitting the experimental data
to an appropriate combination of “pure” secondary structure spectra. Utilization of two different fitting procedures,
CONTIN (32) and CDSSTR (33), gave similar values for the secondary structure content of C-XPC: 33% and 37% alpha-helix, respectively.
Protein: DP01626 (UniProt Q01831)
Region: residues 847	to 863
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The peptide alone exhibits a CD spectrum characteristic for a highly disordered structure, as is generally the case for linear polypeptides of this size.
Protein: DP01626 (UniProt Q01831)
Region: residues 847	to 863
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Therefore, the large variation of the negative band intensity at 222 nm, the most characteristic for the α structure, suggests that a fragment of the peptide undergoes a random coil-to-helix structural transition upon binding to the protein, bringing a significant contribution to the α-helix CD band.
Protein: DP01626 (UniProt Q01831)
Region: residues 847	to 863
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Adding of P1-XPC, at a 1:1 molar ratio, to SC-HsCen2/Ca2+ induces a considerable enhancement of the CD signal (by ∼50%) with a rough conservation of the relative intensities of different bands (Fig. 5A).
Protein: DP01627 (UniProt P47480)
Region: residues 150	to 166
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
For the N-terminal stretch (Ser12 to Lys29), only intra-residual and sequential NOEs could be detected. This type of NOE signature is typical of unstructured polypeptide chains.
Cross-references: PDB:1HXV
Protein: DP01628 (UniProt P14736)
Region: residues 633	to 754
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Limited proteolysis of the insect-cellexpressed 754-residue Rad4 showed that the 100 N-terminal (residues 1–100) and 122 C-terminal (633–754) residues are highly susceptible to digestion, suggesting that they are unstructured or loosely folded.
Protein: DP01628 (UniProt P14736)
Region: residues 1	to 100
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Limited proteolysis of the insect-cellexpressed 754-residue Rad4 showed that the 100 N-terminal (residues 1–100) and 122 C-terminal (633–754) residues are highly susceptible to digestion, suggesting that they are unstructured or loosely folded.
Protein: DP01629 (UniProt P32628)
Region: residues 77	to 147
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
The L1, L2, and L3 regions of Rad23, consisting of amino acids 77-147, 185-265, and 311-355, respectively, were attached to the C terminus of Rad23. Rad23-L3 was degraded efficiently but Rad23-L1 and Rad23-L2 were degraded more slowly.
Protein: DP01629 (UniProt P32628)
Region: residues 77	to 147
Annotation: flexible linker (Disorder function)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
These four domains have well-defined structures but are connected by flexible linker regions ranging in length from 45 to 82 amino acids.
Protein: DP01629 (UniProt P32628)
Region: residues 185	to 265
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
The L1, L2, and L3 regions of Rad23, consisting of amino acids 77-147, 185-265, and 311-355, respectively, were attached to the C terminus of Rad23. Rad23-L3 was degraded efficiently but Rad23-L1 and Rad23-L2 were degraded more slowly.
Protein: DP01629 (UniProt P32628)
Region: residues 185	to 265
Annotation: flexible linker (Disorder function)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
These four domains have well-defined structures but are connected by flexible linker regions ranging in length from 45 to 82 amino acids.
Protein: DP01629 (UniProt P32628)
Region: residues 230	to 254
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The refined model contains residues 126–300, 304–515, 528–599 and 606–632 of Rad4, residues 255–309 and 347–395 of Rad23, and 250 water molecules.
The final models of the ternary complexes contain residues 123–517 and 526–632 of Rad4, and 256–369 of Rad23.
According to the PDB entries, the region 230-254 is unstructured both in the Rad4-Rad23 complex as in the ternary complex with DNA.
Cross-references: PDB:2QSF
PDB:2QSG
PDB:2QSH
Protein: DP01629 (UniProt P32628)
Region: residues 311	to 355
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
The L1, L2, and L3 regions of Rad23, consisting of amino acids 77-147, 185-265, and 311-355, respectively, were attached to the C terminus of Rad23. Rad23-L3 was degraded efficiently but Rad23-L1 and Rad23-L2 were degraded more slowly.
Protein: DP01629 (UniProt P32628)
Region: residues 311	to 355
Annotation: flexible linker (Disorder function)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
These four domains have well-defined structures but are connected by flexible linker regions ranging in length from 45 to 82 amino acids.
Protein: DP01629 (UniProt P32628)
Region: residues 310	to 346
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The refined model contains residues 126–300, 304–515, 528–599 and 606–632 of Rad4, residues 255–309 and 347–395 of Rad23, and 250 water molecules.
Cross-references: PDB:2QSF
Protein: DP01629 (UniProt P32628)
Region: residues 310	to 398
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final models of the ternary complexes contain residues 123–517 and 526–632 of Rad4, and 256–369 of Rad23.
According to the PDB entries, this region is unstructured in the Rad4-Rad23-DNA complexes. In the Methods section the authors states the end of the structured region is the residue 369 but this might be a typographical error considering that in the PDB structure the structured region is 256-309.
Cross-references: PDB:2QSH
PDB:2QSG
Protein: DP01629 (UniProt P32628)
Region: residues 347	to 395
Annotation: order to disorder (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The refined model contains residues 126–300, 304–515, 528–599 and 606–632 of Rad4, residues 255–309 and 347–395 of Rad23, and 250 water molecules.
The final models of the ternary complexes contain residues 123–517 and 526–632 of Rad4, and 256–369 of Rad23.
In the Methods section the authors states the limit of the structured region of the Rad4-Rad23-DNA complexes as the residue 369 but this might be a typographical error considering that in the PDB the structured region is 256-309. According to the PDB entries, the region 347-395 is unstructured in the Rad4-Rad23-DNA complexes but structured in the Rad4-Rad23, when there is no DNA present. 
The UBA2 domain is disordered in the DNA-bound Rad4–Rad23 crystal forms. It is conceivable that the ordered nature of UBA2 in the apoRad4–Rad23 crystals is due to the extensive crystal-packing contacts it makes. In the DNA-bound crystal forms, the area where UBA2 would be is open to a large solvent channel that would not provide any crystal packing contacts.
Cross-references: PDB:2QSH
PDB:2QSG
PDB:2QSF
Protein: DP01629 (UniProt P32628)
Region: residues 347	to 395
Annotation: order (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The refined model contains residues 126–300, 304–515, 528–599 and 606–632 of Rad4, residues 255–309 and 347–395 of Rad23, and 250 water molecules.
Cross-references: PDB:2QSF
Protein: DP01629 (UniProt P32628)
Region: residues 310	to 346
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The refined model contains residues 126–300, 304–515, 528–599 and 606–632 of Rad4, residues 255–309 and 347–395 of Rad23, and 250 water molecules.
The 310-346 disordered regions constitutes a linker between the R4BD (253-309) and UBA2 (347-398) domains.
Cross-references: PDB:2QSF
Protein: DP01631 (UniProt P07276)
Region: residues 642	to 690
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Rad2642–690 exists in an extended conformation devoid of any regular secondary structural element with residues 664–678 forming the interface with Tfb1PH.
Cross-references: PDB:2LOX
Protein: DP01631 (UniProt P07276)
Region: residues 664	to 678
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Rad2642–690 exists in an extended conformation devoid of any regular secondary structural element with residues 664–678 forming the interface with Tfb1PH. This is consistent with the 1H–15N HSQC spectra of the titration of 15N-labeled Rad2642–690 with Tfb1PH as it is these residues that display significant changes in their 1H and 15N chemical shifts (Supplementary Figure S4).
Cross-references: PDB:2LOX
Protein: DP01631 (UniProt P07276)
Region: residues 642	to 760
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
NMR studies with a longer segment of the Rad2 spacer region (Rad2642–760) indicate that this segment does not contain a folded domain in the free form (Supplementary Figure S2), as observed with the free form of TFIIEαCTD.
Protein: DP01631 (UniProt P07276)
Region: residues 642	to 690
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
By ITC, we determine that Rad2642–690 (Kd = 190 nM) binds with much higher affinity to Tfb1PH than Rad2692–760 (Kd = 4.6 µM).
Protein: DP01631 (UniProt P07276)
Region: residues 669	to 673
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
The ITC studies show that neither the F670P nor V673P mutant of Rad2642–690 bind with appreciable affinity.
Protein: DP01631 (UniProt P07276)
Region: residues 642	to 690
Annotation: protein binding (Molecular function)
Evidence: competitive binding evidence used in manual assertion
Supporting statements:
When mapped onto the structure of Tfb1PH, the residues exhibiting significant chemical shift changes are located in strands β5, β6, β7 and the helix H1 (Figure 5b) and the changes are very similar to those observed with Rad2642–690 (Figure 3a). NMR competition experiments further demonstrate that Rad2359–383 and Rad2642–690 compete for binding to Tfb1PH (Figure 5c and d).
Taken together with previous results showing that TFIIEαCTD and p53TAD2 compete for binding to Tfb1PH (19), these results demonstrate that TFIIEαCTD, p53TAD2 and Rad2642–690 all share for a common binding site on Tfb1PH.