LiteFold/DisProt huggingface dataset:
Protein: DP02163 (UniProt Q02388)
Region: residues 1940	to 1978
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
To gain insight into the potential function of the hinge region we investigated a heterologous expressed peptide by CD and NMR spectroscopy. CD spectroscopy implies that the hinge region is intrinsically disordered. Resonance assignment was performed and allowed secondary structure analysis based on the chemical shift values. Seven amino acids in the N-terminal moiety show residual α-helical conformation.
In the 1H,15N-HSQC of the hinge peptide the signals corresponding to the peptide backbone amide protons are not dispersed (Fig. 4). This lack of dispersion is characteristic for unfolded proteins. Resonance assignment of the backbone chemical shifts is nearly complete enabling determination of the secondary structure (Fig. 5 b)
For a patch of about 10 amino acids in the N-terminal moiety of the hinge peptide, the chemical shifts indicate an α-helical conformation for several amino acids. All other residues of the hinge peptide do not adopt neither α-helix nor β-strand conformation
Moreover, the CD-spectrum of the hinge region is typical for an intrinsically disordered protein. The negative shoulder at 220 nm can be interpreted as residual α-helical structure. This is in line with data obtained by NMR spectroscopy: (I) there is no signal dispersion observed in an 1H,15N-HSQC spectrum indicating the absence of secondary structure and (II) secondary structure prediction based on chemical shifts identified only seven amino acids (R24, L25, E27, T28, K32, A33, and S34) with dihedral angles corresponding to an α-helical conformation. The presence of residual secondary structure is commonly observed in disordered proteins (Dunker et al., 2002, Tompa, 2002).
Protein: DP02164 (UniProt Q8WUM0)
Region: residues 252	to 269
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
A disordered 20-residue insertion is present in the DA loop connecting blades 3 and 4 (DA34).
Cross-references: PDB:1XKS
Protein: DP02164 (UniProt Q8WUM0)
Region: residues 478	to 514
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows this region lacks electron density, indicating it is disordered. 
Cross-references: PDB:1XKS
Protein: DP02164 (UniProt Q8WUM0)
Region: residues 1	to 70
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy structures of the Human nuclear pore complex (both dilated and constricted), shows this region from the NUP133 protein lacks electron density, indicating it is disordered. 
Cross-references: PDB:7R5J
PDB:7R5K
EMDB:EMD-14321
EMDB:EMD-14322
Protein: DP02164 (UniProt Q8WUM0)
Region: residues 1	to 70
Annotation: flexible N-terminal tail (Disorder function)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy structures of the Human nuclear pore complex (both dilated and constricted), shows this region from the NUP133 protein lacks electron density, indicating it is disordered.
Cross-references: PDB:7R5K
PDB:7R5J
EMDB:14322
EMDB:14321
Protein: DP02165 (UniProt F0ZBA6)
Region: residues 19	to 32
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The ECD of D. purpureum nicastrin (DpNCT; residues 19–611) yielded well-diffracting crystals in the space group P41212 (Table S1). The structure was determined by a combination of molecular replacement and bromide-based single-wavelength anomalous dispersion (SAD). The atomic model was refined to 1.95-Å resolution (Fig. 1A, Fig. S1, and Table S1). Residues 33–605 were assigned in the structure; 20 residues at the N and C termini are disordered in the crystals.
Cross-references: PDB:4R12
Protein: DP02167 (UniProt Q8N726-1)
Region: residues 1	to 132
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Figure 1C,D show the CD spectrum of p14arf and its thermal denaturation, respectively. The shape of the spectrum is that typical of unstructured proteins, and the thermal denaturation profile suggests the absence of cooperative transitions from folded to unfolded species.
Protein: DP02167 (UniProt Q8N726-1)
Region: residues 57	to 132
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The longitudinal (R1), and transverse (R2) 15N-amide relaxation rates (Fig. 2B), the 15N-nuclear overhauser effect (NOE; Fig. 2C) and the neighbor-corrected secondary structure propensity values calculated from the backbone chemical shifts (Fig. 2D) all indicate that the C-terminal fragment 57–132 of p14arf is intrinsically unstructured and does not have any secondary structure propensity in solution.
Protein: DP02167 (UniProt Q8N726-1)
Region: residues 1	to 14
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Circular dichroism (CD) spectropolarimetry shows that isolated peptides comprised of the A1 and H1 motifs (p14Arf 1−14 and Hdm2 240−254, respectively) are highly disordered in solution (Figure 1A and B, red and violet traces, respectively).
Protein: DP02167 (UniProt Q8N726-1)
Region: residues 1	to 14
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
However, when combined, the components of the binary mixture self-assemble, forming β-strand-containing supramolecular structures of low solubility (Figure 1A and B, other traces). The appearance of a minimum in the CD spectra of the assemblies at 216 nm and the increase in ellipticity at 193 nm are consistent with the formation of β-strand-containing structures. 
When either peptide was titrated into a solution of the other, both NMR and CD spectra revealed that binding was saturable.
Protein: DP02167 (UniProt Q8N726-1)
Region: residues 1	to 14
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
However, when combined, the components of the binary mixture self-assemble, forming β-strand-containing supramolecular structures of low solubility (Figure 1A and B, other traces). The appearance of a minimum in the CD spectra of the assemblies at 216 nm and the increase in ellipticity at 193 nm are consistent with the formation of β-strand-containing structures. 
Maximal β-strand character was observed when the molar ratio of A1:H1 was 1:1 (Figure 1A and B, green trace versus others).
Protein: DP02167 (UniProt Q8N726-1)
Region: residues 1	to 14
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The solution of binary assemblies is characterized by visible turbidity and the disappearance of 1H NMR resonances that, before mixing, were observed for the monodisperse, free peptides (data not shown). When either peptide was titrated into a solution of the other, both NMR and CD spectra revealed that binding was saturable.
Protein: DP02167 (UniProt Q8N726-1)
Region: residues 1	to 14
Annotation: amyloid fibril formation (Biological process)
Evidence: electron microscopy evidence used in manual assertion
Supporting statements:
Figure 3A shows that A1/H1 co-assemblies are networks of short, thin fibrils that are 10−20 nm long and less than 5 nm wide. These structures are morphologically similar to amyloid protofibrils derived from the β-amyloid peptide,24 insulin,23 lysozyme, 25 and an SH3 domain.
To test their stability and potential for further self-assembly, A1/H1 protofibrils were heated. The structure of A1/H1 co-assemblies became more organized after treatment (Figure 3B), appearing as distinct fibrils that were hundreds of nanometers in length. The long fibrils appeared to be bundled together into parallel, flat ribbons comprised of 3−6 individual fibrils.
Protein: DP02167 (UniProt Q8N726-1)
Region: residues 84	to 103
Annotation: protein binding (Molecular function)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
A broad peak is observed in the chromatogram of a 1 : 2 mixture of NPM1-Nter:p14arf-NoLS, at a smaller elution volume than free pentameric NPM1-Nter. This peak has a calculated MW of 200–500 kDa, consistent with the formation of large aggregates, while the MW calculated on the peak of pentameric NPM1-Nter increases from 72 kDa to 95 kDa, suggesting that a complex could be formed between a NPM1 pentamer and several p14arf-NoLS peptides.
Protein: DP02167 (UniProt Q8N726-1)
Region: residues 84	to 103
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Under these conditions, small chemical shift variations were observed, together with an increase in line-width, indicative of an exchange between the free protein and the aggregated, high molecular weight complex, which could be mapped to the NPM1-Nter structure (Fig. 8B).
Protein: DP02167 (UniProt Q8N726-1)
Region: residues 1	to 22
Annotation: MDM2/MDM4 family protein binding (Molecular function)
Evidence: immunoprecipitation evidence used in manual assertion
Supporting statements:
Analysis of smaller p14ARF peptides showed that residues 1–22 retained the ability to bind MDM2, whereas Tx–ARF23–44 and Tx–ARF56–64 showed no evidence of binding (Figure 1b, left).
MDM2 is an E3 ubiquitin-protein ligase that mediates ubiquitination of p53/TP53, leading to its degradation by the proteasome.
Protein: DP02167 (UniProt Q8N726-1)
Region: residues 1	to 22
Annotation: protein localization to nucleolus (Biological process)
Evidence: immunofluorescence evidence used in manual assertion
Supporting statements:
Analysis of proteins containing amino-terminal p14ARF peptides showed that each protein that contained the first 22 amino acids localized to the nucleolus (Figure 2e–h,k,l). In contrast, constructs expressing p14ARF peptides that failed to interact with MDM2 (Tx–ARF35–64, Tx–ARF23–44 and Tx–ARF56–64) also failed to localize to the nucleolus (Figure 2i,j,m–p).
Expression of each of the amino-terminal Tx–ARF proteins that retained the ability to bind MDM2 and localize to the nucleolus also resulted in relocalization of MDM2 to the nucleolus (Figure 3e–h,k,l). MDM2 expressed with non-binding thioredoxin-p14ARF proteins (Tx–ARF35–64, Tx–ARF23–44 and Tx–ARF56–64) remained in the nucleoplasm, with evidence of nucleolar exclusion (Figure 3i,j,m–p).
Protein: DP02167 (UniProt Q8N726-1)
Region: residues 1	to 34
Annotation: regulation of ubiquitin protein ligase activity (Biological process)
Evidence: immunoprecipitation evidence used in manual assertion
Supporting statements:
MDM2-mediated degradation of p53 was efficiently inhibited by coexpression of full-length p14ARF (Figure 4a). Analysis of smaller regions of p14ARF showed that each amino-terminal p14ARF peptide that retained the ability to bind and relocalize MDM2 to the nucleolus inhibited the degradation of p53 (Figure 4a), although the smallest peptide (1–22) was reproducibly slightly less efficient than the full-length protein. In contrast, proteins containing p14ARF peptides that failed to bind MDM2 (Tx–ARF35–64 and Tx–ARF56–64) did not prevent MDM2-mediated degradation of p53 (Figure 4a). 
MDM2 is an E3 ubiquitin-protein ligase that mediates ubiquitination of p53/TP53, leading to its degradation by the proteasome.
Protein: DP02167 (UniProt Q8N726-1)
Region: residues 85	to 101
Annotation: protein localization to nucleus (Biological process)
Evidence: green fluorescent protein fusion protein localization evidence used in manual assertion
Supporting statements:
These experiments identified a sequence—between residues 83 and 101 within exon 2 of ARF—necessary for localizing ARF to the nucleolus.
The ARF85–101-GFP fusion protein exhibited significant accumulation both in the nucleoplasm and nucleolus (Figure 1Db and 1Dd), demonstrating that residues 85 through 101 are also sufficient for localizing a heterologous protein to the nucleus and nucleolus.
Protein: DP02167 (UniProt Q8N726-1)
Region: residues 1	to 132
Annotation: regulation of protein stability (Biological process)
Evidence: quantitative western immunoblotting evidence used in manual assertion
Supporting statements:
The p53 protein level was increased about 150% when cotransfected with an ARF-expressing plasmid (lane 2). However, when cotransfected with equal amounts of plasmid DNA expressing the exon 1β–encoded ARF N-terminal domain (lane 3) or tumor-associated ARFR98L (lane 4) and ARFR98Q (lane 5) mutant proteins, the level of p53, albeit still higher than that accumulated in the absence of ARF, is reproducibly half that seen with wild-type ARF cotransfection.
These results indicate that the ARF N-terminal domain is capable of inhibiting MDM2-mediated p53 degradation when overexpressed, but deletion or tumor-derived mutations in the exon 2 domain reduce ARF’s ability to stabilize p53. Hence, the full activity of ARF in stabilizing p53 requires both the N- and C-terminal domains.
Mutations in Exon 2 Reduce ARF’s Ability to Stabilize p53
Protein: DP02167 (UniProt Q8N726-1)
Region: residues 1	to 132
Annotation: nuclear body organization (Biological process)
Evidence: immunofluorescence evidence used in manual assertion
Supporting statements:
ARF Colocalizes with MDM2 in the Nucleoplasm to Form Nuclear Bodies
The MDM2 and ARF nuclear bodies display identical punctate patterns, suggesting MDM2 and ARF colocalized in the nuclear bodies, which were not seen in control virus–infected cells (Figure 3C) or in ARF-negative (uninfected) cells in the same viewing field of Ad-E2F1-infected populations. 
p53 was also relocalized, from an even distribution in the nucleoplasm to colocalization with MDM2 and ARF in the nuclear bodies (Figure 3C, α-p53 staining).
RF-MDM2-p53 nuclear bodies were also observed in cells triply transfected with plasmid DNAs expressing each of the three proteins (Figure 4B, column 1).
Thus, both the MDM2-binding activity, encoded by the exon 1β, and the nucleolus-localizing activity residing in the exon 2 domain are important for ARF, p53, and MDM2 to form nuclear bodies.
Protein: DP02168 (UniProt Q72J05)
Region: residues 304	to 319
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The region with the highest mobility in TmrAB is indeed located in TM6 of TmrA right above the elbow helix and spans roughly 16 aa (residues 304–319). The weak electron density in this region, which includes a proline and glycine, reflects its high mobility.
Cross-references: PDB:5MKK
Protein: DP02169 (UniProt P37028)
Region: residues 217	to 232
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The disordered amino acid residue stretch (217 to 232) is indicated with a dashed black line.
Cross-references: PDB:5m29
Protein: DP02170 (UniProt O15234)
Region: residues 195	to 215
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The refined model consists of MAGO residues 4–146, Y14 residues 66–154, eIF4AIII residues 22–411, two segments of BTZ comprising residues 169–194 and 216–248, and the C-terminal region of UPF3b encompassing residues 418–432 (Fig. 1). Other portions of the proteins are not present in the structure, and are either poorly ordered or were separated upon proteolysis.
After a disordered linker of about 20 residues, BTZ extends onto the first RecA-like domain.
Cross-references: PDB:2XB2
Protein: DP02170 (UniProt O15234)
Region: residues 198	to 213
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The dotted line in red shows the approximate path of a portion of Btz not present in the electron density (residues 198–213; Figure 1).
Cross-references: PDB:2J0S
PDB:2J0Q
Protein: DP02170 (UniProt O15234)
Region: residues 137	to 168
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The refined model consists of MAGO residues 4–146, Y14 residues 66–154, eIF4AIII residues 22–411, two segments of BTZ comprising residues 169–194 and 216–248, and the C-terminal region of UPF3b encompassing residues 418–432 (Fig. 1). Other portions of the proteins are not present in the structure, and are either poorly ordered or were separated upon proteolysis.
Cross-references: PDB:2XB2
Protein: DP02170 (UniProt O15234)
Region: residues 249	to 286
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The refined model consists of MAGO residues 4–146, Y14 residues 66–154, eIF4AIII residues 22–411, two segments of BTZ comprising residues 169–194 and 216–248, and the C-terminal region of UPF3b encompassing residues 418–432 (Fig. 1). Other portions of the proteins are not present in the structure, and are either poorly ordered or were separated upon proteolysis.
Cross-references: PDB:2XB2
Protein: DP02170 (UniProt O15234)
Region: residues 195	to 215
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The refined model consists of MAGO residues 4–146, Y14 residues 66–154, eIF4AIII residues 22–411, two segments of BTZ comprising residues 169–194 and 216–248, and the C-terminal region of UPF3b encompassing residues 418–432 (Fig. 1). Other portions of the proteins are not present in the structure, and are either poorly ordered or were separated upon proteolysis.
After a disordered linker of about 20 residues, BTZ extends onto the first RecA-like domain.
Cross-references: PDB:2XB2
Protein: DP02170 (UniProt O15234)
Region: residues 1	to 169
Annotation: disorder (Structural state)
Evidence: curator inference based on intrinsic disorder prediction used in manual assertion
Supporting statements:
Cryo-EM structure of the human spliceosome just prior to exon ligation show this region of the MLN51protein lacks electron density. In combination with prediction data from MobiDB and AlphaFold, is posible to infer this region is likely disordered.
Cross-references: PDB:5XJC
Protein: DP02170 (UniProt O15234)
Region: residues 195	to 703
Annotation: disorder (Structural state)
Evidence: curator inference based on intrinsic disorder prediction used in manual assertion
Supporting statements:
Cryo-EM structure of the human spliceosome just prior to exon ligation show this region of the MLN51protein lacks electron density. In combination with prediction data from MobiDB and AlphaFold, is posible to infer this region is likely disordered.
Cross-references: PDB:5XJC
Protein: DP02170 (UniProt O15234)
Region: residues 216	to 246
Annotation: DEAD/H-box RNA helicase binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Residues 216 to 246 contact patches C, D, and E in eIF4AIII domain 1 (Fig. 1C and fig. S2), explaining why the mutation of MLN51 Tyr240 and Gly241 disrupts formation of the EJC core (3). 
Cross-references: PDB:2HYI
Protein: DP02170 (UniProt O15234)
Region: residues 216	to 246
Annotation: disorder to pre-molten globule (Structural transition)
Evidence: combinatorial experimental and curator inference evidence used in manual assertion
Supporting statements:
For the MLN51 fragment expressed for this study (residues 137 to 283), only residues 170 to 194 and 216 to 246 could be traced, and the fragment only contains limited secondary structure (Fig. 1A). Residues 216 to 246 contact patches C, D, and E in eIF4AIII domain 1 (Fig. 1C and fig. S2), explaining why the mutation of MLN51 Tyr240 and Gly241 disrupts formation of the EJC core (3). Residues 170 to 194 are located at the 5′ end of the bound RNA and contact eIF4AIII domain 2 (Fig. 1C).
The flexible non-conserved linker (10) between the two ordered MLN51 fragments allows the protein to remain associated with rather different conformations of eIF4AIII.
Cross-references: PDB:2HYI
Protein: DP02170 (UniProt O15234)
Region: residues 216	to 246
Annotation: flexible linker (Disorder function)
Evidence: combinatorial experimental and curator inference evidence used in manual assertion
Supporting statements:
For the MLN51 fragment expressed for this study (residues 137 to 283), only residues 170 to 194 and 216 to 246 could be traced, and the fragment only contains limited secondary structure (Fig. 1A). Residues 216 to 246 contact patches C, D, and E in eIF4AIII domain 1 (Fig. 1C and fig. S2), explaining why the mutation of MLN51 Tyr240 and Gly241 disrupts formation of the EJC core (3). Residues 170 to 194 are located at the 5′ end of the bound RNA and contact eIF4AIII domain 2 (Fig. 1C).
The flexible non-conserved linker (10) between the two ordered MLN51 fragments allows the protein to remain associated with rather different conformations of eIF4AIII.
Cross-references: PDB:2HYI
Protein: DP02170 (UniProt O15234)
Region: residues 170	to 194
Annotation: pre-molten globule (Structural state)
Evidence: combinatorial experimental and curator inference evidence used in manual assertion
Supporting statements:
For the MLN51 fragment expressed for this study (residues 137 to 283), only residues 170 to 194 and 216 to 246 could be traced, and the fragment only contains limited secondary structure (Fig. 1A).
Residues 170 to 194 are located at the 5′ end of the bound RNA and contact eIF4AIII domain 2 (Fig. 1C).
Cross-references: PDB:2HYI
Protein: DP02170 (UniProt O15234)
Region: residues 216	to 246
Annotation: pre-molten globule (Structural state)
Evidence: combinatorial experimental and curator inference evidence used in manual assertion
Supporting statements:
or the MLN51 fragment expressed for this study (residues 137 to 283), only residues 170 to 194 and 216 to 246 could be traced, and the fragment only contains limited secondary structure (Fig. 1A). Residues 216 to 246 contact patches C, D, and E in eIF4AIII domain 1 (Fig. 1C and fig. S2), explaining why the mutation of MLN51 Tyr240 and Gly241 disrupts formation of the EJC core (3).
Cross-references: PDB:2HYI
Protein: DP02170 (UniProt O15234)
Region: residues 1	to 703
Annotation: exon-exon junction complex (Cellular component)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Here, we present the crystal structure of a tetrameric exon junction core complex containing the DEAD-box adenosine triphosphatase (ATPase) eukaryotic initiation factor 4AIII (eIF4AIII) bound to an ATP analog, MAGOH, Y14, a fragment of MLN51, and a polyuracil mRNA mimic.
To shed light on both the EJC core architecture and the molecular mechanism of DEAD-box proteins, we determined the crystal structure of a minimal reconstituted EJC core assembled on a poly(U) oligonucleotide mimicking the mRNA at 2.3 Å resolution (8) (table S1).
Cross-references: PDB:2HYI