LiteFold/DisProt huggingface dataset:
Protein: DP03702 (UniProt A0A1D5PXA5)
Region: residues 2	to 134
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy 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).  Chemical shift based secondary structure predictions showed that the TRPV4 IDR contains no appreciable secondary structure5.
Cross-references: BMRB:51172
Protein: DP03702 (UniProt A0A1D5PXA5)
Region: residues 2	to 134
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
Small angle X-ray scattering (SAXS) probes the molecular shape of a molecule in solution. An IDR-containing protein is best described as a structural ensemble, rather than as a single structure, which can be analyzed by SEC-coupled small-angle X-ray scattering (SEC-SAXS) and subsequent Ensemble Optimization Method (EOM) analysis37,38. The isolated TRPV4 IDR is highly flexible and fluctuates between numerous conformations that, as a population, produce a skewed real-space scattering pair-distance distribution function, or p(r) profile that extends to ~12.5–15 nm (Fig. 1f, Supplementary Fig. 3).
Protein: DP03702 (UniProt A0A1D5PXA5)
Region: residues 2	to 134
Annotation: disorder (Structural state)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
For the IDR, rapid high HDX was apparent in the resolved parts (residues 3–24, 29–55, and 72–105) substantiating its unstructured character.
Protein: DP03702 (UniProt A0A1D5PXA5)
Region: residues 2	to 134
Annotation: lipid binding (Molecular function)
Evidence: co-sedimentation assay evidence used in manual assertion
Supporting statements:
Indeed, neither the isolated ARD, nor NTDΔN120, also containing the proline-rich region, interacted with POPC/POPG liposomes in a sedimentation assay (Fig. 7a, b, Supplementary Fig. 10a, b). In contrast, ~75% of the native NTD was found bound to liposomes.
Protein: DP03702 (UniProt A0A1D5PXA5)
Region: residues 2	to 134
Annotation: lipid binding (Molecular function)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
NMR chemical shift perturbation assays allowed identification of the lipid-interacting IDR residues (Fig. 7c–e, see Supplementary Fig. 11 for 13C, 15N-labeled IDRAAWAA backbone assignments). In the native IDR, ~75% of all residues showed line-broadening in the presence of POPG-containing liposomes.
Protein: DP03702 (UniProt A0A1D5PXA5)
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 121	to 134
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Neither the isolated PRR (residues 121–134) nor the PRR with the PBD (PBD-PRR, residues 105–134) contain α-helices or β-sheets (Fig. S2).
Protein: DP03702 (UniProt A0A1D5PXA5)
Region: residues 105	to 134
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Neither the isolated PRR (residues 121–134) nor the PRR with the PBD (PBD-PRR, residues 105–134) contain α-helices or β-sheets (Fig. S2).
Protein: DP03702 (UniProt A0A1D5PXA5)
Region: residues 105	to 134
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The absence of α-helices or β-sheets in the TRPV4-PBD-PRR region is also supported by the secondary structure analysis based on the PBD-PRR NMR backbone assignment. Here, the chemical shift-based prediction of the torsion angles indicates that a polyproline helix contribution may be present (Fig. S3).
As expected for an unstructured peptide, the PBD-PRR peptide shows overall high flexibility in the absence of the PACSIN3 SH3 domain, with very high mobility in the C-terminus.
Protein: DP03702 (UniProt A0A1D5PXA5)
Region: residues 121	to 134
Annotation: SH3 domain binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
To obtain a high-resolution view of the interaction of TRPV4 with a desensitizing protein, we determined the solution NMR structure of the chicken PACSIN3 SH3 domain in complex with the TRPV4-PRR (Fig. 3A, S4, Table 1).
Using 15N-labeled PACSIN1 and 2 SH3 domains as reporters, we performed chemical shift perturbation experiments to map the TRPV4-PRR interacting residues. All three PACSIN SH3 domains share the same binding interface with the TRPV4-PRR. 
Cross-references: PDB:6F55
Protein: DP03702 (UniProt A0A1D5PXA5)
Region: residues 105	to 134
Annotation: SH3 domain binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Upon binding of PACSIN3 SH3, the entire peptide becomes less flexible. In agreement with the complex structure, the effects are most pronounced in the PRR, particularly for K122, G123, A125 and N127. 
As expected, PACSIN3 SH3 domain binding to the 15N-TRPV4-PBD-PRR induces chemical shift changes for residues in the PRR, particularly K122, G123, A125 and N127 (Fig. 4A, red line). Chemical shift perturbations are also observed for residues in the linker between the PBD and PRR (e.g. V120 and R112) and even within the PBD (e.g. W109).
Protein: DP03702 (UniProt A0A1D5PXA5)
Region: residues 107	to 111
Annotation: phosphatidylinositol binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In contrast to the effects of the PACSIN3 SH3 domain, when PIP2 is added, it exclusively affects residues in and around the previously identified PIP2 binding domain (107KRWRR111) in the PBD-PRR (Garcia-Elias et al., 2013), as indicated by strong shifts and peak broadening of the corresponding NMR resonances (Fig. 4A, yellow line).
PI(4,5)P2 gives rise to three peaks in the 31P spectrum corresponding to the three phosphate groups at the 1, 4, and 5 positions of the lipid headgroup (Fig. 4E-G). PIP2 was titrated with PBDKRWRR-PRR or the mutant PBDAAWAA-PRR. While the PBDKRWRR-PRR peptide interacts with PIP2 with a KD in the μM range (139.8±1.9 μM), the PBDAAWAA-PRR affinity is more than one order of magnitude lower (2.7±0.1 mM) (Fig. 4D).
Protein: DP03703 (UniProt Q8N660)
Region: residues 174	to 247
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We confirmed the disordered nature of CON1 due to the limited peak dispersion shown in the 15N-1H HSQC (Figs. 2a and 3a). The CON1 sequence has low complexity and comprises many stretches of repeated residues or repeated sequences of amino acids. Due to this there is poor dispersion and many overlapping peaks.
The Secondary Structure Propensity score (SSP) (Marsh et al. 2006) gives an estimation of the secondary structure of a protein using available chemical shifts (a score of 1 indicates a fully formed α-helix, while a score of -1 indicates a fully formed β-sheet). IDPs often have scores between − 0.2 and 0.2 indicating no secondary structure elements are present. The SSP scores for CON1, calculated using HN, N, Cα, and Cβ atoms, both at 25 °C and 5 °C show most residues fall within this disordered range (Fig. 4a).
Cross-references: BMRB:51015
Protein: DP03703 (UniProt Q8N660)
Region: residues 338	to 552
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 15N-1H HSQC of the HSL1-3 triplet showed a peak dispersion characteristic of a disordered protein.
Protein: DP03703 (UniProt Q8N660)
Region: residues 338	to 412
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 15N-1H HSQC of the HSL1-3 triplet showed a peak dispersion characteristic of a disordered protein.
We divided the triplet into its three domains HLS1, 2 and 3, while keeping the adjacent linker sequences in all the constructs. Owing to the moderate dispersion of the resonances the assignments success was 90 ± 5% (Table 1) with HLS1 higher than HLS2 and 3.
Cross-references: BMRB:27569
Protein: DP03703 (UniProt Q8N660)
Region: residues 401	to 487
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 15N-1H HSQC of the HSL1-3 triplet showed a peak dispersion characteristic of a disordered protein.
We divided the triplet into its three domains HLS1, 2 and 3, while keeping the adjacent linker sequences in all the constructs. Owing to the moderate dispersion of the resonances the assignments success was 90 ± 5% (Table 1) with HLS1 higher than HLS2 and 3.
Cross-references: BMRB:27533
Protein: DP03703 (UniProt Q8N660)
Region: residues 478	to 552
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 15N-1H HSQC of the HSL1-3 triplet showed a peak dispersion characteristic of a disordered protein.
We divided the triplet into its three domains HLS1, 2 and 3, while keeping the adjacent linker sequences in all the constructs. Owing to the moderate dispersion of the resonances the assignments success was 90 ± 5% (Table 1) with HLS1 higher than HLS2 and 3.
Cross-references: BMRB:27775
Protein: DP03704 (UniProt A0A1B0GTR3)
Region: residues 1	to 108
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The signal dispersion in the 1HN dimension is reduced to the region between 8.1 and 8.6 ppm (Fig. ​(Fig.3).3). This limited 1HN chemical shift range is typically observed for proteins or protein parts without a well-defined three-dimensional structure. Therefore, the fast inter-conversion between different conformers or transient states results in ensemble-averaged random coil chemical shift values.
In agreement with the [1H,15N]-HSQC spectrum (Fig. ​(Fig.3),3), the CSI 3.0 web server (Hafsa et al. 2015) predicts an all-coil conformation for CX05A based on our chemical shift assignments (data not shown).
Cross-references: BMRB:50944
Protein: DP03705 (UniProt O05312)
Region: residues 1	to 75
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
During the purification, we noticed that Rv1211 eluted much faster (70 min) than expected by the molecular weight (7.9 kDa) from the size exclusion column.
In addition, Rv1211 eluted much later than the void volume (49 min), excluding it from being a non-specific aggregate. These results suggested that Rv1211 is either a multimer or a natively-unfolded protein. It is well known that a natively-unfolded protein behaves like a much larger protein during a size exclusion chromatography.
Protein: DP03705 (UniProt O05312)
Region: residues 1	to 75
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
To characterize the structure of Rv1211 experimentally, we next carried out circular dichroism (CD) spectroscopy which can give information on secondary structure. The spectrum was typical of an unfolded protein (Fig. 2A).
Protein: DP03705 (UniProt O05312)
Region: residues 1	to 75
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Therefore, we obtained the NMR spectrum of Rv1211 in the absence and presence of Ca2+. The data show that Rv1211's spectrum did not change appreciably according to the presence of Ca2+ (Fig. 3A). In addition, there were no peaks upfield of 0.5 ppm, which is the diagnostic character of natively unfolded proteins, consistent with our CD data. To further confirm the absence of spectral changes by Ca2+ with higher resolution, we obtained two-dimensional 1H–15N HSQC spectra in the presence and absence of Ca2+. The spectra were nearly identical, confirming the absence of Ca2+ binding (Fig. 3B). Again, the narrow chemical shift dispersion on the proton amide region showed that Rv1211 is a natively unfolded protein.
Protein: DP03705 (UniProt O05312)
Region: residues 61	to 74
Annotation: small molecule binding (Molecular function)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
Since we already expressed 15N labeled Rv1211, we employed a 1H–15N HSQC NMR assay to monitor the binding.
To identify the binding site between Rv1211 and TFP, we prepared 15N,13C-uniformly double-labeled protein and obtained triple resonance NMR spectra: HNCA, HN(CO)CA, HNCACB, CBCA(CO)NH, HN(CA)CO, and HNCO. The analysis of these three-dimensional spectra led to the assignment of the peak on the 2D 1H–15N HSQC spectrum. Therefore, the peaks that disappeared upon TFP binding (see Fig. 4A) were identified as originating from residues 61D, 63A, 65A, 67G, 68D, 70L, 72G, 73 V, and 74T. These residues are all in the C-terminal part of the protein (Fig. 4B), which is consistent with the binding as a natively unfolded protein.
Protein: DP03705 (UniProt O05312)
Region: residues 1	to 75
Annotation: small molecule binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
The binding affinity and stoichiometry were also studied using ITC (Fig. 4C). Notably, the binding was endothermic, giving the downward curve. The data analysis shows that the dissociation constant (Kd) is 41 μM, and the binding occurs with a molar ratio of 1 : 2 for Rv1211 and TFP.
Protein: DP03706 (UniProt Q13480)
Region: residues 613	to 694
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The far-UV CD spectrum of Gab1613–694 showed a characteristic spectrum of an IDP with a weak negative ellipticity between 210 and 240 nm and a minimum around 200 nm (Figure 2(A), left). This indicates that Gab1613–694 is disordered under these conditions.
Protein: DP03706 (UniProt Q13480)
Region: residues 613	to 694
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
To investigate the presumed disordered character of Gab613–694 at residue resolution, we measured 1H-15N HSQC spectra. The spectra of nonphosphorylated (Figure S3(A)) and phosphorylated Gab1613–694 (Figure S3(B)) show a low chemical-shift dispersion of the amide protons, which is also indicative of disorder.
Cross-references: BMRB:51019
Protein: DP03706 (UniProt Q13480)
Region: residues 613	to 694
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
To investigate the presumed disordered character of Gab613–694 at residue resolution, we measured 1H-15N HSQC spectra. The spectra of nonphosphorylated (Figure S3(A)) and phosphorylated Gab1613–694 (Figure S3(B)) show a low chemical-shift dispersion of the amide protons, which is also indicative of disorder.
Cross-references: BMRB:51018
Protein: DP03706 (UniProt Q13480)
Region: residues 613	to 694
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
The affinity between nonphosphorylated or double phosphorylated Gab1613–694 and SHP21–216 was investigated by ITC in absence of any crowders (Figure 5(A and B)). The phosphorylated protein shows a high affinity binding with a KDvalue of 4 ± 1 nM and a 1:1 stoichiometry (n = 0.90 ± 0.01), an enthalpic change of –169.3 ± 0.6 kJ/mol, and an entropy loss of –407 ± 34 J/(mol·K).
Protein: DP03706 (UniProt Q13480)
Region: residues 117	to 694
Annotation: disorder (Structural state)
Evidence: author statement used in manual assertion
Supporting statements:
The one common feature of LMD proteins is their structural composition. They have folded N-termini, consisting of a small domain module i.e. pleckstrin homology, PH (Gab1–4), phosphotyrosine-binding, PTB (FRS-2α and 2β) or Src homology 3, SH3 (p130Cas family) domains. A slight variation to this is seen with IRS-1, -2 and -4, and DOK1–7, which have two adjacent folded N-terminal domains (PH and PTB). Beyond the folded N-terminus, there is a long C-terminal extension ostensibly devoid of major structural elements, and hence LMD proteins represent lesser-studied examples of intrinsically disordered (or unstructured) proteins (IDPs or IUPs). 
Authors state that the pleckstrin homology (PH) domain, comprised by the 5-116 residues, is the only structured region in GRB2-associated-binding protein 1 (Gab1).
Protein: DP03707 (UniProt P17706-2)
Region: residues 303	to 387
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 2D [1H,15N] TROSY spectra of TCPTPCAT (TCPTP catalytic domain residues 1–302; Fig. 1a, b) is of high quality, which allowed the sequence-specific backbone assignment to be readily completed.
We then compared the 2D [1H,15N] TROSY spectra of TCPTPCAT and TCPTP (Fig. 1b; full-length TCPTP residues 1–387; Fig. 1a). The HN/N cross-peaks of TCPTPCAT overlap well with their corresponding peaks in the TCPTP spectrum, demonstrating that the conformation of TCPTPCAT is identical in both constructs. Further, the spectra showed additional peaks in the TCPTP spectrum that clustered in the center of the spectrum between 7.5 and 8.5 ppm (1H dimension). This is typical for flexible, mostly unstructured amino acids, demonstrating that the C-terminal tail of TCPTP is an intrinsically disordered region (IDR) and thus mirrors the behavior of the C-terminal tail of PTP1B.
Protein: DP03707 (UniProt P17706-2)
Region: residues 303	to 387
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
In contrast, the Rg value for TCPTP was 37.3 ± 0.1 Å, ~10 Å larger than that measured for TCPTPCAT and larger than that expected for a mostly globular protein of ~45 kDa. Thus, these SAXS data are in full agreement with the NMR data and confirm that the TCPTP C-terminal IDR region is extended and dynamic in solution (Supplementary Fig. 2a, b and Supplementary Table 1).
Protein: DP03707 (UniProt P17706-2)
Region: residues 303	to 387
Annotation: self-inhibition (Disorder function)
Evidence: enzymatic activity assay evidence used in manual assertion
Supporting statements:
For both substrate peptides, the rate of dephosphorylation by TCPTP was ~3-fold slower than that measured for TCPTPCAT (Fig. 2a and Supplementary Fig. 3a). Michaelis-Menten analysis revealed that the C-terminal tail of TCPTP affects both the kcat and KM (Table 1 and Supplementary Table 2). These data are consistent with an autoinhibitory function of the TCPTP C-terminal tail and suggest that the change in activity is not achieved by completely blocking the TCPTP active site, but instead via a yet unknown mechanism.
An in trans interaction of the IDR C-terminal tail of TCPTP leads to a dose-dependent inhibition of the TCPTP catalytic activity29.
Protein: DP03707 (UniProt P17706-2)
Region: residues 344	to 385
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
An in trans interaction of the IDR C-terminal tail of TCPTP leads to a dose-dependent inhibition of the TCPTP catalytic activity29. Thus, we tested if the TCPTPTail peptide interacts directly, in trans, with TCPTPCAT. The addition of increasing amounts of TCPTPCAT (1:0 to 1:20, TCPTPTAIL: TCPTPCAT) resulted in reduced intensities of multiple peaks, corresponding to residues 344–385, in the 2D [1H,15N] HSQC spectrum of TCPTPTail (Supplementary Fig. 4).
Protein: DP03707 (UniProt P17706-2)
Region: residues 344	to 385
Annotation: protein binding (Molecular function)
Evidence: cross-linking evidence used in manual assertion
Supporting statements:
Finally, the lysine residues in the C-terminal tail observed to be cross-linked most frequently to lysines in TCPTPCAT correspond to K358, K364 and K369, i.e., the same residues determined to bind TCPTPCAT using NMR spectroscopy (residues 344–385). Together, the cross-linking and NMR-based interaction studies show that TCPTP dynamic C-terminal IDR residues 344–385 interact directly with the TCPTPCAT domain.
As a final control, we repeated the cross-linking experiment between the autoinhibitory and catalytic domains in trans using the individual TCPTPCAT and TCPTPTail domains, i.e. in an experimental manner identical to that used for the NMR experiments. As expected, the results were fully consistent with both the NMR spectroscopy and the in cis cross-linking data. Namely, as observed for full-length TCPTP, TCPTPCAT residues K38, K107, and K118 were again cross-linked to multiple lysines in the TCPTPTail peptides, with the greatest number of cross-links observed for TCPTPTail residues K358, K364, and K369 (cross-links were also observed for K290 and K294, but this is likely due to the increased accessibility of these residues in the free IDP [TCPTPTail] versus the same residues within the context of the full-length protein) (Supplementary Fig. 5a, b and Supplementary Table 4).
Protein: DP03709 (UniProt O96018)
Region: residues 1	to 214
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Circular dichroism (CD) experiments were performed to measure the composition of the secondary structure of Mint3NT. Consequently, a negative peak at 200 nm, which is the hallmark of the random coil, was observed, and significant peaks that originate in secondary structures, especially α-helices and β-sheets, could not be observed (Fig. 1B). The result is suggesting that the isolated N-terminus of Mint3 is mostly composed of a random coil (10).
Protein: DP03709 (UniProt O96018)
Region: residues 1	to 214
Annotation: disorder (Structural state)
Evidence: differential scanning calorimetry evidence used in manual assertion
Supporting statements:
Following that, differential scanning calorimetry (DSC) was performed to analyze the protein folding of Mint3NT. No significant peak caused by the collapse of the higher-order structure was observed in the thermal denaturation experiment (Fig. S1).
Protein: DP03709 (UniProt O96018)
Region: residues 1	to 214
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We measured the 1H-15N HSQC spectrum of Mint3NT and found that the dispersion of resonance peaks was very poor particularly along the 1H-axis, suggesting the absence of strong hydrogen-bonding interactions (Fig. 1D). Furthermore, the superposition of two HSQC spectra separately recorded for the fragment proteins of Mint3NT (Mint3(1–117) and Mint3(101–214)), Figure 1E reproduced the spectrum of whole protein (Mint3NT) very well, suggesting the absence of significant interaction between the N- and C-terminal regions of Mint3NT.