LiteFold/DisProt huggingface dataset:
Protein: DP03688 (UniProt Q6DD88)
Region: residues 1	to 21
Annotation: disorder (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
In all preceding structures, the N-terminal residues leading from the initiator
methionine to the G domain were largely disordered. The conservation of this region across different species is strong within distinct isoforms, but highly divergent when isoforms within a particular species are compared with each other (Fig. 1 A).
Figure 9. Phosphorylation of conserved serine residues in the ATL1 HVR. (A) Cartoon representation of the ATL1 catalytic core structure presented in Fig. 1 (G domain, blue; middle domain, purple; structured portion of the HVR spanning residues 18–31, pink; S22 and S23, red; residues 1–17, disordered).
Cross-references: PDB:6XJO
Protein: DP03689 (UniProt P07250)
Region: residues 287	to 316
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Several loop regions in the Ipk2 structure are disordered, and we have not included the corresponding residues in our current model. These loop regions comprise residues 1-26, 46-57 (between α1 and α2), and 76-110 (between β2 and β3) in the N-terminal domain and 287-316 in the C-terminal domain. Not surprisingly, the unique aspartate-rich poly-D loop region between residues 287 and 316 is disordered in our structure and was omitted from the final model.
The position of the disordered poly-D loop is indicated by a black line.
Cross-references: PDB:2IF8
PDB:2IEW
Protein: DP03689 (UniProt P07250)
Region: residues 76	to 110
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Several loop regions in the Ipk2 structure are disordered, and we have not included the corresponding residues in our current model. These loop regions comprise residues 1-26, 46-57 (between α1 and α2), and 76-110 (between β2 and β3) in the N-terminal domain and 287-316 in the C-terminal domain.
Cross-references: PDB:2IF8
PDB:2IEW
Protein: DP03689 (UniProt P07250)
Region: residues 46	to 57
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Several loop regions in the Ipk2 structure are disordered, and we have not included the corresponding residues in our current model. These loop regions comprise residues 1-26, 46-57 (between α1 and α2), and 76-110 (between β2 and β3) in the N-terminal domain and 287-316 in the C-terminal domain.
Cross-references: PDB:2IF8
PDB:2IEW
Protein: DP03689 (UniProt P07250)
Region: residues 1	to 24
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Several loop regions in the Ipk2 structure are disordered, and we have not included the corresponding residues in our current model. These loop regions comprise residues 1-26, 46-57 (between α1 and α2), and 76-110 (between β2 and β3) in the N-terminal domain and 287-316 in the C-terminal domain.
However, the first 26 residues are disordered in both Ipk2 structures, and we did not observe a similar order-disorder transition between the apoenzyme and the ADP-bound form.
Residues 1-24 are disordered in all structures.
Cross-references: PDB:2IF8
PDB:2IEW
Protein: DP03689 (UniProt P07250)
Region: residues 287	to 303
Annotation: protein stabilization (Biological process)
Evidence: deletion mutation phenotypic evidence used in manual assertion
Supporting statements:
We show here that Mcm1p and Arg80p chaperoning by Arg82p does not involve the inositol polyphosphate kinase activity of Arg82p, but requires its polyaspartate domain. Our results indicate that Arg82p is a bifunctional protein whose inositol kinase activity plays a role in multiple signalling cascades, and whose acidic domain protects two MADS-box proteins against degradation.
In this study we also show that the control of NCR and PHO genes require the kinase domains of Arg82p and Kcs1p, but not the polyaspartate stretch in Arg82p involved in Mcm1p stabilization.
A mutation in Arg82p (D131A) abolishing its IP kinase activity had no effect on the expression of MFα1 (lane 6), whereas the deletion of the polyaspartate residues (lane 5) impaired its expression.
The polyaspartate domain of Arg82p was shown to be crucial for its role in the arginine regulation (Qiu et al., 1990; Dubois et al., 2000) indicating that this region could be important for the interaction between Arg82p and the MADS-box proteins Mcm1p and Arg80p. To address this point, two-hybrid assays were used to examine the interaction between Arg80p or Mcm1p and arg82p mutated proteins (arg82D131A, arg82Δ282-303). Deletion of the polyaspartate domain and not mutation impairing the IP kinase activity caused a significant decrease in the interaction with Mcm1p or Arg80p (Table 2).
The stability of Mcm1p and Arg80p was impaired in the arg82Δasp strain to the same extent as in a arg82Δ strain.
One function requires the presence of the polyaspartate domain, essential for Mcm1p and Arg80p stabilization, suggesting a role of chaperone for Arg82p, and the other function which is to produce inositol polyphosphates, is independent of the polyaspartate domain.
Protein: DP03690 (UniProt P30518)
Region: residues 343	to 371
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
far-UV circular dichroism (CD) spectra (colored lines) present a minimum around 200 nm (black dashed line) and a shoulder at 220 nm (black dashed and dotted line) characteristic of disordered proteins with transient secondary structure content
In addition, far UV CD spectra showed a minimum around 198 nm, characteristic of unfolded proteins [58] (Figure 2b), and a negative shoulder around 222 nm, suggesting the presence of residual secondary structures [59] (Figure 2b).
Protein: DP03690 (UniProt P30518)
Region: residues 343	to 371
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
15N-HSQC spectra display a low proton spectral dispersion (~1 ppm) typical of IDPs.
Additionally, 15N-HSQC spectra of the three C-terminal regions showed a reduced amide proton spectral dispersion (around 1 ppm) typical of a disordered protein (Figure 2c) [18,19].
Protein: DP03690 (UniProt P30518)
Region: residues 343	to 371
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The Kratky plots extracted from SAXS data were typical of disordered regions with no clear maximum and a monotonic increase along the momentum transfer range.
Protein: DP03691 (UniProt Q92847)
Region: residues 339	to 366
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In addition, far UV CD spectra showed a minimum around 198 nm, characteristic of unfolded proteins [58] (Figure 2b), and a negative shoulder around 222 nm, suggesting the presence of residual secondary structures [59] (Figure 2b).
far-UV circular dichroism (CD) spectra (colored lines) present a minimum around 200 nm (black dashed line) and a shoulder at 220 nm (black dashed and dotted line) characteristic of disordered proteins with transient secondary structure content
Protein: DP03691 (UniProt Q92847)
Region: residues 339	to 366
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Additionally, 15N-HSQC spectra of the three C-terminal regions showed a reduced amide proton spectral dispersion (around 1 ppm) typical of a disordered protein.
15N-HSQC spectra display a low proton spectral dispersion (~1 ppm) typical of IDPs. HSQCs were recorded on 300 µM samples at 700 MHz and 20 °C, in 50 mM Bis-Tris pH 6.7, 150 mM NaCl buffer.
Protein: DP03691 (UniProt Q92847)
Region: residues 339	to 366
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The Kratky plots extracted from SAXS data were typical of disordered regions with no clear maximum and a monotonic increase along the momentum transfer range.
Protein: DP03692 (UniProt P07550)
Region: residues 342	to 413
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In addition, far UV CD spectra showed a minimum around 198 nm, characteristic of unfolded proteins, and a negative shoulder around 222 nm, suggesting the presence of residual secondary structures.
far-UV circular dichroism (CD) spectra (colored lines) present a minimum around 200 nm (black dashed line) and a shoulder at 220 nm (black dashed and dotted line) characteristic of disordered proteins with transient secondary structure content
Protein: DP03692 (UniProt P07550)
Region: residues 342	to 413
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Additionally, 15N-HSQC spectra of the three C-terminal regions showed a reduced amide proton spectral dispersion (around 1 ppm) typical of a disordered protein.
15N-HSQC spectra display a low proton spectral dispersion (~1 ppm) typical of IDPs. HSQCs were recorded on 300 µM samples at 700 MHz and 20 °C, in 50 mM Bis-Tris pH 6.7, 150 mM NaCl buffer.
Protein: DP03692 (UniProt P07550)
Region: residues 342	to 413
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The Kratky plots extracted from SAXS data were typical of disordered regions with no clear maximum and a monotonic increase along the momentum transfer range.
Protein: DP03693 (UniProt P01732)
Region: residues 128	to 182
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
A 1H, 15N HSQC experiment performed on 15N-labeled CD8α H was acquired to detect the amide groups. The resulting spectrum lacked chemical shift dispersion, with clustering of CD8α signals in the center of the spectrum (Fig. 2D, with ubiquitin for comparison on the right [56]. This phenomenon reflects lack of secondary structure, as we observed previously for other intrinsically disordered proteins [53], [54] and is consistent with the AF2 prediction (Fig. 1E).
Protein: DP03693 (UniProt P01732)
Region: residues 128	to 182
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Similarly, CD spectroscopy, which informs on secondary structure, indicated intrinsic disorder both with and without DTT, with negative ellipticity observed near 200 nm and low ellipticity at 190 and 222 nm (Fig. 3E), similar to the intrinsically disordered proteins Pup and SocB [53], [54].
Protein: DP03694 (UniProt Q8IY63)
Region: residues 178	to 384
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The far ultra-violet (UV) circular dichroism (CD) spectrum of A123 (Figure 1b) shows a strong signal at 204 nm, suggestive of random coil-like structure, and a relatively weak signal at 222 nm indicative of nascent helical structure.
Protein: DP03694 (UniProt Q8IY63)
Region: residues 178	to 384
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H-15N heteronuclear single quantum coherence (HSQC) spectrum of A123 shows poor dispersion in the NH-region, as expected for a protein with random coil-like and/or helical structure (Figure 2a).
Protein: DP03694 (UniProt Q8IY63)
Region: residues 186	to 204
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
A123 residues involved in binding YWWTD were mapped by NMR titration experiments in which unlabeled YWWTD and isotopically labeled A123 were mixed at molar ratios in the range of 0.25:1–2:1 (YWWTD:A123). As a reporter of the binding interactions, we monitored changes in the intensities of peaks corresponding to the tyrosine residues, Y191, Y313, and Y370, at the 3 PPxY sites.
At the 0.75:1 molar ratio (Figure 3b, upper panel), missing cross-peaks map to residues in the sequence vicinity of P1 (186–204), H2 (261, 265, 268 and 273), P2 (305–317), P3 (365–371), and the linker segment between P2 and P3 (322, 335, 340, 342).
Protein: DP03694 (UniProt Q8IY63)
Region: residues 305	to 317
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
A123 residues involved in binding YWWTD were mapped by NMR titration experiments in which unlabeled YWWTD and isotopically labeled A123 were mixed at molar ratios in the range of 0.25:1–2:1 (YWWTD:A123). As a reporter of the binding interactions, we monitored changes in the intensities of peaks corresponding to the tyrosine residues, Y191, Y313, and Y370, at the 3 PPxY sites.
At the 0.75:1 molar ratio (Figure 3b, upper panel), missing cross-peaks map to residues in the sequence vicinity of P1 (186–204), H2 (261, 265, 268 and 273), P2 (305–317), P3 (365–371), and the linker segment between P2 and P3 (322, 335, 340, 342).
Protein: DP03694 (UniProt Q8IY63)
Region: residues 365	to 371
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
A123 residues involved in binding YWWTD were mapped by NMR titration experiments in which unlabeled YWWTD and isotopically labeled A123 were mixed at molar ratios in the range of 0.25:1–2:1 (YWWTD:A123). As a reporter of the binding interactions, we monitored changes in the intensities of peaks corresponding to the tyrosine residues, Y191, Y313, and Y370, at the 3 PPxY sites.
At the 0.75:1 molar ratio (Figure 3b, upper panel), missing cross-peaks map to residues in the sequence vicinity of P1 (186–204), H2 (261, 265, 268 and 273), P2 (305–317), P3 (365–371), and the linker segment between P2 and P3 (322, 335, 340, 342).
Protein: DP03694 (UniProt Q8IY63)
Region: residues 261	to 273
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
A123 residues involved in binding YWWTD were mapped by NMR titration experiments in which unlabeled YWWTD and isotopically labeled A123 were mixed at molar ratios in the range of 0.25:1–2:1 (YWWTD:A123). As a reporter of the binding interactions, we monitored changes in the intensities of peaks corresponding to the tyrosine residues, Y191, Y313, and Y370, at the 3 PPxY sites.
At the 0.75:1 molar ratio (Figure 3b, upper panel), missing cross-peaks map to residues in the sequence vicinity of P1 (186–204), H2 (261, 265, 268 and 273), P2 (305–317), P3 (365–371), and the linker segment between P2 and P3 (322, 335, 340, 342).
Protein: DP03694 (UniProt Q8IY63)
Region: residues 178	to 384
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
Binding of the two proteins is enthalpically driven, occurs with a binding stoichiometry (N) close to 1:1 and has an effective dissociation constant (Kd) of 0.26 ± 0.01 μM. Because there are two putative binding sites on the YWWTD polypeptide (2 WW domains) and three putative binding sites on the A123 polypeptide (3 PPxY motifs), binding of a single WW-PPxY site or of both WW sites to two PPxY sites will result in a binding stoichiometry of 1:1.
Protein: DP03695 (UniProt P70365)
Region: residues 368	to 385
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The lack of electron density, as shown in the PDB, indicates this region is disordered.
Cross-references: PDB:1OJ5
Protein: DP03695 (UniProt P70365)
Region: residues 371	to 385
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Solution state NMR revealed that the C-terminal residues from Leu371 show very sharp 15N as well as 1H lines indicative of a highly flexible C-terminal part (data not shown).
Protein: DP03695 (UniProt P70365)
Region: residues 367	to 385
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
All RDC values throughout the entire protein, apart from the additional C-terminal tail, which is missing in the crystal structure, are in good agreement with the crystal structure as reflected by the Q factor value (Q = 0.20) and by the Pearson’s correlation coefficient (R = 0.96) (Fig. 4C).
Cross-references: PDB:5NWX
Protein: DP03695 (UniProt P70365)
Region: residues 368	to 385
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
In the complex the PAS-B domain adopts a well-defined globular fold (rmsdBackboneAtoms 260–367 = 0.485 Å) (Fig. 6A) ranging from Glu260 to Glu367 and a dynamically disordered tail at the C-terminus as confirmed by 15N-1H heteronuclear NOE values (SI Fig. 4).
Protein: DP03697 (UniProt Q07820)
Region: residues 192	to 201
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The lack of electron density in this region, as shown in the PDB, indicates it is disordered.
Cross-references: PDB:5W89
Protein: DP03697 (UniProt Q07820)
Region: residues 192	to 201
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The lack of electron density in this region, as shown in the PDB, indicates it is disordered.
Cross-references: PDB:5FC4
Protein: DP03697 (UniProt Q07820)
Region: residues 193	to 203
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The final ensemble (Fig. 4C) of structures with the lowest energies and the fewest violations had a mean root mean square deviation from the average of 0.38 Å for backbone atoms, excluding the residues at the termini (residues 167–172 and 320–326 in cMCL-1; residues 76–78 and 100–106 in BID-BH3) and the ones in the disordered loop between helices α1 and α2 (cMCL-1 residues 193–203).
Cross-references: PDB:2KBW
Protein: DP03698 (UniProt Q8IEU1)
Region: residues 130	to 148
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with high relative B-factor values used in manual assertion
Supporting statements:
Residues from 130 –148 form a random coil (C1) at the N terminus, and this is followed by an alpha-helix (H1, residues 149 –169).
Cross-references: PDB:2VWA
Protein: DP03698 (UniProt Q8IEU1)
Region: residues 83	to 129
Annotation: disorder (Structural state)
Evidence: in vitro cleavage assay evidence used in manual assertion
Supporting statements:
Analysis of the PfUIS3 dimer-monomer transition using gel filtration chromatography and SDS-PAGE suggested that dimeric PfUIS3 underwent proteolysis and reduced to a stable, soluble domain spanning residues 130 –229 (Fig. 1a).
Cross-references: PDB:2VWA
Protein: DP03698 (UniProt Q8IEU1)
Region: residues 83	to 129
Annotation: self-assembly (Disorder function)
Evidence: in vitro cleavage assay evidence used in manual assertion
Supporting statements:
Analysis of the PfUIS3 dimer-monomer transition using gel filtration chromatography and SDS-PAGE suggested that dimeric PfUIS3 underwent proteolysis and reduced to a stable, soluble domain spanning residues 130 –229 (Fig. 1a). This suggests that residues within residues 83–129 of PfUIS3
are likely to be involved in dimerization of PfUIS3.
Cross-references: PDB:2VWA
Protein: DP03698 (UniProt Q8IEU1)
Region: residues 83	to 129
Annotation: self-assembly (Disorder function)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
Purified PfUIS3 (residues 83–229) was dimeric in solution
as shown by protein cross-linking experiments and gel filtration
chromatography (Fig. 1).
Cross-references: PDB:2VWA
Protein: DP03700 (UniProt Q9H9R9)
Region: residues 1	to 158
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In agreement with a predicted low overall secondary structure content, the [1H,15N]-HSQC spectrum of human DBNDD1 shows limited signal dispersion in the 1HN dimension (Fig. 2).
An overall intrinsic disorder of DBNDD1 is supported by the application of secondary chemical shifts and the sequence specific SSP method.
Cross-references: BMRB:51301
Protein: DP03701 (UniProt Q9HBA0)
Region: residues 2	to 148
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In line with a low overall secondary structure content, the [1H, 15N]-TROSY-HSQC spectra of 13C, 15N-labeled human and chicken TRPV4-IDR (Fig. 2 A, B) show a narrow chemical shift dispersion.
The finding that both human and chicken TRPV4-IDR are highly disordered is further supported by the single residue-specific secondary structure propensities (SSP) calculated from the Cα, Cβ and Hα chemical shifts.
Cross-references: BMRB:51147
Protein: DP03701 (UniProt Q9HBA0)
Region: residues 2	to 68
Annotation: self-inhibition (Disorder function)
Evidence: experimental phenotypic evidence used in manual assertion
Supporting statements:
 In contrast, hsTRPV4ΔN68 was hypersensitive to osmotic stimuli and its Ca2+ influx far exceeded that of the native channel, indicating that the IDR N-terminus acts as a dominant autoinhibitory element.
Protein: DP03701 (UniProt Q9HBA0)
Region: residues 1	to 134
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
With increasing length of the N-terminus, the degree of unstructured contributions increases, indicating that the regions preceding the ARD are largely unstructured. The comparison with the respective N-terminal constructs from chicken and human TRPV4 confirms that this architecture is observed across species (Fig. 1, S1).
Protein: DP03702 (UniProt A0A1D5PXA5)
Region: residues 2	to 134
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In line with a low overall secondary structure content, the [1H, 15N]-TROSY-HSQC spectra of 13C, 15N-labeled human and chicken TRPV4-IDR (Fig. 2 A, B) show a narrow chemical shift dispersion.
The finding that both human and chicken TRPV4-IDR are highly disordered is further supported by the single residue-specific secondary structure propensities (SSP) calculated from the Cα, Cβ and Hα chemical shifts.
Cross-references: BMRB:51172
Protein: DP03702 (UniProt A0A1D5PXA5)
Region: residues 2	to 134
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Analytical size-exclusion chromatography (SEC) and SEC-MALS (SEC multi-angle light scattering) showed that these constructs are monomeric, while circular dichroism (CD) spectroscopy and the narrow chemical shift dispersion of the [1H, 15N]-TROSY-HSQC NMR spectra of the 15N-labeled TRPV4 IDR in isolation or in the context of the NTD confirmed its high amount of disorder5 (Fig. 1c–e; Supplementary Fig. 2).