LiteFold/DisProt huggingface dataset:
Protein: DP02842 (UniProt Q09683)
Region: residues 101	to 116
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Binding of the NFKxFxK motif at the Mre11 dimer interface is mediated by the eukaryote–specific insertion loops (one from each Mre11 protomer). As a result, these loops undergo a substantial structural change and a disorder to order transition, leading us to name these as “latching loops”. 
In the free state Mre11, residues 101-116 from the "latching loop" are disordered
Cross-references: PDB:4FCX
Protein: DP02842 (UniProt Q09683)
Region: residues 101	to 116
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Binding of the NFKxFxK motif at the Mre11 dimer interface is mediated by the eukaryote–specific insertion loops (one from each Mre11 protomer). As a result, these loops undergo a substantial structural change and a disorder to order transition, leading us to name these as “latching loops”. 
The second part, unique to eukaryotic Mre11, comprises the latching loops that interact with each other via an extended loop in the presence (but not absence) of Nbs1. As seen from the structures of Nbs1mir–Mre11cd and apo–Mre11cd, Nbs1 induces a disorder–to–order transition and geometric rearrangement of the latching loops (Fig. 4b–d), flipping them almost 180° towards the basal phosphodiesterase core.
In the free state Mre11 (4FCX), residues 101-116 from the "latching loop" are disordered. In the complex (4FBQ), only residues 103-108 remain disordered
Cross-references: PDB:4FCX
PDB:4FBQ
Protein: DP02842 (UniProt Q09683)
Region: residues 101	to 116
Annotation: molecular function regulator (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Binding of the NFKxFxK motif at the Mre11 dimer interface is mediated by the eukaryote–specific insertion loops (one from each Mre11 protomer). As a result, these loops undergo a substantial structural change and a disorder to order transition, leading us to name these as “latching loops”. 
The second part, unique to eukaryotic Mre11, comprises the latching loops that interact with each other via an extended loop in the presence (but not absence) of Nbs1. As seen from the structures of Nbs1mir–Mre11cd and apo–Mre11cd, Nbs1 induces a disorder–to–order transition and geometric rearrangement of the latching loops (Fig. 4b–d), flipping them almost 180° towards the basal phosphodiesterase core.
In the free state Mre11 (4FCX), residues 101-116 from the "latching loop" are disordered. In the complex (4FBQ), only residues 103-108 remain disordered
In contrast, our data suggest that telomere maintenance depends on a stable interaction between the NFKxFxK motif of Xrs2/Nbs1 and the latching loops of Mre11 [...] The asymmetric bridging of Mre11 dimers by a single Nbs1 subunit, paired with the uncovered intrinsic flexibility of the eukaryotic Mre11 dimer, is perhaps the most significant and unexpected finding of our structural and functional analyses. 
Cross-references: PDB:4FCX
PDB:4FBQ
Protein: DP02847 (UniProt P47110)
Region: residues 117	to 350
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Pol32C harboring the C-terminus PIP motif is disordered, but the spatial position of Pol32N is such that it would allow for the PIP motif of Pol32C to extend to the downstream portion of the DNA duplex for interactions with PCNA (Fig. 1a and Supplementary Fig. 3).
Cross-references: PDB:6P1H
Protein: DP02847 (UniProt P47110)
Region: residues 337	to 345
Annotation: protein binding (Molecular function)
Evidence: experimental phenotypic evidence used in manual assertion
Supporting statements:
To analyze the roles of PIP motifs individually, we purified Polδ complexes that carry either (1) the F1002A, I1003A mutations in the Pol3 PIP, (2) the Y327A, F328A mutations in the Pol31 PIP, or (3) where the PIP of Pol32 had been inactivated by deleting C-terminal residues 337–350 of the protein (1–336) or by changing the conserved F344, F345 residues to alanines (Fig. 3B). As shown in Fig. 3C, Polδ harboring a mutation in the Pol3 PIP (lane 5) or lacking the Pol32 PIP (lane 9) exhibits a reduction in PCNA-stimulated DNA synthesis and the formation of fully extended product was impaired by these mutations, similar to that observed for mutations in the Pol31 PIP (lane 7). Thus PCNA binding motifs in all three subunits affect Polδ’s ability to synthesize DNA with PCNA, and they all appear to affect it to about the same degree.
Protein: DP02847 (UniProt P47110)
Region: residues 337	to 345
Annotation: molecular function regulator (Molecular function)
Evidence: experimental phenotypic evidence used in manual assertion
Supporting statements:
To analyze the roles of PIP motifs individually, we purified Polδ complexes that carry either (1) the F1002A, I1003A mutations in the Pol3 PIP, (2) the Y327A, F328A mutations in the Pol31 PIP, or (3) where the PIP of Pol32 had been inactivated by deleting C-terminal residues 337–350 of the protein (1–336) or by changing the conserved F344, F345 residues to alanines (Fig. 3B). As shown in Fig. 3C, Polδ harboring a mutation in the Pol3 PIP (lane 5) or lacking the Pol32 PIP (lane 9) exhibits a reduction in PCNA-stimulated DNA synthesis and the formation of fully extended product was impaired by these mutations, similar to that observed for mutations in the Pol31 PIP (lane 7). Thus PCNA binding motifs in all three subunits affect Polδ’s ability to synthesize DNA with PCNA, and they all appear to affect it to about the same degree.
Protein: DP02847 (UniProt P47110)
Region: residues 337	to 345
Annotation: molecular function regulator (Molecular function)
Evidence: mutant phenotype evidence used in manual assertion
Supporting statements:
This is a PCNA interacting PIP Box motif

The observed defects in mutagenesis were less severe with pol32– 10, a C-terminal 7 aa truncation (F344FKRKAK), than with the internal deletion mutant pol32–9 deleting aa 310–343 which include QGTLES343 of the motif, suggesting the existence of residual interactions between Pol32–10 and PCNA in vivo.
Protein: DP02848 (UniProt P15436)
Region: residues 1007	to 1051
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Polδ CysAD is disordered, suggestive of a flexible region that may only become ordered when it interacts with other components of the replication fork, including PCNA18 (Supplementary Fig. 3)[...]The paucity of interactions between the catalytic and regulatory modules behooves a relatively flexible complex able to accommodate changes in DNA direction. In a previous low resolution SAXS analysis of the Polδ holoenzyme in the absence of DNA, we observed significant flexibility between the catalytic and regulatory modules35. From the current cryo-EM analysis, flexibility between the modules appears to be a feature even when Polδ is complexed to DNA. 
Cross-references: PDB:6P1H
Protein: DP02848 (UniProt P15436)
Region: residues 1007	to 1051
Annotation: molecular adaptor activity (Molecular function)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
Polδ CysAD is disordered, suggestive of a flexible region that may only become ordered when it interacts with other components of the replication fork, including PCNA18 (Supplementary Fig. 3)[...]The paucity of interactions between the catalytic and regulatory modules behooves a relatively flexible complex able to accommodate changes in DNA direction. In a previous low resolution SAXS analysis of the Polδ holoenzyme in the absence of DNA, we observed significant flexibility between the catalytic and regulatory modules35. From the current cryo-EM analysis, flexibility between the modules appears to be a feature even when Polδ is complexed to DNA. 
From the structure, the interface between the catalytic and regulatory modules is relatively sparse and suggestive of a relatively flexible complex able to accommodate changes in DNA direction.

Flexibility between the regulatory and catalytic modules, coupled with the proximity of the regulatory module to the exo and thumb domains, appears to be important for the 3′→5′ exonuclease activity of Polδ

Local flexibility between the catalytic and regulatory modules may also facilitate the binding of various DNA substrates in these diverse pathways.


Cross-references: PDB:6P1H
Protein: DP02849 (UniProt O43521)
Region: residues 1	to 41
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Bim, Bad and Bmf: intrinsically unstructured BH3-only proteins that undergo a localized conformational change upon binding to prosurvival Bcl-2 targets
We show, using spectroscopic methods, that the BH3-only proteins Bim, Bad and Bmf are unstructured in the absence of binding partners. Detailed sequence analyses are consistent with this observation and suggest that most BH3-only proteins are unstructured
The CD spectra obtained for BimLDC27 over the range 5–651C is characteristic of an unstructured protein, although the slight inflection near 222nm may indicate some residual a-helical structure
Protein: DP02849 (UniProt O43521)
Region: residues 1	to 41
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Bim, Bad and Bmf: intrinsically unstructured BH3-only proteins that undergo a localized conformational change upon binding to prosurvival Bcl-2 targets
We show, using spectroscopic methods, that the BH3-only proteins Bim, Bad and Bmf are unstructured in the absence of binding partners. Detailed sequence analyses are consistent with this observation and suggest that most BH3-only proteins are unstructured
Analysis of NMR spectra for BimLDC27 support this conclusion (Figure 2c). In the 1H-15N-HSQC spectrum (Figure 2c), the backbone amide resonances fall between 8.0 and 8.5 p.p.m., and there is little dispersion in the aliphatic region in the 1D 1H NMR spectrum (data not shown). The sharp resonances and lack of chemical shift dispersion reflect the intrinsic mobility and lack of long-range order in BimLDC27. The absence of stable tertiary structure is supported by the complete absence of any HN–HN cross peaks in both proton 2D NOESY and a three-dimensional (3D) 15N-NOESY spectra (data not shown). In heteronuclear
{1H}15N, NOEs spectra, most of the resonances were of negative intensity (data not shown), indicating mobility on the ps–ns time scale, features typical of IUPs.28
Protein: DP02849 (UniProt O43521)
Region: residues 1	to 41
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Bim, Bad and Bmf: intrinsically unstructured BH3-only proteins that undergo a localized conformational change upon binding to prosurvival Bcl-2 targets
We show, using spectroscopic methods, that the BH3-only proteins Bim, Bad and Bmf are unstructured in the absence of binding partners. Detailed sequence analyses are consistent with this observation and suggest that most BH3-only proteins are unstructured

During purification, BimLDC27 was observed to be highly protease sensitive and behaved as a larger protein, migrating in sodium dodecyl sulfatepolyacrylamide gel electrophoresis (SDS-PAGE) as an approximately 16 kDa protein and eluting from gel filtration columns with an apparent molecular weight of B25 kDa (see Figure 3a). However, when analyzed by sedimentation
velocity centrifugation and evaluated in terms of a single class of noninteracting solute, a molecular mass (Mr) of 13.2 kDa was obtained (Figure 2a).
Protein: DP02849 (UniProt O43521)
Region: residues 97	to 164
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Bim, Bad and Bmf: intrinsically unstructured BH3-only proteins that undergo a localized conformational change upon binding to prosurvival Bcl-2 targets
We show, using spectroscopic methods, that the BH3-only proteins Bim, Bad and Bmf are unstructured in the absence of binding partners. Detailed sequence analyses are consistent with this observation and suggest that most BH3-only proteins are unstructured
During purification, BimLDC27 was observed to be highly protease sensitive and behaved as a larger protein, migrating in sodium dodecyl sulfatepolyacrylamide gel electrophoresis (SDS-PAGE) as an approximately 16 kDa protein and eluting from gel filtration columns with an apparent molecular weight of B25 kDa (see Figure 3a). However, when analyzed by sedimentation velocity centrifugation and evaluated in terms of a single class of noninteracting solute, a molecular mass (Mr) of 13.2 kDa was obtained (Figure 2a).
Protein: DP02849 (UniProt O43521)
Region: residues 97	to 164
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Bim, Bad and Bmf: intrinsically unstructured BH3-only proteins that undergo a localized conformational change upon binding to prosurvival Bcl-2 targets
We show, using spectroscopic methods, that the BH3-only proteins Bim, Bad and Bmf are unstructured in the absence of binding partners. Detailed sequence analyses are consistent with this observation and suggest that most BH3-only proteins are unstructured
Analysis of NMR spectra for BimLDC27 support this conclusion (Figure 2c). In the 1H-15N-HSQC spectrum (Figure 2c), the backbone amide resonances fall between 8.0 and 8.5 p.p.m., and there is little dispersion in the aliphatic region in the 1D 1H NMR spectrum (data not shown). The sharp resonances and lack of chemical shift dispersion reflect the intrinsic mobility and lack of long-range order in BimLDC27. The absence of stable tertiary structure is supported by the complete absence of any HN–HN cross peaks in both proton 2D NOESY and a three-dimensional (3D) 15N-NOESY spectra (data not shown). In heteronuclear
Protein: DP02849 (UniProt O43521)
Region: residues 97	to 164
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Bim, Bad and Bmf: intrinsically unstructured BH3-only proteins that undergo a localized conformational change upon binding to prosurvival Bcl-2 targets
We show, using spectroscopic methods, that the BH3-only proteins Bim, Bad and Bmf are unstructured in the absence of binding partners. Detailed sequence analyses are consistent with this observation and suggest that most BH3-only proteins are unstructured

The CD spectra obtained for BimLDC27 over the range 5–651C is characteristic of an unstructured protein, although the slight inflection near 222nm may indicate some residual a-helical structure
Protein: DP02849 (UniProt O43521)
Region: residues 142	to 164
Annotation: disorder to order (Structural transition)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Bim, Bad and Bmf: intrinsically unstructured BH3-only proteins that undergo a localized conformational change upon binding to prosurvival Bcl-2 targets
We show, using spectroscopic methods, that the BH3-only proteins Bim, Bad and Bmf are unstructured in the absence of binding partners. Detailed sequence analyses are consistent with this observation and suggest that most BH3-only proteins are unstructured. When Bim binds and inactivates prosurvival proteins, most residues remain disordered, only the BH3 element becomes structured, and the short ahelical molecular recognition element can be considered to behave as a ‘bead on a string’. Coupled folding and binding is typical of many IUPs that have important signaling roles, such as BH3-only proteins, as the inherent structural plasticity favors interaction with multiple targets.
Partial proteolysis experiments were used to further evaluate the conformational changes associated with complex formation. When treated with trypsin, BimLDC27 was rapidly degraded to small peptides (Figure 3b, lanes 3 and 4), whereas Bcl-w was relatively resistant although after 60 min digestion. When Bcl-wDC10 and BimLDC27 were mixed before trypsin digestion, a different proteolytic profile was obtained (Figure 3b, lanes 8 and 9). Mass spectrometry analysis of the peptide mixtures revealed changes consistent with complex formation […] The mass of the new peptide corresponds to that expected for a peptide derived from the C-terminus of BimLDC27 (sequence shown at the bottom of Figure 3b). This peptide includes the BH3 domain and suggests that interaction with the hydrophobic binding groove protects the BH3 domain and the hydrophobic groove of Bcl-w from proteolysis
The curator assigns the residues based on the known crystal structures
Protein: DP02849 (UniProt O43521)
Region: residues 143	to 165
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
We report the crystal structure of human Mcl-1 bound to a BH3 peptide derived from human Bim and the structures for three complexes that accommodate large physicochemical changes at conserved Bim sites.
To provide a structural context for interpreting changes in binding, we solved the structure of human Mcl-1, consisting of residues corresponding to the Bcl-2 fold without the PEST or transmembrane domains, in complex with a peptide consisting of the BH3 region from human Bim. Single-wavelength anomolous diffraction (SAD) phasing using a selenomethionine derivative provided the native structure at a resolution of 2.0 Å, with an Rfree of 0.23. The model includes residues 172–197, 203–321 of Mcl-1, and 0–22 of Bim.
Residues 0-22  mentioned by the authors correspond to residues 143-165 of the uniprot entry
Cross-references: PDB:3KJ0
PDB:3KJ1
PDB:3KJ2
Protein: DP02849 (UniProt O43521)
Region: residues 143	to 165
Annotation: molecular function regulator (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
We report the crystal structure of human Mcl-1 bound to a BH3 peptide derived from human Bim and the structures for three complexes that accommodate large physicochemical changes at conserved Bim sites.
To provide a structural context for interpreting changes in binding, we solved the structure of human Mcl-1, consisting of residues corresponding to the Bcl-2 fold without the PEST or transmembrane domains, in complex with a peptide consisting of the BH3 region from human Bim. Single-wavelength anomolous diffraction (SAD) phasing using a selenomethionine derivative provided the native structure at a resolution of 2.0 Å, with an Rfree of 0.23. The model includes residues 172–197, 203–321 of Mcl-1, and 0–22 of Bim.
Residues 0-22  mentioned by the authors correspond to residues 143-165 of the uniprot entry
Cross-references: PDB:3KJ0
PDB:3KJ1
PDB:3KJ2
Protein: DP02849 (UniProt O43521)
Region: residues 142	to 165
Annotation: protein binding (Molecular function)
Evidence: experimental evidence used in manual assertion
Supporting statements:
We report the crystal structure of human Mcl-1 bound to a BH3 peptide derived from human Bim and the structures for three complexes that accommodate large physicochemical changes at conserved Bim sites.
Fluorescence spectroscopy
The BH3 region of Bim has been used extensively for studies exploring the relationship between sequence, structure, and binding in the Bcl-2 family.23–25 This work focused on the analysis of two positions in Bim that have the potential to influence binding specificity. As defined in Table TableI,I, these are positions 2d (isoleucine) and 4a (phenylalanine). 

Table I: Binding Affinity of Bim Peptides for Mcl-1 and Bcl-xL
reveals the affinity of the wild type sequence is < 2nM for both Mcl-1 and Bcl-XL
Protein: DP02849 (UniProt O43521)
Region: residues 141	to 165
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The study strategy is twofold: while BAX oligomerization was monitored through spectral changes of spin-labeled BAX, the binding kinetics was studied by observing time-dependent changes of spin-labeled BimBH3. Meanwhile, conformational transition between the unstructured and structured BimBH3 was measured. We show that helical propensity of the BimBH3 is increased upon binding to BAX but is then reduced after being released from the activated BAX;

BH3 domain of Bim is an IDP. […]From the spectra of circular dichroism (CD) spectroscopy, the studied peptides are largely disordered, having very low α- helicity relative to the CD spectrum of the BimBH3 in 90/10 (v/v) TFE/PB solvent (Fig. 1C). The CD result is consistent with the low predicted helicity (ca. 1 − 3%) of the peptides (Fig. 1D)
Legand Fig 1. (C) CD spectra of the BimBH3 mutants. BimBH3 and its mutants are largely disordered compared to BimBH3-C in 90/10 (v/v) TFE/PB buffer.
Protein: DP02849 (UniProt O43521)
Region: residues 141	to 165
Annotation: disorder to order (Structural transition)
Evidence: electron paramagnetic resonance evidence used in manual assertion
Supporting statements:
Here we study the interaction of BAX with an intrinsically
disordered BH3 motif of Bim protein (BimBH3) using ESR techniques. Upon incubation with
BAX, BimBH3 binds to BAX at helices 1/6 trigger site to initiate conformational changes of
BAX, which in turn promotes the formation of BAX oligomers. Study strategy is two-fold: while
BAX oligomerization was monitored through spectral changes of spin-labeled BAX, the binding
kinetics was studied by observing time-dependent changes of spin-labeled BimBH3. Meanwhile,
conformational transition between the unstructured and structured BimBH3 was measured. We
show that helical propensity of the BimBH3 is increased upon binding to BAX, but is then
reduced after being released from the activated BAX;
This comparison indicates that the helicity of the peptides is not a prerequisite for the binding to BAX. Taken together, it suggests that BAX oligomerization can be initiated either by the binding of the structured BimBH3 (i.e., Bim SAHB) through a conformational selection mechanism or by the interaction of the unstructured BimBH3 through an induced-fit mechanism.
Specifically, the results from the present study i) reveal new insights into how the induced-fit reaction of an IDP triggers the oligomerization of BAX, ii) report BAX oligomerization can be initiated by BimBH3 through an induced-fit mechanism, and iii) provide a tool to design experiments that can discriminate between the different functional states of an IDP.
Protein: DP02850 (UniProt O60239)
Region: residues 266	to 452
Annotation: disorder (Structural state)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
To define the dynamics of the full-length SH3BP5 protein, we used hydrogen deuterium exchange mass spectrometry (HDX-MS).
We carried out HDX experiments with a short pulse of deuterium exposure (3 s at 1 °C) for the full-length SH3BP5, with both the N terminus and C terminus of SH3BP5 having > 50% deuterium incorporation, indicating limited secondary structure (Supplementary Figure 3a). HDX-MS results were used to generate a crystal construct of SH3BP5, with all of the C-terminal disordered region removed (SH3BP5 1–265).
Cross-references: PDB:6DJL
Protein: DP02851 (UniProt Q5FWF5)
Region: residues 740	to 753
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Notably, the segment of the loop connecting these strands (residues 740–753) could not be traced in the electron density map and is presumably disordered.
Cross-references: PDB:5T53