LiteFold/DisProt huggingface dataset:
Protein: DP01193 (UniProt Q9H211)
Region: residues 356	to 410
Annotation: flexible linker (Disorder function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
We used Dynamic Light Scattering (DLS) to estimate the radius of hydration (R(h)) as well as polydispersity of Cdt1 in solution. Ovalbumin showed similar R(h) values in our system as with published results (60). For Cdt1, DLS demonstrated the protein was 99% monomeric, had a calculated R(h) of 3.7 nm, and was 40% polydisperse (Figure 3A). This relatively high level of polydispersity is consistent with a mixed-folded protein with many different conformations and also is consistent with thermally instability at relatively low temperatures (61).
We used both circular dichroism (CD) and intrinsic fluorescence (Ex280, Em330/350) to measure the changes in secondary and tertiary elements, respectively. Our thermal stability data for ovalbumin (Figure 2B & 2C) was similar to previously published data (48) given the difference in buffers (Table 1 & 2). For both DSF and DSCD, Cdt1 followed a simple two-state unfolding process. In fluorescence detection, we observed a melting temperature (Tm) of 43 °C (Figure 2B). In CD, we calculated a Tm of 42 °C (Figure 2C).
We also performed 1H/15N HSQC NMR to validate our CD results. The number of peaks, their broadness and their location similarly demonstrate a high disorder content (56). This data confirms all but the WH domains are disordered in human Cdt1.
Using our experimental secondary structure content analysis, we defined the N-terminal and linker regions as entirely flexible.
The authors define the WH domains as those spanning the residues 159-356 and 410-546.
Protein: DP01201 (UniProt Q47184)
Region: residues 1	to 30
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
If the unsolved regions in the EspA–CesA complex structure are disordered, the a-helical content of EspA should be 37.5%. This value is highly consistent with the a-helical content estimated here from far-UV CD spectra of EspA at pH 7.0 (39.6%). It is generally considered that the native-like secondary structures are present in the partially folded state of a protein.
Protein: DP01201 (UniProt Q47184)
Region: residues 1	to 30
Annotation: order to disorder (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
EspA is shown to spontaneously associate into oligomeric structures at neutral pH. However, two distinctive partially unfolded species occur at lower pH. Based on these results, a phase diagram, illustrating potential EspA conformational transitions, was constructed.
Protein: DP01201 (UniProt Q47184)
Region: residues 1	to 30
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The experimental electron density map only showed clear density for the N-terminal region (Asp31–Leu59) and the C-terminal region (Leu148–Leu190) of EspA.
Cross-references: PDB:1XOU
Protein: DP01201 (UniProt Q47184)
Region: residues 1	to 30
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
CesA is the recently proposed chaperone of EspA,
and we demonstrate that CesA traps EspA in a monomeric state and inhibits its polymerization. Crystallographic analysis of the
heterodimeric CesA–EspA complex at a resolution of 2.8 Å reveals that EspA contains two long -helices, which are involved in
extensive coiled-coil interactions with CesA.
Protein: DP01201 (UniProt Q47184)
Region: residues 60	to 147
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
If the unsolved regions in the EspA–CesA complex structure are disordered, the a-helical content of EspA should be 37.5%. This value is highly consistent with the a-helical content estimated here from far-UV CD spectra of EspA at pH 7.0 (39.6%). It is generally considered that the native-like secondary structures are present in the partially folded state of a protein.
Protein: DP01201 (UniProt Q47184)
Region: residues 60	to 147
Annotation: order to disorder (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
EspA is shown to spontaneously associate into oligomeric structures at neutral pH. However, two distinctive partially unfolded species occur at lower pH. Based on these results, a phase diagram, illustrating potential EspA conformational transitions, was constructed.
Protein: DP01201 (UniProt Q47184)
Region: residues 60	to 147
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The experimental electron density map only showed clear density for the N-terminal region (Asp31–Leu59) and the C-terminal region (Leu148–Leu190) of EspA.
Cross-references: PDB:1XOU
Protein: DP01202 (UniProt O55000)
Region: residues 309	to 433
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
A 2D [1H,15N] heteronuclear single
quantum coherence (HSQC) spectrum showed that PNUTS, like most PP1 regulatory proteins, is an
IDP, based on the significantly limited chemical-shift dispersion
Protein: DP01202 (UniProt O55000)
Region: residues 309	to 433
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Isothermal titration
calorimetry of PNUTS394–433 and PP1α7–330,
confirming that the intrinsically unstructured PNUTS
PP1 binding domain is functional and interacts
strongly with PP1.
Cross-references: PDB:4MOY
Protein: DP01202 (UniProt O55000)
Region: residues 309	to 433
Annotation: disorder (Structural state)
Evidence: temperature-induced protein unfolding evidence used in manual assertion
Supporting statements:
PNUTS’s high temperature stability (80 °C).
Protein: DP01203 (UniProt O75807)
Region: residues 513	to 631
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Our studies showed that GADD34513-631 is heat stable (80°C, 15 min; Fig. S1) and that its 2D [1H,15N] HSQC spectrum lacked chemical shift dispersion in the 1HN dimension, confirming that the GADD34 PP1-binding domain is an intrinsically disordered protein (IDP).
Protein: DP01203 (UniProt O75807)
Region: residues 513	to 631
Annotation: disorder (Structural state)
Evidence: temperature-induced protein unfolding evidence used in manual assertion
Supporting statements:
GADD34 (513–631) is heat stable.
Protein: DP01203 (UniProt O75807)
Region: residues 1	to 674
Annotation: disorder (Structural state)
Evidence: in vitro cleavage assay evidence used in manual assertion
Supporting statements:
As expected for natively unstructured proteins41, R15A and R15B were sensitive to a limited trypsin proteolysis (Fig. 4c).
Protein: DP01203 (UniProt O75807)
Region: residues 554	to 674
Annotation: protein phosphatase 1 binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
PP1 was found to interact with the R15A derivatives that encompassed residues 554–674, which contains the RVxF motif (figure 1a; electronic supplementary material, figure S2).
Protein: DP01203 (UniProt O75807)
Region: residues 325	to 554
Annotation: eukaryotic initiation factor eIF2 binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
 eIF2α was enriched in the R15A325–554 and R15A325–674 pulldowns as well as in the pulldown of the full-length R15A1–674, albeit to a lesser extent (figure 1a; electronic supplementary material, figure S2). We found no enrichment of eIF2α upon immunoprecipitation of R15A1–325 or R15A554–674 (figure 1a; electronic supplementary material, figure S2). This reveals that R15A325–554 encodes the substrate recruitment region.
Protein: DP01203 (UniProt O75807)
Region: residues 1	to 674
Annotation: protein phosphatase type 1 complex (Cellular component)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
 eIF2α was enriched in the R15A325–554 and R15A325–674 pulldowns as well as in the pulldown of the full-length R15A1–674, albeit to a lesser extent (figure 1a; electronic supplementary material, figure S2). We found no enrichment of eIF2α upon immunoprecipitation of R15A1–325 or R15A554–674 (figure 1a; electronic supplementary material, figure S2). This reveals that R15A325–554 encodes the substrate recruitment region.
PP1 was found to interact with the R15A derivatives that encompassed residues 554–674, which contains the RVxF motif (figure 1a; electronic supplementary material, figure S2).
Protein: DP01203 (UniProt O75807)
Region: residues 355	to 674
Annotation: protein phosphatase regulator activity (Molecular function)
Evidence: quantitative western immunoblotting evidence used in manual assertion
Supporting statements:
Overexpression of full-length R15A1–674 led to a robust decrease in the levels of phosphorylated eIF2α (figure 3a). Overexpression of R15A325–674 also led to nearly complete dephosphorylation of eIF2α (figure 3a).
The amino-terminal regions of R15s, which do not bind the substrate nor PP1, as well as R15A325–554 and R15B340–639, which bind the substrate but not PP1, did not decrease phosphorylation of eIF2α (figure 3a,b).
Protein: DP01205 (UniProt P02263)
Region: residues 1	to 13
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Histone N-terminal tail regions extend to Lys15 on the H2As, Ser36 on the H2Bs, Tyr41 on the H3s and Arg23 on the H4s. The C-terminal tails of the H2As extend from Pro117. Most of the amino-acid residues in the tails in our structure are disordered.
Cross-references: PDB:1HQ3
Protein: DP01205 (UniProt P02263)
Region: residues 120	to 129
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Histone N-terminal tail regions extend to Lys15 on the H2As, Ser36 on the H2Bs, Tyr41 on the H3s and Arg23 on the H4s. The C-terminal tails of the H2As extend from Pro117. Most of the amino-acid residues in the tails in our structure are disordered.
Cross-references: PDB:1HQ3
Protein: DP01206 (UniProt Q15797)
Region: residues 217	to 267
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The linker region (residues 217 to 267) is not visible due to structural disordering.
Protein: DP01224 (UniProt O43312)
Region: residues 739	to 753
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
We made a synthetic peptide corresponding to this WH2, comprising amino acids Asp 724 to the C-terminus (Ser 755) of human MIM. The structure of the WH2 of MIM can be conceptually subdivided into two parts, an N-terminal amphiphilic α-helix, comprising amino acids Gly 728 to Gly 738, and a C-terminal extended region from Val 739 to Arg 753.
Cross-references: PDB:2D1K
Protein: DP01224 (UniProt O43312)
Region: residues 739	to 753
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The crystal structure of this WH2 was determined as a ternary complex with actin-DNase I.
Protein: DP01236 (UniProt P55735)
Region: residues 305	to 316
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No electron density was
observed for the N-terminal 14 and C-terminal 12 residues, the residues 165 to 172 in Sec13,
and the N-terminal 6 residues of Nup145C. These residues are presumed to be disordered and
therefore have been omitted from the final model
Protein: DP01236 (UniProt P55735)
Region: residues 1	to 14
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No electron density was
observed for the N-terminal 14 and C-terminal 12 residues, the residues 165 to 172 in Sec13,
and the N-terminal 6 residues of Nup145C. These residues are presumed to be disordered and
therefore have been omitted from the final model
Protein: DP01239 (UniProt P20591)
Region: residues 438	to 447
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
A putative loop L2 (amino acids 438–447) opposite the deduced position of the G domain is not visible in our structure.
Cross-references: PDB:3LJB
Protein: DP01239 (UniProt P20591)
Region: residues 532	to 572
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The 40-amino-acid-long loop L4 (residues 532–572) is at the equivalent sequence position as the pleckstrin homology (PH) domain of dynamin (Fig. 1a and Supplementary Fig. 3) and is absent in our model.
Cross-references: PDB:3LJB
Protein: DP01240 (UniProt Q9UJX2)
Region: residues 1	to 25
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
However, the 
intrinsically disordered regions of some APC/C subunits were not visible in the EM map 
(defined in Extended Data Table 2).
Protein: DP01240 (UniProt Q9UJX2)
Region: residues 558	to 597
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
However, the 
intrinsically disordered regions of some APC/C subunits were not visible in the EM map 
(defined in Extended Data Table 2).
Protein: DP01241 (UniProt P19634)
Region: residues 680	to 815
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Secondary structure analysis by NMR spectroscopy revealed severaltransient helices (THs) in the intrinsically disordered NHE1cdt
Thesewere located at P694-R700 (TH1), P727-G743 (TH2), D758-S766 (TH3), andP786-L795 (TH4), where TH1 and TH4 were rather short and lowly populated.
Protein: DP01241 (UniProt P19634)
Region: residues 686	to 815
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
When presented as a Kratky plot, the SAXS profile of hNHE1 cdt increased throughout its range (Figure 2C), a pattern characteristic for unfolded proteins.
Protein: DP01241 (UniProt P19634)
Region: residues 686	to 815
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The secondary structure and overall fold analyses of hNHE1 cdt by far-UV CD spectroscopy showed a distinct minimum at ~200 nm and a shoulder at 220-230 nm, indicating the absence of regular secondary structures (Figure 2B).
Protein: DP01241 (UniProt P19634)
Region: residues 786	to 795
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The Δδircfor the phosphorylated state showed similar proﬁle as for the unphosphorylated state,but with increased helicity for TH4.
To assess whether the local sequence is responsible for the stabilizing eﬀect of phosphorylation and whether it is independent of the nearby T779 phosphorylation we next assigned the NMR chemical shifts of the TH4pepWTwith and without phosphorylation by natural abundance NMR spectroscopy.
Protein: DP01241 (UniProt P19634)
Region: residues 686	to 815
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Finally, the [1H, 15N]-HSQC NMR spectrum of hNHE1 cdt showed a significant lack of dispersion in the proton dimension (Figure 2D), demonstrating in unison with the other data that the regulatory distal domain of NHE1 is intrinsically disordered.
Protein: DP01241 (UniProt P19634)
Region: residues 786	to 795
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
While for all variants, including the WT peptide, the ellipticity at 190 nm increased uponphosphorylation, indicating less disorder, the negative ellipticity at 222 nm,indicating an increase in helicity, was only increased for the WT and theD784A variants. 
change at 222 nm clearly indicated R790 to be important for conferring the phosphorylation-induced helix stabilisation.
Protein: DP01241 (UniProt P19634)
Region: residues 680	to 815
Annotation: disorder to pre-molten globule (Structural transition)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
We found that the Rh of NHE1 reduced more severely by ~8 Å (25.6%) upon calcium addition (Figure 4C), again related to the position of the binding site at mid-sequence.
These data suggest that in some cases, the position of the Ca2+-binding site can affect the extension of the IDP by inducing a conformational shift, seen here for both NHE1 and ANAC046
Protein: DP01241 (UniProt P19634)
Region: residues 745	to 766
Annotation: calcium ion binding (Molecular function)
Evidence: small molecule detection assay evidence used in manual assertion
Supporting statements:
NHE1680-815 similarly bound calcium at a 1:1 ratio (Figure 1G,I), again with micromolar affinity (~130 μM; Figure 1H).
Protein: DP01241 (UniProt P19634)
Region: residues 745	to 766
Annotation: calcium ion binding (Molecular function)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
Subsequently, we used the C-terminal disordered tail of the sodium-proton exchanger 1 (NHE1680-815) to address the interaction between calcium and a protein with high negative charge at the center of the sequence, finding that this was indeed the region (S745–S766) with the highest CSPs (Figure 1C).
Protein: DP01243 (UniProt P25638)
Region: residues 92	to 111
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The last 20 C-terminal
residues of Tah1 (residues 92–111) are unstructured
Protein: DP01243 (UniProt P25638)
Region: residues 93	to 111
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 19-amino acid C-terminal region (positions 93–111)
located immediately downstream from helix C displays the
characteristic features of an unstructured region
Protein: DP01243 (UniProt P25638)
Region: residues 93	to 111
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Our NMR spectrum of the Tah1:Pih1(257–
344) complex strongly suggests that the C-terminal part of
Tah1 folds upon interaction with Pih1.
Protein: DP01243 (UniProt P25638)
Region: residues 93	to 111
Annotation: protein binding (Molecular function)
Evidence: yeast 2-hybrid evidence used in manual assertion
Supporting statements:
Therefore, in Y2H assays, the short unstructured C-terminal region of Tah1 was sufficient to bind Pih1 and the strength of the interaction was similar to that for full-length Tah1.
Protein: DP01244 (UniProt O76074)
Region: residues 128	to 145
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Most residues in the structures have a good electron density and are traced without ambiguity, except for disordered residues 128–145, 395–406, and 436–445 in subunit A and residues 131–146, 209–217, 395–408, and 435–446 in subunit B in both structures. In addition, residues 89–100 in the PDE5A89 structure are disordered.
Cross-references: PDB:3LFV
Protein: DP01244 (UniProt O76074)
Region: residues 395	to 406
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Most residues in the structures have a good electron density and are traced without ambiguity, except for disordered residues 128–145, 395–406, and 436–445 in subunit A and residues 131–146, 209–217, 395–408, and 435–446 in subunit B in both structures. In addition, residues 89–100 in the PDE5A89 structure are disordered.
Cross-references: PDB:3LFV
Protein: DP01244 (UniProt O76074)
Region: residues 840	to 850
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 840–850 of the M-loop have not been modeled due to disorder and are indicated by a dotted line
Protein: DP01245 (UniProt P12823)
Region: residues 1	to 20
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The NMR structure of DENV-2 C protein (PDB ID: 1R6R) reveals a homodimer that contains a well-folded core domain (residues 21–100) and a conformationally labile N-terminal region (residues 1–20), which is absent from the reported coordinates.
Cross-references: PDB:1R6R
Protein: DP01245 (UniProt P12823)
Region: residues 1	to 20
Annotation: entropic chain (Disorder function)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The N-terminal tails of the DENV C protein are essential for efficient viral particle formation as well as for recognition of different ligands during the life cycle of the virus
Protein: DP01245 (UniProt P12823)
Region: residues 1	to 21
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The secondary structure of DEN2C is composed of four alpha helices. The most N-terminal helix (helix I, amino acids 26 to 31) is followed by a 14-residue loop and a second helix (helix II, amino acids 45 to 55). Helix II contains the start of an internal hydrophobic region that has been previously implicated in membrane association (underlined residues of DEN2C sequence in Fig. ​Fig.4B).4B). Following helix II is a loop region (amino acids 56 to 62) that is followed by helix III (amino acids 63 to 69) and then a fourth short loop region (amino acids 70 to 73). The longest helix in DEN2C (helix IV) occurs at the C terminus of the protein (amino acids 74 to 96). The N terminus of DEN2C (amino acids 1 to 21) does not appear to possess secondary structure.
Cross-references: PDB:1R6R