LiteFold/DisProt huggingface dataset:
Protein: DP01443 (UniProt Q9UJX4)
Region: residues 170	to 205
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The regions are detailed in the Extended Data Table 2.
Cross-references: PDB:4UI9
Protein: DP01443 (UniProt Q9UJX4)
Region: residues 353	to 413
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Figure S5. Missing electron density, conformational flexibility.
Cross-references: PDB:5KHU
PDB:5KHR
Protein: DP01445 (UniProt P30260)
Region: residues 171	to 450
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The regions are detailed in the Extended Data Table 2
Cross-references: PDB:4UI9
PDB:5A31
PDB:5G05
PDB:5G04
Protein: DP01445 (UniProt P30260)
Region: residues 767	to 824
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The regions are detailed in the Extended Data Table 2
Cross-references: PDB:4UI9
PDB:5A31
PDB:5G05
PDB:5G04
Protein: DP01445 (UniProt P30260)
Region: residues 180	to 447
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
"Several  lines of evidence suggested that residues 182-453 are mobile and/or disordered, and not part of the signature TPR folded region of human APC3"
Cross-references: PDB:4RG6
PDB:4RG7
PDB:4RG9
Protein: DP01445 (UniProt P30260)
Region: residues 769	to 824
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
"...the subsequent residues 775-830 are not visible in the electron density and are presumably disordered"
Cross-references: PDB:4RG6
PDB:4RG7
PDB:4RG9
Protein: DP01446 (UniProt Q9Y239)
Region: residues 111	to 138
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Residues 111–138 of NOD1 are located in an unstructured carboxy-terminal extension where unfavourable dynamic properties resulted in a low signal to noise in the NMR spectra.
Cross-references: PDB:2B1W
Protein: DP01447 (UniProt P30281)
Region: residues 255	to 292
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The equivalent protein sequence of cyclin D3 (residues 255–C terminus) is not apparent in the electron density, presumably because of disorder.
Cross-references: PDB:3G33
Protein: DP01447 (UniProt P30281)
Region: residues 1	to 22
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
N-terminal region characterized by missing electron density in the crystal structure.
Cross-references: PDB:3G33
Protein: DP01447 (UniProt P30281)
Region: residues 281	to 285
Annotation: phosphorylation display site (Disorder function)
Evidence: in vitro protein kinase assay evidence used in manual assertion
Supporting statements:
We found that phosphorylation of His-cyclin D3 (wt) in vitro by GSK-3β reached a stoichiometry of approximately 0.6 mol phosphate per mol of His-cyclin D3 (wt) (data not shown), indicating that GSK-3β effectively phosphorylates cyclin D3 in vitro. To determine whether Thr-283 in cyclin D3 is phosphorylated by GSK-3β, a bacterially produced His-tagged cyclin D3 mutant containing an Ala for Thr-283 substitution [His-cyclin D3 (T283A)] was used as a substrate in an in vitro kinase reaction with purified GSK-3β. Fig. 6B shows that GSK-3β phosphorylated His-cyclin D3 (wt) but not His-cyclin D3 (T283A).
Taken together, these results indicate that cyclin D3 is a specific substrate for GSK-3β, and map the site of GSK-3β phosphorylation to Thr-283 in cyclin D3.
Protein: DP01448 (UniProt P10923)
Region: residues 17	to 294
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The far-ultraviolet CD spectral data indicated that mouse OPN largely lacks secondary structures.
Protein: DP01448 (UniProt P10923)
Region: residues 17	to 294
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The HSQC peaks of OPN were observed within narrow spectral region (7.5–8.5 ppm of the 1H chemical shifts), confirming that they are largely unstructured in solution.
Protein: DP01449 (UniProt Q15637)
Region: residues 1	to 25
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
NMR spectra of free SF1(1-25) display characteristics of a random coil conformation.
Protein: DP01449 (UniProt Q15637)
Region: residues 1	to 25
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Upon addition of unlabeled U2AF65-RRM3 to 15N-labeled SF1(1-25), tight binding is observed.
Protein: DP01449 (UniProt Q15637)
Region: residues 69	to 95
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
NMR data demonstrate that
SF1NTD comprises a structured domain consisting of
two a-helical regions that are interrupted by a long disordered
linker (residues 69–95)
Protein: DP01449 (UniProt Q15637)
Region: residues 69	to 95
Annotation: phosphorylation display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
SF1HH comprises
a helix-hairpin motif with two a-helices in an anti-parallel
arrangement that are connected by a flexible linker
(Figure 2), which contains the SPSP tandem phosphorylation
motif.
Protein: DP01450 (UniProt Q9UKT4)
Region: residues 1	to 318
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Region 1-318 is described as disordered in Extended Data Table 2.
Cross-references: PDB:4UI9
Protein: DP01450 (UniProt Q9UKT4)
Region: residues 332	to 355
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Region 336-355 is described as disordered in Extended Data Table 2, although upon examination of the associated cryo-EM PDB structure it appears that the region is invisible starting from Ala332.
Cross-references: PDB:4UI9
Protein: DP01450 (UniProt Q9UKT4)
Region: residues 437	to 447
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Region 437-447 in the LR tail appears to be disordered.
Cross-references: PDB:4UI9
Protein: DP01450 (UniProt Q9UKT4)
Region: residues 305	to 374
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
NMR studies indicate that other than the 45-residue ZBR, the 143-residue C-terminal EMI1 inhibitory region lacks fixed tertiary structure.
The APC/C inhibitory domain of EMI1 contains two intrinsically disordered segments separated by a zinc-dependent folded domain
Overall, the data suggest that EMI1DLZT is substantially intrinsically unfolded, with predominantly disordered D-box, Linker, and Tail regions separated by a folded ZBR.
Backbone resonance assignments revealed that the chemical shifts were consistently dispersed for the ZBR residues in EMI1DLZT, EMI1ZT, and EMI1Z constructs, indicating that the ZBR is an autonomously folded domain (Fig. 1b). Notably, the remaining resonances in EMI1DLZT displayed poor dispersion, low or negative {1H}-15N heteronuclear NOE (HetNOE) values, and relatively lower differences in Cα chemical shifts compared to values predicted for a random coil (Fig. 1c).
Cross-references: PDB:2M6N
Protein: DP01450 (UniProt Q9UKT4)
Region: residues 421	to 447
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
NMR studies indicate that other than the 45-residue ZBR, the 143-residue C-terminal EMI1 inhibitory region lacks fixed tertiary structure.
The APC/C inhibitory domain of EMI1 contains two intrinsically disordered segments separated by a zinc-dependent folded domain
Overall, the data suggest that EMI1DLZT is substantially intrinsically unfolded, with predominantly disordered D-box, Linker, and Tail regions separated by a folded ZBR.
Backbone resonance assignments revealed that the chemical shifts were consistently dispersed for the ZBR residues in EMI1DLZT, EMI1ZT, and EMI1Z constructs, indicating that the ZBR is an autonomously folded domain (Fig. 1b). Notably, the remaining resonances in EMI1DLZT displayed poor dispersion, low or negative {1H}-15N heteronuclear NOE (HetNOE) values, and relatively lower differences in Cα chemical shifts compared to values predicted for a random coil (Fig. 1c).
Cross-references: PDB:2M6N
Protein: DP01450 (UniProt Q9UKT4)
Region: residues 421	to 447
Annotation: disorder (Structural state)
Evidence: dynamic light scattering assay evidence used in manual assertion
Supporting statements:
To further characterize the biophysical properties of EMI1DLZT, we measured the hydrodynamic radius (Rh) to be 3.1 nm and 2.9 nm by dynamic light scattering (DLS) and analytical ultracentrifugation, respectively (Fig. 1f, g). A globular protein would have to be ~46 kDa, rather than the 16.0 kDa of EMI1DLZT to yield an Rh value of 3.1 nm by DLS. The best-fit weight-average anhydrous frictional ratio (f/f0)w values of 1.73 and 1.85 obtained from two analytical ultracentrifugation experiments indicate that EMI1DLZT is elongated in solution (Supplementary Fig. 1). Overall, the data suggest that EMI1DLZT is substantially intrinsically unfolded, with predominantly disordered D-box, Linker, and Tail regions separated by a folded ZBR.
Protein: DP01450 (UniProt Q9UKT4)
Region: residues 305	to 374
Annotation: disorder (Structural state)
Evidence: dynamic light scattering assay evidence used in manual assertion
Supporting statements:
To further characterize the biophysical properties of EMI1DLZT, we measured the hydrodynamic radius (Rh) to be 3.1 nm and 2.9 nm by dynamic light scattering (DLS) and analytical ultracentrifugation, respectively (Fig. 1f, g). A globular protein would have to be ~46 kDa, rather than the 16.0 kDa of EMI1DLZT to yield an Rh value of 3.1 nm by DLS. The best-fit weight-average anhydrous frictional ratio (f/f0)w values of 1.73 and 1.85 obtained from two analytical ultracentrifugation experiments indicate that EMI1DLZT is elongated in solution (Supplementary Fig. 1). Overall, the data suggest that EMI1DLZT is substantially intrinsically unfolded, with predominantly disordered D-box, Linker, and Tail regions separated by a folded ZBR.
Protein: DP01450 (UniProt Q9UKT4)
Region: residues 321	to 330
Annotation: protein binding (Molecular function)
Evidence: microscopy evidence used in manual assertion
Supporting statements:
An obvious key functional element is EMI1’s D-box. In examining the EM data, there are differences between APC/CCDH1 and the EMI1–SKP1- and EMI1DLZT-bound complexes in the vicinity of CDH1 and APC10, consistent with EMI1’s D-box binding the coreceptors (Supplemental Fig. 2). We were unable to generate stoichiometric complexes for mutants lacking EMI1’s D-box. Furthermore, alanine substitutions in place of Arg322 and Leu325 in EMI1DLZT’s D-box “RxxL” motif decreased inhibition of cycB-NT* in reactions with UBCH10 to the point that we could not measure a Ki under the initial rate conditions (Table 1). The apparent Ki increased by over two orders-of-magnitude for UbcycB-NT* ubiquitination by APC/CCDH1 and UBE2S.
The intrinsically disordered D-box, linker and tail elements, together with a structured zinc-binding domain, bind distinct regions of APC/C(CDH1) to synergistically both block the substrate-binding site and inhibit ubiquitin-chain elongation.
Protein: DP01450 (UniProt Q9UKT4)
Region: residues 321	to 330
Annotation: molecular function inhibitor activity (Molecular function)
Evidence: mutant phenotype evidence used in manual assertion
Supporting statements:
Furthermore, alanine substitutions in place of Arg322 and Leu325 in EMI1DLZT’s D-box “RxxL” motif decreased inhibition of cycB-NT* in reactions with UBCH10 to the point that we could not measure a Ki under the initial rate conditions (Table 1). The apparent Ki increased by over two orders-of-magnitude for UbcycB-NT* ubiquitination by APC/CCDH1 and UBE2S.
The functional importance of intrinsic structural disorder is explained by the D-box, Linker, ZBR, and Tail synergistically blocking both Ub ligation to a substrate and Ub chain elongation by APC/C.
The intrinsically disordered D-box, linker and tail elements, together with a structured zinc-binding domain, bind distinct regions of APC/C(CDH1) to synergistically both block the substrate-binding site and inhibit ubiquitin-chain elongation. 
The functional importance of intrinsic structural disorder is explained by enabling a small inhibitory domain to bind multiple sites to shut down multiple functions of a “molecular machine” nearly 100 times its size.
Protein: DP01450 (UniProt Q9UKT4)
Region: residues 421	to 447
Annotation: molecular function inhibitor activity (Molecular function)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Although the Ki for full-length EMI1 increased substantially, presumably due to lack of its D-box recruitment by CDH1, the isolated EMI1 Tail inhibited APC/C-UBE2S-mediated ubiquitination of UbcycB-NT* equally well in the presence or absence of CDH1 (Table 1, Fig. 6a, b).
The functional importance of intrinsic structural disorder is explained by enabling a small inhibitory domain to bind multiple sites to shut down multiple functions of a “molecular machine” nearly 100 times its size.
Protein: DP01450 (UniProt Q9UKT4)
Region: residues 421	to 447
Annotation: molecular function regulator (Molecular function)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
The indifference to CDH1 implied that the isolated EMI1 Tail targets a catalytic function of APC/C-UBE2S independently of blocking APC/C binding to a D-box substrate.
Furthermore, between the EM data showing EMI1 contacting the APC/C Catalytic core and biochemical data analyzing reactions inhibited by EMI1, we also uncovered a function for the unstructured C-terminal tail of EMI1 in blocking catalysis of Ub chain elongation by UBE2S
Protein: DP01450 (UniProt Q9UKT4)
Region: residues 338	to 359
Annotation: molecular function inhibitor activity (Molecular function)
Evidence: mutant phenotype evidence used in manual assertion
Supporting statements:
Prompted by the structural data showing that an insertion maps to the central location between the D-box coreceptor APC10, the Arc lamp, and the Platform (Fig. 4a), we considered that the Linker might be functionally important. Indeed, the Linker is not simply a spatial connector joining the D-box and ZBR effectors: deleting 20 Linker residues impairs EMI1DLZT-mediated inhibition, which is not restored by replacement with a 20-residue glycine-rich sequence (Fig. 4c, d). As a first attempt to address whether this sequence or structure may be important, we tested two 10-residue deletions, and found only one to be severely impaired for inhibition. Triply mutating conserved Leu345, Tyr356, and Arg358 within the essential sequence to alanines, either in the context of the benign 10-residue deletion or in EMI1DLZT, is sufficient to substantially impair inhibition. Thus, specific side-chains within the Linker contribute to inhibition (Fig. 4d).
The intrinsically disordered D-box, linker and tail elements, together with a structured zinc-binding domain, bind distinct regions of APC/C(CDH1) to synergistically both block the substrate-binding site and inhibit ubiquitin-chain elongation.
Protein: DP01450 (UniProt Q9UKT4)
Region: residues 338	to 359
Annotation: molecular function inhibitor activity (Molecular function)
Evidence: deletion mutation phenotypic evidence used in manual assertion
Supporting statements:
Prompted by the structural data showing that an insertion maps to the central location between the D-box coreceptor APC10, the Arc lamp, and the Platform (Fig. 4a), we considered that the Linker might be functionally important. Indeed, the Linker is not simply a spatial connector joining the D-box and ZBR effectors: deleting 20 Linker residues impairs EMI1DLZT-mediated inhibition, which is not restored by replacement with a 20-residue glycine-rich sequence (Fig. 4c, d). As a first attempt to address whether this sequence or structure may be important, we tested two 10-residue deletions, and found only one to be severely impaired for inhibition. 
Thus, specific side-chains within the Linker contribute to inhibition (Fig. 4d).
The intrinsically disordered D-box, linker and tail elements, together with a structured zinc-binding domain, bind distinct regions of APC/C(CDH1) to synergistically both block the substrate-binding site and inhibit ubiquitin-chain elongation.
Protein: DP01450 (UniProt Q9UKT4)
Region: residues 338	to 359
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The linker region connects the D-box and ZBR domains of Emi1.
Protein: DP01451 (UniProt Q9UBU9)
Region: residues 102	to 118
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
"The N-terminal glycine and arginine-rich portion of the molecule (residues 102–118) is disordered and may therefore be flexible in the absence of RNA."
Cross-references: PDB:1FT8
Protein: DP01451 (UniProt Q9UBU9)
Region: residues 96	to 117
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
"Similar to previously reported structures of free TAP-NTD, N-terminal amino acids 96–117 were disordered in the crystal structure of the complex with hCTE."
Cross-references: PDB:3RW6
Protein: DP01452 (UniProt Q13042)
Region: residues 96	to 126
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The regions are specified in the Extended Data Table 2
Cross-references: PDB:4UI9
Protein: DP01452 (UniProt Q13042)
Region: residues 96	to 123
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The regions are specified in the Extended Data Table 2
Cross-references: PDB:4UI9
Protein: DP01452 (UniProt Q13042)
Region: residues 528	to 620
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The regions are specified in the Extended Data Table 2
Cross-references: PDB:4UI9
Protein: DP01452 (UniProt Q13042)
Region: residues 94	to 126
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
"These sites lie within disordered regions of the APC/C (Ref. 23)."
Cross-references: PDB:5G05
Protein: DP01452 (UniProt Q13042)
Region: residues 528	to 620
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
"These sites lie within disordered regions of the APC/C (Ref. 23)."
Cross-references: PDB:5G05
Protein: DP01452 (UniProt Q13042)
Region: residues 534	to 620
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The regions are specified in the Extended Data Table 2
Cross-references: PDB:4UI9
Protein: DP01453 (UniProt Q8NHZ8)
Region: residues 26	to 85
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:5G05
PDB:5G04
Protein: DP01454 (UniProt P60006)
Region: residues 57	to 121
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:5G05
PDB:5G04
Protein: DP01455 (UniProt Q96DE5)
Region: residues 1	to 51
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:5G05
PDB:5G04
Protein: DP01456 (UniProt Q01081)
Region: residues 38	to 152
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The small chemical shift dispersion clearly
indicates that the protein adopts a random coil conformation
and is unstructured in aqueous solution.
Protein: DP01456 (UniProt Q01081)
Region: residues 38	to 152
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In the present paper, we found that the
monomeric free form of U2AF35 RRM is unstructured in
solution and that its three-dimensional structure is induced
upon binding to its native protein partner U2AF65.
Protein: DP01456 (UniProt Q01081)
Region: residues 38	to 152
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In the present paper, we found that the
monomeric free form of U2AF35 RRM is unstructured in
solution and that its three-dimensional structure is induced
upon binding to its native protein partner U2AF65.
Protein: DP01457 (UniProt Q92973)
Region: residues 319	to 371
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In Transportin-1 the H8 loop (residue 312-374) defined as a long loop connecting H8A and H8B helices. 
"The loops are disordered in the regions between K319 and S371 for NLS-free Trn1, and in the regions between K319 and D366 for Trn1 bound to hnRNP D NLS"
Cross-references: PDB:2Z5M
Protein: DP01458 (UniProt Q9Y3B4)
Region: residues 100	to 125
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The flanking N- (residues 1–
20) and C-terminal regions (residues 100–125) are unstructured