LiteFold/DisProt huggingface dataset:
Protein: DP01513 (UniProt P53378)
Region: residues 439	to 473
Annotation: phosphorylation display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The in vivo phosphorylation of an evolutionarily conserved Tyr (Y445) residue in the gamma-tubulin orthologue of the budding yeast was identified. Mutation of Y445 to an acidic residue alters microtubule dynamics and perturbs the function of the mitotic spindle but does not appear to alter microtubule nucleation, suggesting the S.c. gamma-CT may function in postnucleation organization and function of microtubules.
Protein: DP01515 (UniProt P25344)
Region: residues 187	to 249
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The initial construct corresponding to the predicted Ste50p-RA domain showed a well-dispersed 1H-15N HSQC spectrum indicative of a folded protein (data not shown), with the exception of the N-terminal region that was unfolded.
To verify that the “missing strands” are not located in more distal regions of the protein, we analyzed a longer Ste50p fragment corresponding to aa187-346 was by NMR, and no additional folded elements were detected.
Protein: DP01516 (UniProt Q06810)
Region: residues 194	to 333
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Sequence analysis predicted that the cytoplasmic tail of Opy2p is intrinsically unstructured (Supplemental Figure S2A). This prediction was confirmed by NMR spectroscopy of a recombinant 15N-enriched fragment of Opy2p encompassing amino acid residues 194-333, which showed a 1H-15N HSQC spectrum indicative of an unstructured polypeptide (Supplemental Figure S2B).
Protein: DP01516 (UniProt Q06810)
Region: residues 267	to 345
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
The HSQC spectra of 15N-labeled Opy2p SID (aa 267-345) shows this region is unstructured.
Protein: DP01516 (UniProt Q06810)
Region: residues 325	to 339
Annotation: protein binding (Molecular function)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
The HSQC spectra of this fragment titrated with the unlabeled Ste50p-RA domain revealed that only signals corresponding to residues 325-339 of SIDOpy2p showed significant changes in the presence of the Ste50p-RA domain (Figure 4A), suggesting that these residues contribute to the interaction.
Protein: DP01516 (UniProt Q06810)
Region: residues 325	to 339
Annotation: protein binding (Molecular function)
Evidence: fluorescence polarization evidence used in manual assertion
Supporting statements:
To quantify the strength of this interaction, we used fluorescence polarization and isothermal titration calorimetry (ITC) measurements and determined that the affinity (apparent Kd) is in the range of 20–80 μM (Figure 4B).
Protein: DP01516 (UniProt Q06810)
Region: residues 325	to 339
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
To quantify the strength of this interaction, we used fluorescence polarization and isothermal titration calorimetry (ITC) measurements and determined that the affinity (apparent Kd) is in the range of 20–80 μM (Figure 4B).
Protein: DP01517 (UniProt Q06710)
Region: residues 64	to 86
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
NOE data and chemical shift differences from random coil values (60) support the random coil nature of the linker (Figs. ​(Figs.22 and supplemental S4). Furthermore, the backbone chemical shifts of the linker are consistent with a highly flexible backbone, according to the random coil index (65) (supplemental Fig. S5).
Cross-references: PDB:2K27
Protein: DP01517 (UniProt Q06710)
Region: residues 64	to 86
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The tertiary organization of the free Pax-8 DNA binding domain shows the characteristics of a canonical Prd domain: two HTH motifs are connected by an unstructured linker region. NOE data and chemical shift differences from random coil values (60) support the random coil nature of the linker (Figs. ​(Figs.22 and supplemental S4). Furthermore, the backbone chemical shifts of the linker are consistent with a highly flexible backbone, according to the random coil index (65) (supplemental Fig. S5).
Protein: DP01517 (UniProt Q06710)
Region: residues 135	to 146
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Additionally, the random coil index indicates a random coil-like structure and high backbone flexibility for the C- and N-terminal regions flanking the two HTH domains.
Cross-references: PDB:2K27
Protein: DP01517 (UniProt Q06710)
Region: residues 1	to 28
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Additionally, the random coil index indicates a random coil-like structure and high backbone flexibility for the C- and N-terminal regions flanking the two HTH domains.
Cross-references: PDB:2K27
Protein: DP01520 (UniProt Q02297-10)
Region: residues 1	to 75
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
Atypical mobility of pure NRG1-III-Nct on SDS-PAGE was observed, which is an indication of a disordered nature of the protein.
Protein: DP01520 (UniProt Q02297-10)
Region: residues 1	to 75
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
Two types of synchroton SAXS experiments were done: a highly concentrated batch of the protein was directly analysed, and the protein was also subjected to an online SAXS experiment on a SEC column. The featureless scattering curve suggests a lack of globular folded domains, which is confirmed by the Kratky plot, clearly lacking any defined maximum characteristic for a folded protein.
Protein: DP01520 (UniProt Q02297-10)
Region: residues 1	to 75
Annotation: disorder (Structural state)
Evidence: synchrotron radiation circular dichroism evidence used in manual assertion
Supporting statements:
The folding of NRG1-III-Nct was studied by SRCD spectroscopy. In aqueous solution, the protein showed a typical spectrum for disordered proteins, with a strong negative minimum at 200 nm. This result fits well to the sequence-based predictions of disorder.
Protein: DP01520 (UniProt Q02297-10)
Region: residues 1	to 75
Annotation: nickel cation binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
To further investigate metal binding by NRG1-III-Nct, ITC experiments were performed. The binding assays (Fig. 4; Table 1) showed that the protein binds to Zn2+ as well as to Ni2+ with a dissociation constant Kd in the low micromolar range. No binding was observed with Mg2+ or Fe2+.
Protein: DP01520 (UniProt Q02297-10)
Region: residues 1	to 75
Annotation: zinc ion binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
To further investigate metal binding by NRG1-III-Nct, ITC experiments were performed. The binding assays (Fig. 4; Table 1) showed that the protein binds to Zn2+ as well as to Ni2+ with a dissociation constant Kd in the low micromolar range. No binding was observed with Mg2+ or Fe2+.
Protein: DP01521 (UniProt Q5RJL0)
Region: residues 1	to 282
Annotation: disorder (Structural state)
Evidence: synchrotron radiation circular dichroism evidence used in manual assertion
Supporting statements:
Synhrotron radiation circular dichroism (SRCD) spectra were recorded for full-length juxtanodin and truncated variants. All spectra exhibited a negative minimum close to 200 nm and a relatively low ellipticity above 210 nm, a typical observation for disordered proteins.
Protein: DP01521 (UniProt Q5RJL0)
Region: residues 1	to 282
Annotation: protein binding (Molecular function)
Evidence: synchrotron radiation circular dichroism evidence used in manual assertion
Supporting statements:
Juxtanodin, also called ermin, is a 282-residue actin-binding protein, which co-localizes with filamentous actin (F-actin) and promotes the formation of cell protrusions during the differentiation of oligodendrocytes.
Protein: DP01521 (UniProt Q5RJL0)
Region: residues 1	to 282
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
The mmunoblotting results showed a discrepancy between the calculated molecular mass (32.2 kDa) and the actual migration of JN on SDS/PAGE. Further tests attributed this atypical migration of JN largely to its residues 101-247. In vitro expression of FLAG-tagged JN, JN247, JN141, and JNc yielded products that, on Western blots, measured heavier than predicted by 30%, 41%, 16%, and 44%, respectively.
Protein: DP01521 (UniProt Q5RJL0)
Region: residues 1	to 282
Annotation: disorder (Structural state)
Evidence: static light scattering assay evidence used in manual assertion
Supporting statements:
The SLS analysis clearly illustrates that juxtanodin is monomeric in solution, with a molecular weight of 32 kDa, which is essentially identical to the expected value of 32.2 kDa for a monomer. The small elution volume indicates a large hydrodynamic radius, i.e. juxtanodin has an extended and non-globular shape.
Protein: DP01521 (UniProt Q5RJL0)
Region: residues 1	to 282
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
We performed SAXS experiments. The Rg values derived from the Guinier plot, the distance distribution functions and Debye functions showed highly extended particle shapes. The large maximum particle dimensions (Dmax) also support a disordered nature. The Kratky plot revealed the typical behavior of disordered proteins, with a short plateau followed by a monotonic increase, and the lack of a clear maximum.
Protein: DP01524 (UniProt Q9UM11)
Region: residues 1	to 41
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The region is specified in the Extended Data Table 2
Cross-references: PDB:4UI9
Protein: DP01524 (UniProt Q9UM11)
Region: residues 68	to 87
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The region is specified in the Extended Data Table 2
Cross-references: PDB:4UI9
Protein: DP01524 (UniProt Q9UM11)
Region: residues 109	to 124
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The region is specified in the Extended Data Table 2
Cross-references: PDB:4UI9
Protein: DP01524 (UniProt Q9UM11)
Region: residues 133	to 145
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The region is specified in the Extended Data Table 2
Cross-references: PDB:4UI9
Protein: DP01526 (UniProt Q9UJX6)
Region: residues 1	to 14
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The region is specified in the Extended Data Table 2
Cross-references: PDB:4UI9
PDB:5A31
PDB:5G04
Protein: DP01526 (UniProt Q9UJX6)
Region: residues 30	to 52
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The region is specified in the Extended Data Table 2
Cross-references: PDB:4UI9
PDB:5G04
Protein: DP01526 (UniProt Q9UJX6)
Region: residues 221	to 231
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The region is specified in the Extended Data Table 2
Cross-references: PDB:4UI9
PDB:5G04
Protein: DP01526 (UniProt Q9UJX6)
Region: residues 459	to 475
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The region is specified in the Extended Data Table 2
Cross-references: PDB:4UI9
PDB:5G04
Protein: DP01526 (UniProt Q9UJX6)
Region: residues 305	to 319
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The region is specified in the Extended Data Table 2
Cross-references: PDB:4UI9
PDB:5G04
Protein: DP01526 (UniProt Q9UJX6)
Region: residues 731	to 822
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The region is specified in the Extended Data Table 2
Cross-references: PDB:4UI9
PDB:5G05
PDB:5G04
Protein: DP01527 (UniProt Q57904)
Region: residues 46	to 101
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
in the article "The corresponding region in Mj0480 is predicted to form a coiled coil but is disordered in the crystal"
Cross-references: PDB:5C8J
Protein: DP01527 (UniProt Q57904)
Region: residues 46	to 101
Annotation: small molecule binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
"we propose that this region facilitates interaction with different hydrophobic substrates"
Protein: DP01528 (UniProt P15273)
Region: residues 20	to 50
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
By examining the R2 values for individual residues (Fig. 4B), we noted that certain residues, mainly located between helices α1 and α2 (residues 19–50), showed considerably greater line broadening of their 15N resonances (up to 15 s−1 excess broadening). This indicates that these regions in the monomeric protein are undergoing conformational exchange (i.e. adopting different conformations) at the milli- to microsecond timescale.
The authors used a different strain (Yersinia pseudotuberculosis serotype I (strain IP32953)). Since the IDR is 100% identical this region is considered disordered.
Protein: DP01528 (UniProt P15273)
Region: residues 21	to 35
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region lacks electron density, indicating it is disordered.
Cross-references: PDB:4GF3
Protein: DP01531 (UniProt O75554)
Region: residues 276	to 376
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The spectrum of FBP 21276–376 showed very low chemical shift dispersion, consistent with an intrinsically disordered protein region (IDPR)
Protein: DP01531 (UniProt O75554)
Region: residues 276	to 376
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The spectrum of the complex suggests that the FBP21 fragment globally retains its unstructured nature when bound to Brr2C-Sec63 and does not adopt a stable fold upon complex formation.
Protein: DP01533 (UniProt Q9NS23-4)
Region: residues 1	to 50
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
(A) Fully annotated 15N-HSQC spectrum of unbound Rassf1C1-50, assigned by 1H13C15Ncorrelation experiments. The polypeptide chain is predominantly disordered as evidenced by limited 1HN dispersion (10 mM sodium phosphate, 0.1 mM EDTA, pH 6.5, 25 °C).
Protein: DP01533 (UniProt Q9NS23-4)
Region: residues 61	to 72
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
(C) Heteronuclear 15N{1H}NOE values of 15N-Rassf1C23-38w free (gray) and bound to DAXX55-144 (black) demonstrate that residues ∼28-38 are unstructured in isolation and become ordered upon complex formation.
Protein: DP01533 (UniProt Q9NS23-4)
Region: residues 61	to 72
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
(C) Heteronuclear 15N{1H}NOE values of 15N-Rassf1C23-38w free (gray) and bound to DAXX55-144 (black) demonstrate that residues ∼28-38 are unstructured in isolation and become ordered upon complex formation.
Protein: DP01533 (UniProt Q9NS23-4)
Region: residues 61	to 72
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
(C) Heteronuclear 15N{1H}NOE values of 15N-Rassf1C23-38w free (gray) and bound to DAXX55-144 (black) demonstrate that residues ∼28-38 are unstructured in isolation and become ordered upon complex formation.
Protein: DP01534 (UniProt Q07889)
Region: residues 1141	to 1300
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Our data show that the far-UV CD spectrum of the PR domain is characterized by a negative band centered around 208nm in the absence of denaturants (Figures 3a and 3b). This strongly suggests that the PR domain predominantly adopts a random coil-like conformation in solution though the possibility of some degree of polyproline II (PPII) helices cannot be completely ruled out.
Protein: DP01534 (UniProt Q07889)
Region: residues 1141	to 1300
Annotation: disorder (Structural state)
Evidence: dynamic light scattering assay evidence used in manual assertion
Supporting statements:
 Accordingly, our hydrodynamic data further substantiate the notion that the PR domain likely adopts a random coil-like conformation in solution.
Protein: DP01534 (UniProt Q07889)
Region: residues 1141	to 1300
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
Strikingly, the Kratky plots for the PR domain at all three concentrations initially rise at low scattering angles but then plateau out at higher scattering angles. Such behavior is consistent with an extended random coil-like conformation characteristic of proteins devoid of a globular structure (59).
Protein: DP01534 (UniProt Q07889)
Region: residues 1117	to 1319
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: fluorescence recovery after photobleaching evidence used in manual assertion
Supporting statements:
pLAT, Grb2, and Sos1 clusters exhibited dynamic liquid-like properties.
We observed multivalent assembly and consequent phase separation of LAT and its binding partners into liquid-like, micron-sized clusters.
Cross-references: PhaSePro:Q07889
Protein: DP01534 (UniProt Q07889)
Region: residues 1117	to 1319
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
Supplementary figure S1 shows this peptide migrates as higher molecular weight protein, probably due to its extended disordered nature.
Protein: DP01535 (UniProt B6KJB6)
Region: residues 337	to 542
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
SAXS was used to determine the average structure of the GRA24DN-p38a complex in solution. The radius of gyration was determined to be 4.85 nm with a Dmax of 16.96 nm and ab initio modeling showing an elongated molecule best described by a disordered protein binding two globular domains.
Protein: DP01535 (UniProt B6KJB6)
Region: residues 337	to 542
Annotation: protein binding (Molecular function)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
One of the effector proteins secreted by T. gondii, GRA24, has been shown to interact with the MAP kinase p38a, promoting its activation and nuclear translocation.
Protein: DP01535 (UniProt B6KJB6)
Region: residues 337	to 542
Annotation: disorder (Structural state)
Evidence: atomic force microscopy evidence used in manual assertion
Supporting statements:
In both AFM and EM data no secondary structure can be observed in GRA24 confirming its disordered nature.
Protein: DP01537 (UniProt O00429-3)
Region: residues 505	to 515
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region lacks electron density in the PDB structure indicating it is disordered.
Cross-references: PDB:4BEJ
Protein: DP01537 (UniProt O00429-3)
Region: residues 503	to 610
Annotation: protein localization to mitochondrion (Biological process)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
When expressed in DNM1L-depleted COS-7 cells, both the 4A and ΔB mutants failed to localize to mitochondria (Figure 3D). Instead, the 4A mutant was diffusely distributed in the cytoplasm, whereas the ΔB mutant was found in large punctate structures in the cytoplasm (Figure 3D, white arrows).
Protein: DP01537 (UniProt O00429-3)
Region: residues 74	to 83
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region lacks electron density in the PDB structure indicating it is disordered.
Cross-references: PDB:4BEJ
Protein: DP01537 (UniProt O00429-3)
Region: residues 503	to 610
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region lacks electron density in the PDB structure indicating it is disordered.
Cross-references: PDB:5WP9
EMDB:8874
Protein: DP01538 (UniProt P04147)
Region: residues 419	to 502
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum of the unfused wild-type P domain is typical of a denatured protein (Fig. 5A), and we observe no cooperative thermal unfolding transition from 4 to 80°C.
Protein: DP01538 (UniProt P04147)
Region: residues 419	to 502
Annotation: disorder (Structural state)
Evidence: temperature-induced protein unfolding evidence used in manual assertion
Supporting statements:
The CD spectrum of the unfused wild-type P domain is typical of a denatured protein (Fig. 5A), and we observe no cooperative thermal unfolding transition from 4 to 80°C.