LiteFold/DisProt huggingface dataset:
Protein: DP00333 (UniProt P27797)
Region: residues 18	to 417
Annotation: nuclear export signal receptor activity (Molecular function)
Evidence: cell permeability assay evidence used in manual assertion
Supporting statements:
These results indicate that nuclear export mediated by CRT requires specific recognition of the NES within PKI. 
Taken together, our data indicate that CRT and Ran cooperate to mediate nuclear export of PKI, and that this pathway involves CRT recognition of the leucine-rich NES of PKI. These properties are consistent with CRT functioning as a nuclear export receptor for PKI.
Thus, CRT and Ran exhibit cooperative binding to the NES. The binding of CRT and Ran in this reaction is specific for a WT NES, since addition of these proteins to a surface containing a mutant NES did not cause a detectable increase in refractive index (light blue tracing).
Protein: DP00333 (UniProt P27797)
Region: residues 261	to 278
Annotation: complement component C1q complex binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
Interestingly, the mapping studies revealed other unique C1q binding sites in the CRT sequence of a non-CH2-like nature; a site in the N-domain of CRT (peptides 35−40, Figure 1B) was observed to bind to C1q encompassing the amino acids TDMHGDSEYNIMFGPDICGPGTKKVHV (amino acids 103−129). The peptide 51 corresponding to the amino acid sequence FTHLYTLIVRPDNTY (amino acids 150−165) also demonstrated strong binding to C1q. As shown in Figure 2, a non-CH2-like region peptide present in the P-domain (peptide 79−82), WEPPVIQNPEYKGEWKPR (amino acids 244−261), bound to C1q in addition to the CH2-like domain present in the P-domain, WDERAKID.
The region 244−261, mentioned by the authors, corresponds to the 261-278 region of the full protein.
Protein: DP00333 (UniProt P27797)
Region: residues 120	to 146
Annotation: complement component C1q complex binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
Interestingly, the mapping studies revealed other unique C1q binding sites in the CRT sequence of a non-CH2-like nature; a site in the N-domain of CRT (peptides 35−40, Figure 1B) was observed to bind to C1q encompassing the amino acids TDMHGDSEYNIMFGPDICGPGTKKVHV (amino acids 103−129). The peptide 51 corresponding to the amino acid sequence FTHLYTLIVRPDNTY (amino acids 150−165) also demonstrated strong binding to C1q. As shown in Figure 2, a non-CH2-like region peptide present in the P-domain (peptide 79−82), WEPPVIQNPEYKGEWKPR (amino acids 244−261), bound to C1q in addition to the CH2-like domain present in the P-domain, WDERAKID.
The region 103−129, mentioned by the authors, corresponds to the 120-146 region of the full protein.
Protein: DP00333 (UniProt P27797)
Region: residues 168	to 182
Annotation: complement component C1q complex binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
Interestingly, the mapping studies revealed other unique C1q binding sites in the CRT sequence of a non-CH2-like nature; a site in the N-domain of CRT (peptides 35−40, Figure 1B) was observed to bind to C1q encompassing the amino acids TDMHGDSEYNIMFGPDICGPGTKKVHV (amino acids 103−129). The peptide 51 corresponding to the amino acid sequence FTHLYTLIVRPDNTY (amino acids 150−165) also demonstrated strong binding to C1q. As shown in Figure 2, a non-CH2-like region peptide present in the P-domain (peptide 79−82), WEPPVIQNPEYKGEWKPR (amino acids 244−261), bound to C1q in addition to the CH2-like domain present in the P-domain, WDERAKID.
The region 150−165, mentioned by the authors, corresponds to the 168-182 region of the full protein.
Protein: DP00333 (UniProt P27797)
Region: residues 219	to 226
Annotation: complement component C1q complex binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
Interestingly, the mapping studies revealed other unique C1q binding sites in the CRT sequence of a non-CH2-like nature; a site in the N-domain of CRT (peptides 35−40, Figure 1B) was observed to bind to C1q encompassing the amino acids TDMHGDSEYNIMFGPDICGPGTKKVHV (amino acids 103−129). The peptide 51 corresponding to the amino acid sequence FTHLYTLIVRPDNTY (amino acids 150−165) also demonstrated strong binding to C1q. As shown in Figure 2, a non-CH2-like region peptide present in the P-domain (peptide 79−82), WEPPVIQNPEYKGEWKPR (amino acids 244−261), bound to C1q in addition to the CH2-like domain present in the P-domain, WDERAKID.
Protein: DP00334 (UniProt Q00987)
Region: residues 1	to 24
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Multiple medium and long-range NOEs were observed for most residues between Glu25 and Tyr104, with gaps falling mainly between the elements of secondary structure.
Few long-range NOEs arising from the residues prior to Glu25 were detected, suggesting that this N-terminal segment of the protein is unlikely to interact extensively with the remainder of the MDM2N domain. The exception is Ile19, which exhibits NOEs to His96, Arg97 and Tyr100 in the N-terminal part of α2′. The measurable heteronuclear (1H,15N) NOEs (Figure 2(a)) are indeed negative or very small for N-terminal residues (Met6–Val8, The10–Val14), and T2 values are elevated (Figure 2(b)), consistent with the presence of fast (picosecond to nanosecond timescale) motion in this region.
Cross-references: PDB:1Z1M
BMRB:6612
Protein: DP00334 (UniProt Q00987)
Region: residues 210	to 304
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Here, we compared spectral resolution and sensitivity for 2D 1H-15N and 13C-15N correlation spectra recorded through direct detection of each of the two correlated nuclei for two protein regions that are entirely disordered (Hdm2-ABD and Surf6-N) and 2D 1H-15N correlation spectra for a ~73 kDa folded, pentameric protein with two short IDRs (N130).
Protein: DP00334 (UniProt Q00987)
Region: residues 215	to 300
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The narrow dispersion observed for the 1H resonances in the MDM2 AD (Fig. 4) is similar to that observed for the MDMX AD that we recently assigned (Song et al. 2022). Such a narrow dispersion with resonances clustered into the central region of the 1H-15N HSQC is typical for intrinsically disordered regions (Dyson and Wright 2021), as was indeed the case for the MDMX AD.
Consistent with an intrinsically disordered region, δ2D analysis of the chemical shift data demonstrates significant random-coil propensity coupled with polyproline II (PPII) propensity along the entire segment (Fig. 5 A).
Heteronuclear NOE enhancement factors < 0.65 are typically held to be indicative of considerable structural flexibility on the ps-ns time scale (Tjandra et al. 1995). The observed enhancement factors for the AD are all well below this threshold, falling in the range of − 0.2 to − 2.1 (Fig. 5B), which indicates that the AD has a high degree of structural flexibility and is consistent with the characteristics of an intrinsically disordered region.
Cross-references: BMRB:51334
Protein: DP00334 (UniProt Q00987)
Region: residues 335	to 437
Annotation: disorder (Structural state)
Evidence: combinatorial experimental and curator inference evidence used in manual assertion
Supporting statements:
The solved structure contained RPL11 and part of MDM2 (Fig. 1A,B; Supplemental Movie 1), most likely because of MDM2 degradation during the crystallization process. The final model included MDM2 residues 293–334, RPL11 residues 13–178 (residues 139–155 were missing), two zinc ions, one imidazole molecule, one β-mercaptoethanol molecule, and 84 water molecules.
The combination of the missing electron density for this region with the data from AlphaFold and MobiDB predictors, indicates this region is disorder rather than missing from the crystal due to degradation.
Cross-references: PDB:4XXB
Protein: DP00334 (UniProt Q00987)
Region: residues 1	to 24
Annotation: flexible N-terminal tail (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Few long-range NOEs arising from the residues prior to Glu25 were detected, suggesting that this N-terminal segment of the protein is unlikely to interact extensively with the remainder of the MDM2N domain. The exception is Ile19, which exhibits NOEs to His96, Arg97 and Tyr100 in the N-terminal part of α2′. The measurable heteronuclear (1H,15N) NOEs (Figure 2(a)) are indeed negative or very small for N-terminal residues (Met6–Val8, The10–Val14), and T2 values are elevated (Figure 2(b)), consistent with the presence of fast (picosecond to nanosecond timescale) motion in this region.
Cross-references: PDB:1Z1M
Protein: DP00337 (UniProt P06968)
Region: residues 137	to 152
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The sequence of residues 137-152 (not visible in the electron density maps) is particularly rich in glycines
Figure 2a and b shows a topology diagram and a ribbon representation of the subunit which consists of a polypeptide chain of 152 amino acid residues; the first 136 of these are visible in the crystal structure. 
Cross-references: PDB:1DUP
Protein: DP00341 (UniProt Q02248)
Region: residues 17	to 48
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Comparison of the NOESY spectra showed significantly less NOEs connectivities for the nonphosphorylated peptide (256 versus 352 for the phosphorylated peptide, Table 5), indicating a less structured state. In the 1HN/1Hα region, the nonphosphorylated peptide showed less dispersed signals for both amide and α protons of the nonphosphorylated peptide.
The global rmsd is high (5.7 Å for the backbone), suggesting an unstructured state, but by superimposing the structures, a general tendency can be detected.
Protein: DP00341 (UniProt Q02248)
Region: residues 17	to 48
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
From the CD spectra, the nonphosphorylated peptide does not appear to show any helical structure, even after the addition of TFE. This peptide appears to be less structured and more flexible than P-β-Cat17–48. In addition, the 205 nm negative band could show a possible type I β-turn structure.
Protein: DP00342 (UniProt P09883)
Region: residues 1	to 83
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H – 15N HSQC spectrum of colicin E9 (Figure 5) has a relatively narrow 1H chemical shift dispersion for the majority of signals, typical of that for a largely unstructured protein
The N-terminal region of colicin E9 is largely unstructured and flexible
chemical shift differences between the Ca, Cb and 13CO resonances of colicin E9 and those of sequence-corrected random coil values suggest that some of the residues in the N-terminal
region of the colicin are not in random coil conformations (Figure 8). The majority of peaks have
low-frequency Ca, Cb and 13CO shifts, indicating a preference for populating the b-region of (phi,psi) space, which is normal for random polypeptide chains.
the data presented here show that colicin E9 has a largely unstructured translocation domain without regular secondary structure, and thus it is not a molten globule
Protein: DP00342 (UniProt P09883)
Region: residues 1	to 61
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Most of the signals of the T1−61 region of the fusion protein had similar chemical shifts to those of intact colicin E9, with chemical shift differences from the sequence-corrected random coil values indicating that it lacked any stable secondary or tertiary structure.
Protein: DP00342 (UniProt P09883)
Region: residues 2	to 18
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Finally, we report the structure of the OmpF- OBS1 complex that shows the colicin bound within the porin lumen spanning the membrane bilayer. Our study explains how colicins exploit porins to deliver epitope signals to the bacterial periplasm and, more broadly, how the inherent flexibility and narrow cross-sectional area of an IUP domain can endow it with the ability to traverse a biological membrane via the constricted lumen of a β-barrel membrane protein
the most important factors in colicin translocation are the flexibility of the polypeptide backbone and the unconstrained nature of the N terminus.
We can now add a further advantage IUPs have over their globular counterparts that centers on their flexibility and lack of structure, characteristics that allow them to traverse a membrane through the narrow channels of a protein pore in order to deliver a signal directly into a cell. The key to this transfer is the intrinsically unstructured nature of an IUP and its narrow cross-sectional area, properties that allow a macromolecule as big as 6,000 Da to pass through a protein pore that has a molecular weight cutoff filter of 600 Da.
The disordered character may also be derived from the fact that each of the 6 copies show different conformations – these are probably induced by the fuzzy interaction.
Cross-references: PDB:3O0E
Protein: DP00342 (UniProt P09883)
Region: residues 2	to 18
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
detecting binding through isothermal titration calorimetry (ITC) (see Fig. S2 and Table S1 for details). We narrowed down the main OmpF-binding site to a 17-residue epitope from the N terminus of the ColE9 IUTD (residues 2–18), for which a peptide encompassing this sequence bound OmpF with a Kd of approximately 2 μM and a stoichiometry of one colicin peptide/OmpF monomer
We denote this IUTD binding epitope as OmpF-Binding Site 1 (OBS1). The interaction of the OBS1 peptide with OmpF is characterized by a large and favorable enthalpy (ΔH = −19.1 kcal∕mol) and an unfavorable entropy change (ΔS = −37.8 cal∕mol/K), consistent with the disordered peptide becoming ordered upon complex formation.
Protein: DP00342 (UniProt P09883)
Region: residues 54	to 63
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
Delineation of OBS2 was confirmed through ITC experiments using a synthetic peptide of residues 54 to 63 of the ColE9 IUTD binding to OmpF (Fig. 1B). Although OBS2 binds 10-fold weaker to OmpF than OBS1 (Kd 1⁄4 24 μM) the thermodynamic parameters of complex formation are similar to those of OBS1 (Table S1). Importantly, when OmpF was incubated with an excess of the OBS1 peptide, OBS2 was no longer able to bind OmpF, suggest- ing the two ColE9 IUTD OmpF-binding sites associate with the same region on the porin (Fig. 1B).
Protein: DP00342 (UniProt P09883)
Region: residues 32	to 47
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
ColE9 yet further, bound TolB with the same equilibrium dissociation constant as intact colicin (Kd = 1 uM) and with very similar thermodynamic parameters. ITC data for Tpep32–47 binding TolB are shown in Fig. 5b and compared with wild-type ColE9 in Table 1. The data show that complex formation is enthalpically driven and has a negative entropy, which is typical of binding-induced disorder–order transitions of natively disordered proteins.
Protein: DP00342 (UniProt P09883)
Region: residues 34	to 46
Annotation: protein binding (Molecular function)
Evidence: cross-linking evidence used in manual assertion
Supporting statements:
MBP-labeled ColE9 mutants could be readily crosslinked to TolB, but surprisingly these were distributed on either side of the previously identified TolB box sequence, appearing instead to form a photocrosslink footprint that spanned residues 34–46
Protein: DP00342 (UniProt P09883)
Region: residues 32	to 47
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
the structure of the ColE9 Tpep32–47–TolB complex was solved to a resolution of 2.0 Å
ColE9 Tpep32–47 binds to the ‘‘top’’ side of the B-propeller domain, distal to the N-terminal domain, with 15 of the 16 residues (32–46) contacting TolB.
Cross-references: PDB:2IVZ
Protein: DP00342 (UniProt P09883)
Region: residues 33	to 44
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
 a reduction in the backbone segmental motions of the residues giving rise to the signals, and TolB- induced chemical shift changes together with intermediate exchange between free and bound colicin E9. Whichever is the most important mechanism, the NMR data (Figure 11) identify clearly that residues 33 – 44 of colicin E9 are affected by the inter- action with TolB.
Protein: DP00342 (UniProt P09883)
Region: residues 2	to 18
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
In order to define this common binding site we crystallized OmpF in the presence of the higher affinity OBS1 peptide, the resulting crystals diffracting to 3.0-Å resolution. The monoclinic asymmetric unit contained two OmpF trimers and the electron density maps revealed electron density in the lumen of all six OmpF molecules, indicating the presence of the OBS1 peptide.
Cross-references: PDB:3O0E
Protein: DP00342 (UniProt P09883)
Region: residues 32	to 47
Annotation: disorder to order (Structural transition)
Evidence: temperature-induced protein unfolding evidence used in manual assertion
Supporting statements:
ColE9 yet further, bound TolB with the same equilibrium dissociation constant as intact colicin (Kd = 1 uM) and with very similar thermodynamic parameters. ITC data for Tpep32–47 binding TolB are shown in Fig. 5b and compared with wild-type ColE9 in Table 1. The data show that complex formation is enthalpically driven and has a negative entropy, which is typical of binding-induced disorder–order transitions of natively disordered proteins.
Protein: DP00343 (UniProt Q9Y6Q9)
Region: residues 1018	to 1088
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
Both the ACTR domain and the CBP domain are intrinsically unfolded in isolation, as indicated by the limited resonance dispersion in 1H–15N correlated NMR spectra (Fig. 1a, b).
Protein: DP00343 (UniProt Q9Y6Q9)
Region: residues 1045	to 1085
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
On formation of the complex, however, the two proteins form a single, highly helical and cooperatively folded entity.
ACTR forms an intimate complex with CBP (Fig. 2), burying 1,500 Å2 in the molecular interface. The structure comprises six helices, three from the ACTR domain (denoted Aα1, Aα2 and Aα3) and three from CBP (Cα1, Cα2 and Cα3). The overall architecture seems to be new, and DALI searches11 failed to find matches in the database of known structures. Residues 1,018–1,045 and 1,084–1,088 of ACTR are unstructured in the complex.
Cross-references: PDB:1KBH
Protein: DP00343 (UniProt Q9Y6Q9)
Region: residues 1018	to 1088
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
High-affinity binding between CBP and ACTR (dissociation constant (Kd) = 3.4 × 10-8 M, measured by isothermal titration calorimetry; Fig. 1d) is driven by enthalpy (ΔH° = -31.7 ± 1.5 kcal mol-1). This large enthalpy decrease is partly offset by the high entropic cost (TΔS° = -21.3 ± 1.5 kcal mol-1) that is associated with the ACTR and CBP domains folding on complex formation.
Protein: DP00343 (UniProt Q9Y6Q9)
Region: residues 1018	to 1045
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
ACTR forms an intimate complex with CBP (Fig. 2), burying 1,500 Å2 in the molecular interface. The structure comprises six helices, three from the ACTR domain (denoted Aα1, Aα2 and Aα3) and three from CBP (Cα1, Cα2 and Cα3). The overall architecture seems to be new, and DALI searches11 failed to find matches in the database of known structures. Residues 1,018–1,045 and 1,084–1,088 of ACTR are unstructured in the complex.
Cross-references: PDB:1KBH
Protein: DP00343 (UniProt Q9Y6Q9)
Region: residues 1045	to 1085
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H–15N NMR spectra of both CBP and ACTR gain significant amide proton dispersion on formation of the complex (Fig. 1a, b).
ACTR forms an intimate complex with CBP (Fig. 2), burying 1,500 Å2 in the molecular interface. The structure comprises six helices, three from the ACTR domain (denoted Aα1, Aα2 and Aα3) and three from CBP (Cα1, Cα2 and Cα3). The overall architecture seems to be new, and DALI searches11 failed to find matches in the database of known structures. Residues 1,018–1,045 and 1,084–1,088 of ACTR are unstructured in the complex.
Cross-references: PDB:1KBH
Protein: DP00344 (UniProt P62152)
Region: residues 74	to 83
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We find that the conformational fluctuations of the interdomain linker, which are largely responsible for the overall interdomain motions of CaM, can be well described by exploiting the information provided by chemical shifts
Protein: DP00345 (UniProt P16535)
Region: residues 884	to 953
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In aqueous solution, the CD spectra of  both HlyA and LktA reflect a predominantly  random conformation (Figures 6 and 7). There is no observed structural change between 23 and 37 “C. A broad range of pH changes (pH 4.5-8) do not affect the structure of  either HlyA or LktA signal  peptide.
The C-terminal signal peptides of HlyA and LktA exhibit similar biophysical behaviors. In aqueous solution, both molecules are mainly in a random conformation.
Protein: DP00345 (UniProt P16535)
Region: residues 884	to 953
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Finally, we tested the conformational behaviors of HlyA and LktA  signal peptides in phospholipid vesicles,  a  lipid bilayer environment which more closely resembles a membrane  compared to the  other  reagents  tested.   Uncharged phospholipids  PC  could not induce an ordered  structure (Figure 7G,H), while  the  anionic  phospholipids  (PS,  PG) induced formation of a-helices in both peptides (Figure 7C- F).
In aqueous solution, both molecules are mainly in a random conformation. Membrane mimetic environments such as TFE/H20, SDS micelles, and negatively charged phospholipid vesicles induce formation of a-helices.