LiteFold/DisProt huggingface dataset:
Protein: DP02901 (UniProt J7QA90)
Region: residues 44	to 88
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
On its own, the C-terminal region of AtaR (AtaRA44–M88) or shorter versions from S60 to M88 (AtaRS60–M88) are largely disordered in solution as shown by circular dichroism spectroscopy (Supplementary Fig. 3b). The circular dichroism spectra of both, AtaRA44–M88 and AtaRS60–M88, show a lack of secondary structure and a distinctive minimum at 205nm typical of disordered proteins. Moreover, AtaRA44–M88 lacks an observable transition from native to denatured state, also a signature feature of IDRs (Supplementary Fig. 3b).
Protein: DP02901 (UniProt J7QA90)
Region: residues 44	to 88
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
In the repressor complex, AtaR intrinsically disordered region interacts with AtaT at two different sites, folding into different structures, that are involved in two separate functional roles, toxin neutralization and placing the DNA-binding domains of AtaR in a binding-compatible orientation. [...] The antitoxin AtaR binds and neutralizes AtaT via its intrinsically disordered C-terminal region (IDR), sufficient to counteract the action of AtaT in vivo10


The structure AtaRA44–M88 in complex with AtaTY144F (Fig. 3a and Supplementary Fig. 3d) showed the intrinsically disordered AtaRA44–M88 wrapped around AtaTY144F (encompassing a large interface of ~1,500Å2 ). AtaRA44–M88 is anchored to the surface of AtaT via four structural motifs—mt1 (β-strand), mt2 (α-helix), a proline-rich fragment (P-rich) and mt3 (α-helix) (Fig. 3a–g)
Evidence is in PDB 6gtr
Cross-references: PDB:6GTS
PDB:6GTQ
PDB:6GTR
Protein: DP02901 (UniProt J7QA90)
Region: residues 44	to 88
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
In the repressor complex, AtaR intrinsically disordered region interacts with AtaT at two different sites, folding into different structures, that are involved in two separate functional roles, toxin neutralization and placing the DNA-binding domains of AtaR in a binding-compatible orientation.


The structure AtaRA44–M88 in complex with AtaTY144F (Fig. 3a and Supplementary Fig. 3d) showed the intrinsically disordered AtaRA44–M88 wrapped around AtaTY144F (encompassing a large interface of ~1,500Å2 ). AtaRA44–M88 is anchored to the surface of AtaT via four structural motifs—mt1 (β-strand), mt2 (α-helix), a proline-rich fragment (P-rich) and mt3 (α-helix) (Fig. 3a–g)
Evidence is in PDB 6gtr
Cross-references: PDB:6GTS
PDB:6GTQ
PDB:6GTR
Protein: DP02901 (UniProt J7QA90)
Region: residues 44	to 88
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
We used AtaR A44–M88 to gain further insights into the mechanism of AtaT neutralization. AtaT Y144F interacts with AtaR A44–M88 with an affinity of 367nM, lower than the affinity for the full length AtaR (Kd=29nM) (Supplementary Fig. 2g,h and Supplementary Table 1).
Protein: DP02901 (UniProt J7QA90)
Region: residues 44	to 88
Annotation: toxin sequestering activity (Molecular function)
Evidence: experimental phenotypic evidence used in manual assertion
Supporting statements:
The antitoxin AtaR binds and neutralizes AtaT via its intrinsically disordered C-terminal region (IDR), sufficient to counteract the action of AtaT in vivo10


Removing the last six residues of AtaR (K83 to M88) has a strong effect on growth and when this is extended to nine residues (R80 to M88) neutralization severely drops. These results indicate the neutralization region of AtaR involves almost entirely the IDR.
AtaR neutralizes AtaT via four functional domains located mainly in the C-terminal IDR
Cross-references: PDB:6GTO
PDB:6GTS
PDB:6GTQ
PDB:6GTR
Protein: DP02903 (UniProt P78953)
Region: residues 1	to 452
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
The low sedimentation coefficient and large Stokes radius are consistent with Mid1p-N452 purified with phosphatase inhibitors being disordered.
Protein: DP02903 (UniProt P78953)
Region: residues 1	to 452
Annotation: disorder (Structural state)
Evidence: analytical ultracentrifugation evidence used in manual assertion
Supporting statements:
The low sedimentation coefficient and large Stokes radius are consistent with Mid1p-N452 purified with phosphatase inhibitors being disordered.
Protein: DP02903 (UniProt P78953)
Region: residues 1	to 452
Annotation: disorder (Structural state)
Evidence: static light scattering assay evidence used in manual assertion
Supporting statements:
The low sedimentation coefficient and large Stokes radius are consistent with Mid1p-N452 purified with phosphatase inhibitors being disordered.
Static light scattering analysis of the peak of Mid1p-N452 gave a molecular weight of 60 kDa (Figure 3A), which is slightly larger than the molecular weight of 52.7 kDa based on the sequence. Therefore, Mid1pN452 is a monomer with a large hydrodynamic radius.
Protein: DP02903 (UniProt P78953)
Region: residues 1	to 308
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
After uniform labeling of Mid1p-N308 with 15N in bacteria and purification, we recorded 1H −15N HSQC NMR spectra. The peaks in the two-dimensional NMR spectra overlapped and were characterized by limited 1H chemical shift dispersion. These features are characteristic of intrinsically disordered proteins (IDPs) where conformational
averaging within the rapidly interconvertible ensembles results in poor dispersion. Flexibility allows significant chemical exchange of 15N with bulk water, resulting in decreases in 1H −15N signal intensities and a poor signal-to-noise ratio.
Protein: DP02903 (UniProt P78953)
Region: residues 1	to 452
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum of Mid1p-N452 purified from insect cells with phosphatase inhibitors (Figure 5C) was typical of a disordered protein53 with a minimum at 205 nm and a shoulder at 220 nm.
Protein: DP02903 (UniProt P78953)
Region: residues 1	to 452
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: microscopy evidence used in manual assertion
Supporting statements:
Differential interference contrast microscopy at room temperature (DIC) revealed that Mid1p-N452 at concentrations from 3.8 to 23 μM formed droplets, which increased in size over time.
Like the wild type protein, Mid1p constructs consisting of residues 1 −50649 or 1 −45220 exit the nucleus during interphase and accumulate in cortical nodes that mature to form cytokinetic nodes and assemble functional contractile rings during mitosis.
Protein: DP02903 (UniProt P78953)
Region: residues 1	to 452
Annotation: protein binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
Mid1p immunoprecipitates with overexpressed full-length Myo2, but not with a construct lacking 132 residues from C-terminus.
Protein: DP02903 (UniProt P78953)
Region: residues 1	to 452
Annotation: protein binding (Molecular function)
Evidence: bait-prey hybrid interaction evidence used in manual assertion
Supporting statements:
Hence, we assessed the binding of purified Mid1p-N452 to GST-Myo2-tail, a fusion of
GST to Myo2p residues 1441 −1526 that we immobilized on glutathione beads. Mid1p-N452 bound to GST-Myo2 tail (1441 −1526) with a Kd of ∼2 μM (n = 2; 1.9 and 2.2).
Protein: DP02904 (UniProt Q8NBI3)
Region: residues 225	to 243
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Crystal structure of Netrin-1 in complex with a Draxin fragment
We show that Draxin is largely unstructured, but that it uses a small C-terminal domain (Draxin-C) to bind DCC N-terminal Ig domains and an upstream conserved peptide motif (Draxin-22) to bind Netrin-1.
Draxin also contains a Netrin-1 binding site, just 20 amino acids N-terminal to Draxin-C, the DCC binding domain. It covers a 22-residue region that is evolutionary conserved, but is intrinsically unstructured.
Cross-references: PDB:6FKQ
Protein: DP02904 (UniProt Q8NBI3)
Region: residues 225	to 243
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Crystal structure of Netrin-1 in complex with a Draxin fragment
We show that Draxin is largely unstructured, but that it uses a small C-terminal domain (Draxin-C) to bind DCC N-terminal Ig domains and an upstream conserved peptide motif (Draxin-22) to bind Netrin-1.
Draxin also contains a Netrin-1 binding site, just 20 amino acids N-terminal to Draxin-C, the DCC binding domain. It covers a 22-residue region that is evolutionary conserved, but is intrinsically unstructured.
Cross-references: PDB:6FKQ
Protein: DP02904 (UniProt Q8NBI3)
Region: residues 25	to 245
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
Draxin is predicted to consist of a signal peptide for secretion, an unstructured region covering residues 25 to 245, and a C-terminal domain
Dimensionless Kratky plot of the SAXS data demonstrating the partially folded nature of hDraxin in solution. Theoretical Kratky representations for compact folded (dotted black line), fully unfolded (solid black line), and the experimentally derived full-length human Draxin (solid red line) are shown.
Cross-references: SASBDB:SASDBZ6
Protein: DP02904 (UniProt Q8NBI3)
Region: residues 225	to 243
Annotation: molecular adaptor activity (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Draxin tethers Netrin-1 and DCC together to promote fasciculation
The relatively strong Draxin/Netrin-1 complex can build a bridge between two axons decorated with DCC, initiating adhesion and therefore fasciculation between the axons. 
Cross-references: PDB:6FKQ
Protein: DP02904 (UniProt Q8NBI3)
Region: residues 225	to 243
Annotation: molecular function regulator (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Draxin tethers Netrin-1 and DCC together to promote fasciculation
The relatively strong Draxin/Netrin-1 complex can build a bridge between two axons decorated with DCC, initiating adhesion and therefore fasciculation between the axons.
Cross-references: PDB:6FKQ
Protein: DP02908 (UniProt P53853)
Region: residues 226	to 264
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
TALOS-N CS analysis of Vps75226–264 in the context of full-length Vps752 shows that the Vps75 tail is disordered. The same narrow CS dispersion is observed in the full complex.
Protein: DP02908 (UniProt P53853)
Region: residues 226	to 264
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
When we compared the 1H-15N CSPs of the Vps75 CTAD in the Asf1–H3:H4–Rtt109–Vps752 and the Asf1–H329–135:H4–Rtt109–Vps752 complexes (relative to free Vps752), we observed that the CSPs of residues 234–246 in the complex assembled with N-terminally truncated H3 were smaller than in that assembled with full-length H3 (Fig. 5b), confirming the interaction between the Vps75 CTAD and the H3 tail. Despite binding to each other, both the H3 N-terminal domain and the Vps75 CTAD remain disordered (Figs. 4b, ​,5c5c and Supplementary Fig. 9), hence conserving a substantial portion of their free-form conformational entropy. In agreement with the structural data, the removal of the Vps75 CTAD severely impacts H3-K9ac, but has no effect on H3-K56ac.
We compared the 2D 1H-15N NMR spectrum of H3 in the free histone dimer H3:H4 with those of H3 in the Asf1–H3:H4 complex and after addition of one equivalent of either Vps752 or Vps7521–225. In the presence of Vps752, the chemical shifts of H3 residues 7–37 differed from those measured in either H3:H4 or Asf1–H3:H4, while in the presence of the C-terminally truncated Vps7521–225, the chemical shifts of the H3 tail were identical to those of the free histone dimer (Fig. 4b). This result demonstrates that the H3 tail interacts with the Vps75 CTAD.
Cross-references: PDB:6O22
Protein: DP02908 (UniProt P53853)
Region: residues 226	to 264
Annotation: protein folding chaperone (Molecular function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
We show that Vps75 promotes K9-acetylation by engaging the H3 N-terminal tail in fuzzy electrostatic interactions with its disordered C-terminal domain, thereby confining the H3 tail to a wide central cavity faced by the Rtt109 active site. These fuzzy interactions between disordered domains achieve localization of lysine residues in the H3 tail to the catalytic site with minimal loss of entropy
The histone chaperone Vps75 belongs to the nucleosome assembly protein (NAP-1) family, which can bind to the four core histones (H2A, H2B, H3, and H4)25. Like Asf1, Vps75 stimulates acetylation of H3 by Rtt10910; however, unlike Asf1, it is critical for H3-K9ac but not for H3-K56ac, and can also facilitate acetylation of K23 and K27.
Vps75 promotes acetylation of K9 via a two-fold mechanism, which differs from a classical interaction between folded and unfolded protein domains. First, the Vps75 dimer acts as a binding platform for both the Asf1–H3:H4 substrate and the Rtt109 enzyme, building a doughnut-like structure with a 25-Å-wide central cavity faced by the Rtt109 catalytic site. Second, the unstructured C-terminal tail of Vps75 (C-terminal acidic domain, CTAD) recruits the similarly unstructured H3 N-terminal tail, containing K9, to this cavity via fuzzy electrostatic interactions. Both the Vps75 CTAD and the H3 N-terminal domain remain disordered, allowing confinement of the H3 tail in proximity to the enzyme active site with minimal entropic penalty.
Protein: DP02910 (UniProt P28023)
Region: residues 108	to 191
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In contrast to the CAP-Gly domain, the signals of other domains in the protein are poorly dispersed. This is an indication that the extended region of p150Glued(1–191) comprising the basic and SP-rich domains is much less structured than the CAP-Gly domain and may have a substantial proportion of random coil. 
Our results thus indicate that despite the presence of some secondary structures in these segments, the basic and SP-rich domains are intrinsically disordered and unfolded in
free state in solution.
Protein: DP02910 (UniProt P28023)
Region: residues 108	to 191
Annotation: protein binding (Molecular function)
Evidence: co-sedimentation assay evidence used in manual assertion
Supporting statements:
The binding affinity of monomeric p150Glued(1–191) to polymerized MTs was assessed by co-sedimentation assay (Fig. 1 C). More than 98% of p150Glued(1–191) binds to
MTs when equivalent molar concentrations of the protein and the tubulin dimer were used (Fig. 1 C). In comparison, as we and others reported previously, under the identical
conditions, less than half of the CAP-Gly domain protein encompassing residues 19–107 (CAP-Gly19–107) binds to MTs (15). Thus, the binding affinity of p150Glued(1–191) to MTs is significantly higher than that of CAP-Gly(19–107). Th is result validates that p150Glued(1–191) contains a second MT-binding domain other than CAP-Gly, and the
extended region comprised of the basic domain and SP-rich domain assists the interactions between the p150Glued and MTs.
Protein: DP02910 (UniProt P28023)
Region: residues 108	to 191
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Our results thus indicate that the rigid segments in the basic domain of p150Glued(1–191), S112–R119, A124–R132, and T141–T146, likely comprise most of the residues at the intermolecular interface with MTs (Fig. 7 C). Together with the CAP-Gly domain, they appear to be responsible for the MT-binding interactions of the p150Glued subunit. This finding is consistent with previous studies demonstrating that the basic domain is the second MT-binding segment of p150Glued 
Residues 108–191 of p150Glued(1–191) enhance the binding affinity and contain a second MT-binding region, albeit it is largely unstructured in solution and dynamic upon binding to MTs. Three short and rigid segments in the basic domain, S111–I116, A124–R132, and K144–T146, are predicted to form a-helical and b-sheet structures and are likely to encompass the MT-binding site.
Protein: DP02910 (UniProt P28023)
Region: residues 115	to 145
Annotation: molecular adaptor activity (Molecular function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
As reported previously, the basic domain of p150Glued (residues 115–145) has the ability to bind with MTs in the absence of CAP-Gly domain and to independently skate along MTs in the absence of dynein (16). In addition, this domain enhances dynein processivity
by fourfold and is responsible for the long-range motility of dynein and its long-time interactions with MTs (16).
Protein: DP02910 (UniProt P28023)
Region: residues 132	to 152
Annotation: molecular function regulator (Molecular function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
More specifically, the K-rich domain (132–152) antagonizes the inhibitory effect of the coiled-coil 1 domain (CC1) (residues 214–547) in the MT-binding affinity of p150Glued (17).
Protein: DP02910 (UniProt P28023)
Region: residues 1	to 18
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In contrast to the CAP-Gly domain, the signals of other domains in the protein are poorly dispersed. This is an indication that the extended region of p150Glued(1–191) comprising the basic and SP-rich domains is much less structured than the CAP-Gly domain and may have a substantial proportion of random coil.
Protein: DP02910 (UniProt P28023)
Region: residues 1	to 18
Annotation: molecular adaptor activity (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We also speculate that the N-terminal tail (1–25) of p150Glued(1–191) may contain
an anchoring point at residue R11 for interacting with the tubulin’s C-terminal tail (Fig. 7). In a previous study, the N-terminal segment 1–25 has been proposed to secure the
binding of CAP-Gly to MTs by wrapping around tubulin’s E-hook (13). According to our results, R11 is the only residue that is detected at 4C and exhibits strong peak intensity in the segment 1–25, indicating that R11 is possibly involved in binding interactions with tubulin.
In the N-terminal segment of p150Glued (residues 1–144), the N-terminal tail (residues 1–25) and the basic patch (residues 106–144) greatly increase the binding affinity of the
segment to MTs, and these patches affect the lateral associations of tubulins by interacting with the tubulin’s E-hook(13).
Protein: DP02910 (UniProt P28023)
Region: residues 1	to 18
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We also speculate that the N-terminal tail (1–25) of p150Glued(1–191) may contain
an anchoring point at residue R11 for interacting with the tubulin’s C-terminal tail (Fig. 7). In a previous study, the N-terminal segment 1–25 has been proposed to secure the
binding of CAP-Gly to MTs by wrapping around tubulin’s E-hook (13). According to our results, R11 is the only residue that is detected at 4C and exhibits strong peak intensity in the segment 1–25, indicating that R11 is possibly involved in binding interactions with tubulin.
In the N-terminal segment of p150Glued (residues 1–144), the N-terminal tail (residues 1–25) and the basic patch (residues 106–144) greatly increase the binding affinity of the
segment to MTs, and these patches affect the lateral associations of tubulins by interacting with the tubulin’s E-hook(13).
Protein: DP02911 (UniProt Q8N3V7)
Region: residues 545	to 613
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
To determine if SYNPO545-613 is disordered as predicted, we used far UV CD and NMR spectroscopy to investigate the solution structure of the polypeptide. A strong negative
signal at 200 nm in the far UV CD spectrum (Fig. 1B) and limited dispersion in the amide proton region of the 1H-15N HSQC spectrum (Fig. 1C) are consistent with a primarily disordered protein.
Protein: DP02911 (UniProt Q8N3V7)
Region: residues 545	to 613
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
To determine if SYNPO545-613 is disordered as predicted, we used far UV CD and NMR spectroscopy to investigate the solution structure of the polypeptide. A strong negative
signal at 200 nm in the far UV CD spectrum (Fig. 1B) and limited dispersion in the amide proton region of the 1H-15N HSQC spectrum (Fig. 1C) are consistent with a primarily disordered protein.
Protein: DP02911 (UniProt Q8N3V7)
Region: residues 545	to 613
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
Isothermal titration calorimetry and CD experiments revealed that the interactions of the disordered WW2 domain with SYNPO are significantly weaker than SYNPO's interactions with the well-folded WW1 domain and that an I81W substitution in the WW2 domain neither enhances binding affinity nor induces substantial WW2 domain folding.
These analyses also disclosed that SYNPO binds the tandem WW domain polypeptide in an antiparallel manner, that is, the WW1 domain binds the second PPXY motif of SYNPO.
Protein: DP02911 (UniProt Q8N3V7)
Region: residues 1	to 929
Annotation: disorder (Structural state)
Evidence: author statement used in manual assertion
Supporting statements:
Synaptopodin family of natively unfolded, actin binding proteins: physical properties and potential biological functions
Critical to the understanding of the function of synaptopodin’s is the appreciation of the fact that they have little secondary or tertiary structure under native conditions.
Protein: DP02913 (UniProt P04004)
Region: residues 48	to 130
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
We utilized far-UV CD to study the effect of osmotic pressure on secondary structure within the IDD. Ethylene glycol (EG) and polyethylene glycol (PEG)-400 were employed to test for structural changes within the IDD that may be induced by changes in osmotic pressure. The results indicated that the SMBIDD fragment alone exhibited ellipticity characteristic of a protein fold devoid of classical secondary structure elements (Figure 2a).
Protein: DP02913 (UniProt P04004)
Region: residues 1	to 130
Annotation: disorder (Structural state)
Evidence: small-angle neutron scattering evidence used in manual assertion
Supporting statements:
This analysis indicates that the isolated SMB-IDD is a significantly flexible structure, existing over a relatively broad Rg range of ~20-55 Å