LiteFold/DisProt huggingface dataset:
Protein: DP01425 (UniProt Q15004)
Region: residues 62	to 69
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
As a disordered protein, p15 yields NMR spectra with sharp signals and poor dispersion in the proton frequency. On addition of excess PCNA, signal intensities decrease generally and most notably for the central residues V53-D75 that even disappear (Fig. 1d). This observation highlights the central region of p15 as the principal binding site for PCNA, which includes the PIP-box motif (62QKGIGEFF69, conserved residues underlined).
Protein: DP01425 (UniProt Q15004)
Region: residues 50	to 77
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
Isothermal titration calorimetry (ITC) measurements could be fitted very well to a model assuming independent p15 binding to equivalent sites in the PCNA trimer, with a dissociation constant of 1.1 μM at 25 °C (Fig. 1c).
Protein: DP01425 (UniProt Q15004)
Region: residues 1	to 31
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
All three p15 fragments bind PCNA, but with decreasing affinity (Supplementary Fig. 1 and Supplementary Table 1). The N-terminal deletion mutant binds PCNA with only slightly lower affinity than p15, implying that any transient interactions of the N-terminal V2-S31 residues stabilize the complex only marginally. The affinity of p1550–77, however, is reduced by a factor of 5 and the shortest core fragment p1559–70 even by a factor of 33. These results indicate that residues G50-T58 and/or L71-E77 strongly contribute to PCNA binding, which is further enhanced by residues A32-G49.
Isothermal titration calorimetry measurements and analysis of p15 and fragments binding to PCNA in PBS, pH 7.0 at 35 °C.
Protein: DP01425 (UniProt Q15004)
Region: residues 51	to 71
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Residues N51-L71 of p1550–77 are well defined in the crystal structure (Supplementary Fig. 6), although the side chains of N51, R70 and L71 could not be reliably modelled (Fig. 2b).
Cross-references: PDB:4D2G
Protein: DP01425 (UniProt Q15004)
Region: residues 1	to 31
Annotation: DNA binding (Molecular function)
Evidence: fluorescence polarization evidence used in manual assertion
Supporting statements:
The p15–DNA interaction is unspecific since any of the DNA molecules tested (single-stranded DNA, primed DNA and flapped DNA) are bound by p15 with similar affinity (Supplementary Fig. 11a). The binding isotherms could be fitted to a 1:1 interaction model, with apparent dissociation constants between 0.2 and 0.4 μM at 25 °C.
The affinity of p15ΔN is reduced by two orders of magnitude, indicating that the basic N-terminal region of p15 contributes most to the DNA affinity (Fig. 5a).
Protein: DP01425 (UniProt Q15004)
Region: residues 50	to 77
Annotation: DNA binding (Molecular function)
Evidence: fluorescence polarization evidence used in manual assertion
Supporting statements:
The p15–DNA interaction is unspecific since any of the DNA molecules tested (single-stranded DNA, primed DNA and flapped DNA) are bound by p15 with similar affinity (Supplementary Fig. 11a). The binding isotherms could be fitted to a 1:1 interaction model, with apparent dissociation constants between 0.2 and 0.4 μM at 25 °C.
The central fragment p1550–77 binds DNA with even lower affinity, and no DNA binding was observed with the core PIP-box fragment p1559–70. When DNA was titrated with PCNA-bound p15, the increase in fluorescence polarization was larger (Fig. 5a), indicating that a ternary complex forms (since the larger the size of the complex the larger the polarization). The slightly reduced DNA affinity shows that PCNA interferes only weakly with p15 binding to DNA. Similarly, when DNA-bound p15 was titrated with PCNA (Fig. 5b) the PCNA affinity was comparable to that of isolated p15 (or p1550–77). Thus, a ternary p15–PCNA–DNA complex forms in solution in which the direct p15–PCNA and p15–DNA interactions are largely independent of each other.
Protein: DP01425 (UniProt Q15004)
Region: residues 50	to 77
Annotation: molecular adaptor activity (Molecular function)
Evidence: fluorescence polarization evidence used in manual assertion
Supporting statements:
The central fragment p1550–77 binds DNA with even lower affinity, and no DNA binding was observed with the core PIP-box fragment p1559–70. When DNA was titrated with PCNA-bound p15, the increase in fluorescence polarization was larger (Fig. 5a), indicating that a ternary complex forms (since the larger the size of the complex the larger the polarization). The slightly reduced DNA affinity shows that PCNA interferes only weakly with p15 binding to DNA. Similarly, when DNA-bound p15 was titrated with PCNA (Fig. 5b) the PCNA affinity was comparable to that of isolated p15 (or p1550–77). Thus, a ternary p15–PCNA–DNA complex forms in solution in which the direct p15–PCNA and p15–DNA interactions are largely independent of each other.
Protein: DP01425 (UniProt Q15004)
Region: residues 1	to 31
Annotation: molecular adaptor activity (Molecular function)
Evidence: fluorescence polarization evidence used in manual assertion
Supporting statements:
The affinity of p15ΔN is reduced by two orders of magnitude, indicating that the basic N-terminal region of p15 contributes most to the DNA affinity (Fig. 5a).
The central fragment p1550–77 binds DNA with even lower affinity, and no DNA binding was observed with the core PIP-box fragment p1559–70. When DNA was titrated with PCNA-bound p15, the increase in fluorescence polarization was larger (Fig. 5a), indicating that a ternary complex forms (since the larger the size of the complex the larger the polarization). The slightly reduced DNA affinity shows that PCNA interferes only weakly with p15 binding to DNA. Similarly, when DNA-bound p15 was titrated with PCNA (Fig. 5b) the PCNA affinity was comparable to that of isolated p15 (or p1550–77). Thus, a ternary p15–PCNA–DNA complex forms in solution in which the direct p15–PCNA and p15–DNA interactions are largely independent of each other.
Protein: DP01425 (UniProt Q15004)
Region: residues 50	to 77
Annotation: molecular adaptor activity (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The poor HN signal dispersion and only minor changes in Cα chemical shifts (Supplementary Fig. 13) indicate that p15 does not acquire a defined structure on binding to the DNA; rather, its backbone remains flexible and disordered. In the presence of PCNA, DNA-bound p15 shows a similar pattern of NMR signal attenuation as in the absence of DNA (Fig. 5c), in line with a ternary complex where the central region of p15 is tightly bound to PCNA.
Protein: DP01425 (UniProt Q15004)
Region: residues 1	to 111
Annotation: molecular adaptor activity (Molecular function)
Evidence: transmission electron microscopy evidence used in manual assertion
Supporting statements:
For an experimental verification of this possibility, PCNA in the presence of p15, DNA or both was stained with uranyl acetate and observed by transmission electron microscopy (Fig. 6b). Two-dimensional analysis of single particle projections yielded class averages for top-, side-, and tilted-views of the PCNA ring, with a larger proportion of tilted-view classes for the ternary p15–DNA–PCNA complex (Supplementary Fig. 15). Most remarkably, many of the top- and tilted-views of the ternary complex show increased density within the PCNA ring compared to both binary mixtures (where only the p15–PCNA mixture, however, is expected to form a complex). The same result is obtained when the rotational power spectra of individual particles in the three data sets are calculated and classified (Supplementary Fig. 16). These observations indicate that p15-bound DNA in the ternary complex is (at least transiently) located within the PCNA ring.
Protein: DP01426 (UniProt P06400)
Region: residues 84	to 93
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Disordered loop in the RbN domain
Cross-references: PDB:2QDJ
Protein: DP01426 (UniProt P06400)
Region: residues 590	to 635
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
The spacer, which is the least conserved region of Rb (Fig. 1a), and is different in the related p107 and p130 pocket proteins, appears to be unstructured or loosely folded based on proteolytic digestion (data not shown).
Cross-references: PDB:1GUX
Protein: DP01426 (UniProt P06400)
Region: residues 590	to 635
Annotation: flexible linker (Disorder function)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
This is the spacer joining the A and B subdomains of RbAB (RbPL)
Protein: DP01426 (UniProt P06400)
Region: residues 500	to 513
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This is a Flexible region in the RbA subdomain that appears disordered in most RbAB structures
Cross-references: PDB:1GUX
Protein: DP01426 (UniProt P06400)
Region: residues 346	to 370
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The work provides evidence that phosphorylation of RbIDL produces a transition from unassociated to self-associated Rb: "This analysis suggests an equilibrium between associated and dissociated RbN and pocket domains, in which phos- phorylation of RbIDL shifts the equilibrium toward the associated conformation. "
Cross-references: undefined:undefined
Protein: DP01426 (UniProt P06400)
Region: residues 346	to 370
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region corresponds to the linker joining the RbN and RbAB domains. T373 phosphorylation induces conformational transitions in the linker region. The larger interface (2277 A ̊ 2 buried surface area) is formed between pocket subdomain A and RbN subdomain B and is mediated by T373 phosphorylation (Fig. 4B)
Cross-references: PDB:4ELJ
Protein: DP01426 (UniProt P06400)
Region: residues 346	to 370
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This is the RbIDL linker region joining the RbN and the RbAB domains (the two main structured domains in Rb).
Protein: DP01426 (UniProt P06400)
Region: residues 346	to 370
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
373 phosphorylation induces interactions of RbIDL with the RbAB domain that also block E2F binding, favouring the autoinhibited conformation. ""
Protein: DP01426 (UniProt P06400)
Region: residues 346	to 370
Annotation: order to disorder (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Here we observe that T356 phosphorylation disorders a helix in RbN.
Protein: DP01426 (UniProt P06400)
Region: residues 355	to 370
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
limited tryptic digestion of Rb residues 1-370 generated two fragments with approximate size of 24.7 and 10.9 kDa (Supplement; Fig S-1A). Mass spectrometry and N-terminal sequencing of these identified three polypeptides encompassing residues 46-251, 263-355 and 266-355 (not shown), indicating trimming from both termini
Protein: DP01426 (UniProt P06400)
Region: residues 245	to 269
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Disordered loop in the RbN domain joining helices alpha 9 and alpha 10 (R-Linker) " limited tryptic digestion of Rb residues 1-370 generated two fragments [...] indicating trimming from both termini and removal of an internal arginine (Arg)-rich linker (aa 251-266)"
Cross-references: PDB:2QDJ
Protein: DP01426 (UniProt P06400)
Region: residues 500	to 511
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This is a Flexible region in the RbA subdomain that appears disordered in most RbAB structures
Cross-references: PDB:4ELL
Protein: DP01426 (UniProt P06400)
Region: residues 577	to 615
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Region is part of the RbPL, a flexible loop connecting the A and B subdomains of the central RbAB domain. This loop can be phosphorylated, inducing a closed conformation that has decreased ability to bind the E2F transcription factor
Cross-references: PDB:4ELL
Protein: DP01426 (UniProt P06400)
Region: residues 577	to 615
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Phosphorylation of S608 in the flexible RbPL loop induces binding to RbAB (residues 600-609) favouring a "closed" autoinhibited conformation which inhibits binding of the E2F transactivation domain to pRb. "In sum, the RbPL–P structure demonstrates that S608 phosphorylation results in a bound and inhibitory conformation of RbPL that directly blocks the E2FTD-binding site."
Protein: DP01426 (UniProt P06400)
Region: residues 578	to 589
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region of the RbPL linker appears disordered in the crystal structure
Cross-references: PDB:1GUX
Protein: DP01426 (UniProt P06400)
Region: residues 786	to 928
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Limited proteolysis of an Rb protein containing the pocket and RbC domains (771-928) suggested that RbC does not contain stable structural domains. However, the region 771-785 is part of the ordered Rb pocket domain and hence not included in the annotation.
Protein: DP01426 (UniProt P06400)
Region: residues 786	to 928
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
NMR data indicate that the isolated RbC (786-928) is unstructured in solution.
Protein: DP01426 (UniProt P06400)
Region: residues 829	to 873
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Here, we demonstrate an interaction between RbC and the CC-MB domains of E2F-DP heterodimers and present the crystal structure of an RbC-E2F1-DP1 complex.
Cross-references: PDB:2AZE
Protein: DP01426 (UniProt P06400)
Region: residues 829	to 873
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Here, we demonstrate an interaction between RbC and the CC-MB domains of E2F-DP heterodimers and present the crystal structure of an RbC-E2F1-DP1 complex.
RbC Binds to E2FCM-DPCM through a Bipartite Interaction
Cross-references: PDB:2AZE
Protein: DP01426 (UniProt P06400)
Region: residues 829	to 873
Annotation: molecular adaptor activity (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Here, we demonstrate an interaction between RbC and the CC-MB domains of E2F-DP heterodimers and present the crystal structure of an RbC-E2F1-DP1 complex.
RbC Binds to E2FCM-DPCM through a Bipartite Interaction
Cross-references: PDB:2AZE
Protein: DP01427 (UniProt Q01094)
Region: residues 200	to 301
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The lack of 15N and particularly 1H chemical shift dispersion in (A) and (B) are consistent with polypeptides lacking significant structure (Dyson and Wright, 2004). The fact that the NMR data suggests that E2F1CM is unstructured in the absence of DP1CM is consistent with the structural and biochemical studies presented in this study, which indicate that the stability of E2F1CM requires heterodimerization. 
In addition, NMR data suggest that E2F1CM is unstructured in the absence of DP1 (Supplemental Data, Section 2). These results confirm the structure-based prediction that the E2F1CM homodimer is less stable than the E2F1CM-DP1CM heterodimer, and they provide an explanation for the observation that the DNA binding and transactivation activities of E2F1 are reduced in the absence of a DP partner
Protein: DP01427 (UniProt Q01094)
Region: residues 200	to 301
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Intermolecular interactions are distributed throughout the E2F1 and DP1 polypeptides and involve the coiled coil, the β sandwich, and essentially all of the additional secondary-structure elements (Figures 2A and 2B).
Cross-references: PDB:2AZE
Protein: DP01427 (UniProt Q01094)
Region: residues 200	to 301
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Here, we demonstrate an interaction between RbC and the CC-MB domains of E2F-DP heterodimers and present the crystal structure of an RbC-E2F1-DP1 complex. 
Cross-references: PDB:2AZE
Protein: DP01427 (UniProt Q01094)
Region: residues 200	to 301
Annotation: molecular adaptor activity (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Here, we demonstrate an interaction between RbC and the CC-MB domains of E2F-DP heterodimers and present the crystal structure of an RbC-E2F1-DP1 complex. 
Cross-references: PDB:2AZE
Protein: DP01429 (UniProt Q09427)
Region: residues 928	to 1000
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
SUR1 had some disordered regions (744-770, 928-1000, 1319-1343), particularly in the linkers
between TMDs and NBDs, and in NBD1, that were not seen in our map.
Cross-references: PDB:5TWV
Protein: DP01429 (UniProt Q09427)
Region: residues 1319	to 1343
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
SUR1 had some disordered regions (744-770, 928-1000, 1319-1343), particularly in the linkers
between TMDs and NBDs, and in NBD1, that were not seen in our map.
Cross-references: PDB:5TWV
Protein: DP01429 (UniProt Q09427)
Region: residues 747	to 770
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
SUR1 had some disordered regions (744-770, 928-1000, 1319-1343), particularly in the linkers
between TMDs and NBDs, and in NBD1, that were not seen in our map.
Cross-references: PDB:5TWV
Protein: DP01429 (UniProt Q09427)
Region: residues 928	to 1000
Annotation: flexible linker (Disorder function)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
SUR1 had some disordered regions (744–770, 928–1000, 1319–1343), particularly in the linkers between TMDs and NBDs, and in NBD1, that were not seen in our map.
Flexible linker connecting ABC transporter 1 domain and ABC transmembrane type-1 2 domain.
Cross-references: PDB:5TWV
Protein: DP01429 (UniProt Q09427)
Region: residues 1319	to 1343
Annotation: flexible linker (Disorder function)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
SUR1 had some disordered regions (744–770, 928–1000, 1319–1343), particularly in the linkers between TMDs and NBDs, and in NBD1, that were not seen in our map.
Flexible linker connecting ABC transmembrane type-1 2 and ABC transporter 2 domain.
Cross-references: PDB:5TWV
Protein: DP01430 (UniProt Q03071)
Region: residues 77	to 99
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
15N HSQC NMR spectra indicate that Elc1 has regions of dynamic instability and/or flexibility. Most peaks missing from the HSQC spectrum and those lacking correlations in triple-resonance and NOESY spectra are from residues at the C terminus of Elc1. Thus, the dynamic instability of Elc1 appears to be most prominent at the C terminus.
Protein: DP01431 (UniProt C6ZFX3)
Region: residues 1	to 94
Annotation: disorder (Structural state)
Evidence: synchrotron radiation circular dichroism evidence used in manual assertion
Supporting statements:
Like unfolded polypeptides, the CD spectrum of LjIDP1 shows a large negative peak at ∼200 nm
Protein: DP01431 (UniProt C6ZFX3)
Region: residues 1	to 94
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
LjIDP1 protease sensitivity is comparable with the intrinsically disordered α-synuclein, whereas the globular protein lysozyme remains intact under the same conditions. This suggests that the amino acid backbone of LjIDP1 is largely accessible to proteolytic attack and in combination with the spectroscopic data unequivocally shows that LjIDP1 is largely disordered along the entire length.
Protein: DP01431 (UniProt C6ZFX3)
Region: residues 1	to 94
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H spectrum of LjIDP1 shows no signal dispersion typical of globular proteins, and the similarity of the spectra in the aliphatic region with and without urea indicates that no major structural transitions occurred and supports the notion that LjIDP1 is intrinsically disordered.
Protein: DP01432 (UniProt E1UJ20)
Region: residues 2	to 109
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Ca2+ depletion from csPA makes it susceptible to the limited proteolysis by bovine α-chymotrypsin at 37 °C.
Protein: DP01432 (UniProt E1UJ20)
Region: residues 2	to 109
Annotation: molten globule to order (Structural transition)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Apo-PA is destabilized due to the highly unfavorable electrostatic repulsion of the nearby carboxylates within Ca2+-binding loops of PA, which turns into favorable electrostatic attraction upon the metal association.
Protein: DP01432 (UniProt E1UJ20)
Region: residues 2	to 109
Annotation: disorder (Structural state)
Evidence: differential scanning calorimetry evidence used in manual assertion
Supporting statements:
The DSC data strongly evidence the absence of rigid tertiary structure in apo-csPA. This conclusion is further supported by the data on GdmCl-induced unfolding of apo-csPA at 20 °C, monitored by its molar ellipticity at 222 nm.