LiteFold/DisProt huggingface dataset:
Protein: DP01319 (UniProt Q15796)
Region: residues 457	to 467
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Compared to the unphosphorylated Smad2 (Wu et al., 2000), the N-terminal extension adopts a different conformation and is more than 12 Å away, whereas the previously flexible C terminus becomes well ordered after phosphorylation (Figure 2B).
Structural comparison of the phosphorylated (green) and unphosphorylated (gold) Smad2-MH2 (PDB code 1DEV). The differences are apparent in two locations; the N-terminal extensions are more than 12 Å apart, and the flexible C terminus in the unphosphorylated Smad2 becomes rigid and ordered upon phosphorylation.
Cross-references: PDB:1DEV
Protein: DP01319 (UniProt Q15796)
Region: residues 463	to 467
Annotation: phosphorylation display site (Disorder function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
To reveal the structural basis of phosphorylation-induced homotrimerization, we crystallized a Smad2-MH2 fragment (residues 241–467) with Ser465 and Ser467 homogeneously phosphorylated.
Cross-references: PDB:1DEV
Protein: DP01319 (UniProt Q15796)
Region: residues 463	to 467
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The phosphorylated Smad2 forms a symmetric homotrimer, with both the phosphorylated C terminus and the N-terminal extension from one MH2 domain reaching out to interact with an adjacent domain (Figure 2C).
Cross-references: PDB:1DEV
Protein: DP01319 (UniProt Q15796)
Region: residues 18	to 33
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The flexibility of this loop was confirmed by low 1H,15N heteronuclear NOE values (Supplemental Fig. S3A) and by the presence of partially overlapped amides as indicated in the 1H-15N HSQC (Fig. 1D; Supplemental Fig. S1D).
Cross-references: BMRB:27742
Protein: DP01319 (UniProt Q15796)
Region: residues 18	to 33
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The loop connecting the α1 and α2 helices (G-loop, Supplemental Fig. S1A), was excluded in the refined model because it is not well defined in the electron density map.
Protein: DP01319 (UniProt Q15796)
Region: residues 18	to 33
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The SAXS data also supports the conformational variability sampled by the G-loop, in agreement with the faster motions detected by NMR, with heteronuclear NOE values below 0.3 (Fig. 3B; Supplemental Fig. S3B).
Protein: DP01320 (UniProt P36152)
Region: residues 234	to 348
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
CD, NMR and fluorescence data confirm the in silico predictions and show that the N-terminus of Dre2 [Dre2 (1–133)] is a stably-folded domain, whereas the C-terminus is intrinsically unstructured, and contains eight cysteines that coordinate the Fe-S clusters.
Protein: DP01320 (UniProt P36152)
Region: residues 234	to 348
Annotation: molecular adaptor activity (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
A tight interaction between the Fe-S-containing Dre2-C-terminus and the two FMN-binding and FAD-binding domains from the reductase Tah18 is essential for yeast viability.
Protein: DP01322 (UniProt Q01924)
Region: residues 396	to 591
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Fibronectin-binding proteins (FnBPs), anchored in the bacterial cell wall, have multiple Fn-binding repeats in an unfolded region of the protein
Protein: DP01322 (UniProt Q01924)
Region: residues 396	to 591
Annotation: order to disorder (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
As well as showing how pathogenic bacteria can adhere to F1 modules in 1–5 F1 of Fn, the consequences of the mechanism, namely the high affinity and specificity of the binding, the significant conformational change undergone by the unfolded region of the FnBP and the presence of multiple Fn-binding sites, are all likely to have a role in bacterial invasion
Protein: DP01323 (UniProt Q8R316)
Region: residues 242	to 255
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
An additional triple-stranded β sheet is made of two antiparallel strands (β6 and β7), and a third strand (β8) that runs parallel to β7. α1 packs against β1 and β2 and is followed by a long unstructured region of 13 amino acids (residues 242–255), whereas α2 packs against β7 and β8.
An additional triple-stranded β sheet is made of two antiparallel strands (β6 and β7), and a third strand (β8) that runs parallel to β7. α1 packs against β1 and β2 and is followed by a long unstructured region of 13 amino acids (residues 242–255), whereas α2 packs against β7 and β8.
Cross-references: PDB:1V06
Protein: DP01323 (UniProt Q8R316)
Region: residues 358	to 380
Annotation: disorder (Structural state)
Evidence: circular dichroism evidence used in manual assertion
Supporting statements:
Like Mad1 SID, the circular dichroism spectrum of unbound HBP1 SID is characterized by the absence of stable secondary structure (data not shown).
Protein: DP01323 (UniProt Q8R316)
Region: residues 366	to 376
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In the complex, however, HBP1 SID forms an amphipathic helix (αA) that extends from Ala366 to Gln376. The regions preceding and following the helix in the NMR structure are poorly defined, most likely owing to a lack of experimental restraints and/or enhanced flexibility (Fig. 4a).
Cross-references: PDB:1S5R
Protein: DP01323 (UniProt Q8R316)
Region: residues 366	to 376
Annotation: order (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In the complex, however, HBP1 SID forms an amphipathic helix (αA) that extends from Ala366 to Gln376. The regions preceding and following the helix in the NMR structure are poorly defined, most likely owing to a lack of experimental restraints and/or enhanced flexibility (Fig. 4a).
Cross-references: PDB:1S5R
Protein: DP01323 (UniProt Q8R316)
Region: residues 366	to 376
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In the complex, however, HBP1 SID forms an amphipathic helix (αA) that extends from Ala366 to Gln376. The regions preceding and following the helix in the NMR structure are poorly defined, most likely owing to a lack of experimental restraints and/or enhanced flexibility (Fig. 4a).
Cross-references: PDB:1S5R
Protein: DP01323 (UniProt Q8R316)
Region: residues 358	to 380
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
We therefore synthesized a peptide corresponding to HBP1 residues 358–380 (henceforth designated HBP1 SID) and assayed for binding to mSin3A PAH2 using isothermal titration calorimetry (ITC). The HBP1 SID peptide bound mSin3A PAH2 with moderate affinity (Kd = 5.2 ± 1.0 μM) and 1:1 stoichiometry (Supplementary Fig. 1 online). A His6-tagged HBP1 construct spanning residues 342–398 also bound mSin3A PAH2 with a similar affinity, implying that the principal affinity determinants for the Sin3 interaction resided within HBP1 residues 358–380.
Protein: DP01324 (UniProt Q9HCJ0)
Region: residues 1592	to 1606
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Here we show that a conserved motif in the human GW182 paralog TNRC6C interacts with the C-terminal domain of polyadenylate binding protein 1 (PABC) and present the crystal structure of the complex.
Protein: DP01324 (UniProt Q9HCJ0)
Region: residues 1587	to 1608
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
1H-15N heteronuclear single quantum correlation spectra of the DUF region showed limited dispersion of signals, which confirms that the peptide is unfolded prior to Mlle binding (supplemental Fig. S1).
Protein: DP01324 (UniProt Q9HCJ0)
Region: residues 1591	to 1606
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Helices α2 and α3 and a small part of helix α5 participate in peptide binding. The electron density map showed the GW182 peptide from residues Asn1384 to Gln1399.
Cross-references: PDB:3KTP
Protein: DP01324 (UniProt Q9HCJ0)
Region: residues 1591	to 1606
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Titration of the 15N-labeled peptide with the Mlle domain produced large chemical shift changes, indicating that the peptide becomes structured upon Mlle binding.
Protein: DP01324 (UniProt Q9HCJ0)
Region: residues 1591	to 1606
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
 Titration of the 15N-labeled peptide with the Mlle domain produced large chemical shift changes, indicating that the peptide becomes structured upon Mlle binding.
Protein: DP01324 (UniProt Q9HCJ0)
Region: residues 1591	to 1606
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Helices α2 and α3 and a small part of helix α5 participate in peptide binding. The electron density map showed the GW182 peptide from residues Asn1384 to Gln1399.
Cross-references: PDB:3KTP
Protein: DP01324 (UniProt Q9HCJ0)
Region: residues 1591	to 1606
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
The affinity of the wild-type GW182-(1380–1401) peptide measured by ITC was 6 μm (Fig. 2a).
Protein: DP01325 (UniProt O43236-6)
Region: residues 248	to 274
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H-NMR spectra of ARTS CTD showed a narrow dispersion of amide resonances. This pattern implies a random coil conformation and is characteristic of disordered regions and peptides.
Protein: DP01325 (UniProt O43236-6)
Region: residues 248	to 274
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We showed that the nine C-terminal residues (266-274) of the proapoptotic ARTS protein mediate its interaction with the Bir3 domain of XIAP.
Protein: DP01325 (UniProt O43236-6)
Region: residues 248	to 274
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The far-UV CD spectrum of ARTS C-terminal domain (CTD) is composed largely of a minimum at 200 nm and is missing the typical signatures of secondary structures, indicating mainly a random coil. This is a characteristic pattern for disordered regions.
Protein: DP01325 (UniProt O43236-6)
Region: residues 248	to 274
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
We showed that the nine C-terminal residues (266-274) of the proapoptotic ARTS protein mediate its interaction with the Bir3 domain of XIAP.
Protein: DP01326 (UniProt Q9Y4P1)
Region: residues 190	to 216
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The four N-terminal residues, 16 C-terminal residues, and four loop regions corresponding to residues 190 –216, 288 –290, 343–346, and 356 –361 lacked defined electron density and were omitted from the model (Fig. 1).
Cross-references: PDB:2CY7
Protein: DP01326 (UniProt Q9Y4P1)
Region: residues 387	to 392
Annotation: protein binding (Molecular function)
Evidence: mutant phenotype evidence used in manual assertion
Supporting statements:
ATG4B contains a C-terminal LIR motif important for binding and efficient cleavage of mammalian orthologs of yeast Atg8.
ATG4B contains a C-terminal LIR motif important for a strong interaction with Atg8-family orthologs
C-terminal sequences of ATG4B constructs carrying mutations affecting the C-terminal LIR motif.
Next, a series of mutant ATG4B constructs, either deleted for the C-terminal LIR region (ΔLIRC) or carrying 2 (2mLIR) or 5 (5mLIR) point mutations affecting the motif (Fig. 1D), were in vitro translated and tested for interaction with Atg8-family orthologs fused to GST. Mutation of 2 residues in the core LIRC motif (F388A and L391A) reduced the interaction of ATG4B with LC3A, LC3B, LC3C and GABARAPL2 to 25% residual binding, and the interactions with GABARAP or GABARAPL1 to 60% (Fig. 1E and F). However, mutation of 5 residues in the LIRC region, or deletion of the LIRC motif, reduced the interactions with GABARAP and GABARAPL1 to 10% to 15% (Fig. 1E and F). The 5 point-mutations included the 3 negatively charged residues located immediately N-terminal to the core LIRC motif (Fig. 1D), in addition to the F388A and L391A mutations. In contrast to mutation of the C-terminal LIR, mutation or deletion of the N-terminal YDTL LIR (LIRN) had only a very minor effect on the interaction with LC3B or GABARAPL1 (Fig. 1G and H). Thus, we identified a LIR motif in the C terminus of ATG4B that contributed strongly to the interaction between ATG4B and Atg8-family proteins.
The C-terminal LIR motif corresponds to residues 388-391 (FEIL).
Protein: DP01326 (UniProt Q9Y4P1)
Region: residues 191	to 215
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structure from residues 191 to 215, which links the auxiliary domain and protease domain, could not be constructed because of the weak electron density.
Cross-references: PDB:2D1I
Protein: DP01326 (UniProt Q9Y4P1)
Region: residues 187	to 217
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Disordered region in ATG4B.
Cross-references: PDB:2Z0E
PDB:2ZZP
PDB:2Z0D
Protein: DP01326 (UniProt Q9Y4P1)
Region: residues 378	to 393
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The four N-terminal residues, 16 C-terminal residues, and four loop regions corresponding to residues 190 –216, 288 –290, 343–346, and 356 –361 lacked defined electron density and were omitted from the model (Fig. 1).
Cross-references: PDB:2CY7
Protein: DP01326 (UniProt Q9Y4P1)
Region: residues 388	to 391
Annotation: protein binding (Molecular function)
Evidence: staining evidence used in manual assertion
Supporting statements:
ATG4B contains a C-terminal LIR motif important for binding and efficient cleavage of mammalian orthologs of yeast Atg8. 
ATG4B contains a C-terminal LIR motif important for a strong interaction with Atg8-family orthologs
The C-terminal LIR motif is important for the interaction of full-length ATG4B with Atg8-family orthologs. Myc-tagged ATG4B constructs were in vitro translated in the presence of [35S]methionine, and tested in GST affinity isolation experiments for binding to the indicated Atg8-family orthologs fused to GST. Bound proteins were detected by autoradiography (AR), and immobilized GST or GST-tagged proteins by Coomassie brilliant blue staining (CBB).
The C-terminal LIR motif corresponds to residues 388-391 (FEIL).
Protein: DP01326 (UniProt Q9Y4P1)
Region: residues 388	to 391
Annotation: selective autophagy (Biological process)
Evidence: quantitative western immunoblotting evidence used in manual assertion
Supporting statements:
ATG4B contains a C-terminal LIR motif important for binding and efficient cleavage of mammalian orthologs of yeast Atg8. 
Strikingly, the LIR motif of ATG4B was required for stabilization of the unlipidated forms of GABARAP and GABARAPL1 in cells.
The LIRC motif of ATG4B is required for stabilization of GABARAP and GABARAPL1. (A) The endogenous level of GABARAP is severely diminished in cells that do not express ATG4B. Extracts of atg4b KO cells reconstituted with the indicated GFP-ATG4 constructs were analyzed by western blotting.
Intriguingly, we observed that GABARAP and GABARAPL1 were degraded and virtually absent in cells lacking ATG4B. Consistently, the levels of these 2 proteins were highly elevated in cells overexpressing WT ATG4B. We propose that binding to ATG4B stabilizes these proteins. Without this stabilization they are rapidly degraded by the proteasome and unavailable for autophagosome formation.
The C-terminal LIR motif corresponds to residues 388-391 (FEIL).
Protein: DP01326 (UniProt Q9Y4P1)
Region: residues 388	to 391
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
ATG4B contains a C-terminal LIR motif important for binding and efficient cleavage of mammalian orthologs of yeast Atg8.
We solved the crystal structures of the GABARAPL1-ATG4B C-terminal LIR complex.
Crystal structures of the complex of GABARAPL1 with 2 LIR peptides at 1.55- and 1.75-Å resolution reveal canonical LIR-LDS interactions with important contributions from electrostatic interactions involving residues both N-terminal to, and within, the core LIR.
To evaluate the interaction between the C-terminal LIR-motif of ATG4B with Atg8-family proteins in more detail, we determined the X-ray structure of GABARAPL1 in complex with a peptide containing the C-terminal 10-amino acid LIRC motif of ATG4B (Fig. S1A).
The structure displays 4 additional interactions: 1) Electrostatic interactions between the acidic N-terminal LIRC residues 384Glu-Asp-Glu-Asp387 of ATG4B and the basic residues GABARAPL1 (K46), GABARAPL1 (K24), GABARAPL1 (K20) and GABARAPL1 (K48), respectively; 2) a salt bridge between ATG4B (E389) and GABARAPL1 (R67); 3) some hydrophobic interactions between ATG4B (I390) in position +2 and GABARAPL1 (L50) as well as GABARAPL1 (Y25); 4) 3 hydrogen bonds between the carbonyls of ATG4B (L391), ATG4B (S392) and the guanidinium group of GABARAPL1 (R28). Except for the C-terminal ATG4B (L393), all residues in the LIRC are contributing to the interaction.
The C-terminal LIR motif corresponds to residues 388-391 (FEIL).
Cross-references: PDB:5LXI
PDB:5LXH
Protein: DP01326 (UniProt Q9Y4P1)
Region: residues 191	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 structure from residues 191 to 215, which links the auxiliary domain and protease domain, could not be constructed because of the weak electron density.
Protein: DP01327 (UniProt Q8IV16)
Region: residues 21	to 54
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
GPIHBP1 is highly asymmetrical with an N-terminal intrinsically disordered region (IDR) rich in acidic residues
Cross-references: SASBDB:SASDHF4
Protein: DP01328 (UniProt Q9C0C7)
Region: residues 527	to 541
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Authors show the region is intrinsically unstructured by its large negative ellipticity at 200 nm and moderate ellipticity at 190 nm, typical of IDR.
Protein: DP01329 (UniProt P28324)
Region: residues 94	to 136
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The 43 amino acids (94–136) linking the B-box to the ETS domain of SAP-1 are unobserved in the electron density map and are therefore likely to be highly disordered.
Cross-references: PDB:1HBX
Protein: DP01329 (UniProt P28324)
Region: residues 94	to 136
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This linker region must be flexible as it accommodates cooperative binding of SAP-1 and SRF on sites disposed with virtually any spacing of up to 10 bp as well as direction reversal of the EBS with respect to the CArG-box
The terminal amino acids and the SAP-1 linker region disordered in the structure are printed in gray.
Protein: DP01330 (UniProt P32639)
Region: residues 1	to 112
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Region could not be traced in the electron density of the present FL Brr2-Jab1 crystals.
Cross-references: PDB:5DCA
Protein: DP01330 (UniProt P32639)
Region: residues 193	to 257
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Region could not be traced in the electron density of the present FL Brr2-Jab1 crystals.
Cross-references: PDB:5DCA
Protein: DP01330 (UniProt P32639)
Region: residues 394	to 419
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Region could not be traced in the electron density of the present FL Brr2-Jab1 crystals.
Cross-references: PDB:5DCA
Protein: DP01332 (UniProt P17931)
Region: residues 20	to 100
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
Small-angle X-ray scattering studies. A, SAXS intensities of galectin-3 as a function of the scattering vector q (Å−1). B, the Kratky plot is typical of that of a partially folded protein.
Protein: DP01332 (UniProt P17931)
Region: residues 1	to 115
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Resonances from the CRD are relatively well dispersed for the canonical β-sheet structure as previously reported for truncated Gal-3 CRD (Umemoto and Leffler 2001), whereas those arising from the N-terminal tail exhibit rather narrow line widths, reflecting comparatively increased internal mobility. In addition, resonances arising from the N-terminal tail are minimally dispersed and fall within the spectral region associated with random coil conformation.
Cross-references: BMRB:19491