LiteFold/DisProt huggingface dataset:
Protein: DP01332 (UniProt P17931)
Region: residues 20	to 100
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: microscopy evidence used in manual assertion
Supporting statements:
The low sequence complexity of the structurally disordered NTD is reminiscent of those recently reported proteins whose low-complexity domains mediate their liquid–liquid phase separation behavior in various cellular functions. Indeed, we found that the NTD (as does a phosphomimetic mutant S6E) undergoes temperature-dependent phase separation.
The text is in the discussion, but the figure showing LLPS is in the supplementary.
Protein: DP01332 (UniProt P17931)
Region: residues 20	to 100
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The MTSL label on the CRD (I250C; the β-strand 11) bleaches a broad range of intensity in the NTD, consistent with the model that the NTD contacts with the CRD fuzzily and that the first ∼20 residues have less contact with this domain
The authors report an intra-protein interaction between the disordered N-terminal domain and the folded C-terminal domain.
Protein: DP01332 (UniProt P17931)
Region: residues 1	to 40
Annotation: carbohydrate binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The present study is focused on human galectin-3 (Gal-3) interactions with a 60 kDa rhamnogalacturonan RG-I-4 that we use as a model to garner information as to how galectins interact with large polysaccharides, as well as to develop this agent as a therapeutic against human disease. Gal-3 is unique among galectins, because as the only chimera-type, it has a long N-terminal tail (NT) that has long puzzled investigators due to its dynamic, disordered nature and presence of numerous prolines. Here, we use 15N-1H heteronuclear single quantum coherence NMR spectroscopy to demonstrate that multiple sites on RG-I-4 provide epitopes for binding to three sites on 15N-labeled Gal-3, two within its carbohydrate recognition domain (CRD) and one at a novel site within the NT encompassing the first 40 residues that are highly conserved among all species of Gal-3.
A number of NT resonances are chemically shifted by the presence of RG-I-4, with the most perturbed ones belonging to residues within the N-terminal part of the NT as observed with the NT in full length Gal-3. These data indicate that the Gal-3 NT (independent of the presence of the CRD) binds to one or more sites within the RG-I-4 polysaccharide.
Although there are some changes that occur within the C-terminal part of the NT (residues ~75–100), the most perturbed resonances belong to residues within the N-terminal part of the NT (residues 1–40). Likewise, seven of the nine Asn/Gln residues in the NT (i.e., N4, N16, N18, Q20, N28, Q29, Q48) perturbed by interactions with RG-I-4.
Protein: DP01332 (UniProt P17931)
Region: residues 1	to 112
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: microscopy evidence used in manual assertion
Supporting statements:
Indeed, a 1 mM NTD sample with 150 mM NaCl condenses at higher temperatures and dissolves at lower ones in a reversible manner.
Protein: DP01332 (UniProt P17931)
Region: residues 1	to 112
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We collected the longitudinal relaxation rates (R1), transverse relaxation rates (R2), and heteronuclear NOEs (hetNOEs) at different protein concentrations. The residues in the NTD have higher R1 values, lower R2 values, and lower hetNOEs than those in the CRD because the intrinsically disordered region is more dynamic.
Protein: DP01333 (UniProt O00522)
Region: residues 118	to 128
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows that this region lacks electron density, indicating that it is disordered.
Cross-references: PDB:4DX8
Protein: DP01334 (UniProt B7T1D9)
Region: residues 215	to 240
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
V3, which is encompassed by the 26-amino-acid disordered region, was not visible
in the structure.
Cross-references: PDB:3NIB
Protein: DP01334 (UniProt B7T1D9)
Region: residues 215	to 240
Annotation: small molecule binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
V3 could not be modeled in the electron-density map. The V3 loop is
part of a larger motif that we have termed the GHL (glycopeptide
helix loop) and is believed to interact extensively with the glycopeptide.
Protein: DP01335 (UniProt O94907)
Region: residues 250	to 260
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
All residues of LRP6(3-4) are visible in both copies in the crystal, except for the loop comprising residues 1006–1012. In both copies, at least one sugar is visible at each of the five predicted N-linked glycosylation sites (Figure S1). The model of Dkk1_C comprises residues 182–264, except that the loop spanning residues 250–258 is disordered.
Cross-references: PDB:3S2K
Protein: DP01336 (UniProt P03709)
Region: residues 42	to 80
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Amide proton chemical shift values consistent with unstructured protein and a lack of medium and long range NOEs indicated that residues 42–80 were unstructured.
Cross-references: PDB:2LSM
Protein: DP01336 (UniProt P03709)
Region: residues 42	to 80
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
A partial trypsin digestion reaction of full-length gpFI by SDS-PAGE revealed the presence of a single band of ∼10 kDa that was resolved as two protein fragments by native PAGE. This further supports the presence of two independently folded domains in this protein with cleavage likely taking place at the single Arg residue present at position 56 in the unstructured loop between the two domains.
Protein: DP01336 (UniProt P03709)
Region: residues 42	to 80
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
A partial trypsin digestion reaction of full-length gpFI by SDS-PAGE revealed the presence of a single band of ∼10 kDa that was resolved as two protein fragments by native PAGE. This further supports the presence of two independently folded domains in this protein with cleavage likely taking place at the single Arg residue present at position 56 in the unstructured loop between the two domains.
Protein: DP01337 (UniProt Q96B02)
Region: residues 136	to 145
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In place of the final
C-terminal helix present in canonical UBC
folds, residues N136–W145 form a disordered
region that occupies positions directly beneath
the active site in all states of the ensemble, as
revealed by the spin label attached to active site
C91.
Cross-references: PDB:2MT6
Protein: DP01339 (UniProt P0A903)
Region: residues 26	to 98
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The most outstanding structural feature of the BamCD complex is the 73-residue-long unstructured N terminus of BamC that has not been observed in previously reported structures (11, 23, 39); it folds into an elongated U-shaped loop structure that interacts extensively with BamD by fitting into a trail of crevices that run along the longitudinal axis of BamD (Fig. 2b and supplemental Fig. 3).
 In this study, we crystallized BamD in a heterodimeric complex with BamCUN, and its structure was solved and refined to 2.9 Å resolution (supplemental Table 2).
Cross-references: PDB:3TGO
Protein: DP01339 (UniProt P0A903)
Region: residues 1	to 100
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The first 100 N-terminal residues are not structured in BamC
Protein: DP01339 (UniProt P0A903)
Region: residues 214	to 227
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
Heteronuclear 15N{1H} NOEs were measured for the backbone amides in BamC101-344 and as seen in Fig. 2a, residues in the N- and C-terminal domains generally had NOE values above 0.7, whereas residues 214 to 227 in the linker had significantly lower 15N{1H} NOE values (0.13 to 0.42), indicating a flexible linker.
Cross-references: PDB:2LAE
Protein: DP01339 (UniProt P0A903)
Region: residues 214	to 227
Annotation: flexible linker (Disorder function)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
Heteronuclear 15N{1H} NOEs were measured for the backbone amides in BamC101-344 and as seen in Fig. 2a, residues in the N- and C-terminal domains generally had NOE values above 0.7, whereas residues 214 to 227 in the linker had significantly lower 15N{1H} NOE values (0.13 to 0.42), indicating a flexible linker.
Cross-references: PDB:2LAE
Protein: DP01339 (UniProt P0A903)
Region: residues 26	to 98
Annotation: protein binding (Molecular function)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Size exclusion chromatography analysis showed that any truncated form of BamC missing the unstructured N terminus (i.e. BamCN, BamCC, and BamCNC) was unable to form the BamCD complex (Fig. 1b and supplemental Fig. 1). On the other hand, BamCUN co-purified with BamD throughout the entire purification process despite missing the C-terminal domain (Fig. 1, c and d).
Together, these results show that the unstructured N terminus of BamC is required for the formation of the BamCD complex.
Protein: DP01339 (UniProt P0A903)
Region: residues 26	to 98
Annotation: order (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The most outstanding structural feature of the BamCD complex is the 73-residue-long unstructured N terminus of BamC that has not been observed in previously reported structures (11, 23, 39); it folds into an elongated U-shaped loop structure that interacts extensively with BamD by fitting into a trail of crevices that run along the longitudinal axis of BamD (Fig. 2b and supplemental Fig. 3).
Cross-references: PDB:3TGO
Protein: DP01339 (UniProt P0A903)
Region: residues 26	to 98
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The most outstanding structural feature of the BamCD complex is the 73-residue-long unstructured N terminus of BamC that has not been observed in previously reported structures (11, 23, 39); it folds into an elongated U-shaped loop structure that interacts extensively with BamD by fitting into a trail of crevices that run along the longitudinal axis of BamD (Fig. 2b and supplemental Fig. 3).
Protein: DP01342 (UniProt P52564)
Region: residues 1	to 43
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
It was likely that the R-factor and R-free values were rather high owing to the highest disordered rate. The npMAP2K6 is composed of 340 residues, with 49 residues disordered in the crystal. Although the N-terminal
region (residues 1-43) and the His 6 -tag were disordered, the kinase domain (residues 44-334) was ordered (Fig. 2A).
Cross-references: PDB:3VN9
Protein: DP01344 (UniProt Q13469)
Region: residues 131	to 294
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
These 15N-detected experiments were used to assign the backbone resonances of human transcription factor nuclear factor of activated T cells (NFATC2) (residues 131–294). This portion of NFAT is disordered.
Protein: DP01344 (UniProt Q13469)
Region: residues 131	to 294
Annotation: molecular adaptor activity (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Our data demonstrate that, upon PKA phosphorylation, 14-3-3 binds to NFAT and blocks access to the nuclear localization sequence (NLS), which may prevent the nuclear transport protein importin from translocating NFAT to the nucleus, thus preventing transcriptional activation
Protein: DP01344 (UniProt Q13469)
Region: residues 131	to 294
Annotation: phosphorylation display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
PKA phosphorylation resulted in downfield shifts of the 1H resonances of two serine residues that are assigned to S-225 and S-255.
Protein: DP01344 (UniProt Q13469)
Region: residues 131	to 294
Annotation: 14-3-3 protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
PKA phosphorylation of NFAT promotes its association with the 14-3-3 chaperone protein, which results in the inhibition of NFAT transcriptional activity (26).
Protein: DP01347 (UniProt Q9UNL4)
Region: residues 119	to 188
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The shape of the spectra of Nt_NLS and NLS_PHD can be explained by the combination of the spectra of Nt
or PHD, respectively, and the spectrum of a random-coil chain: less negative ellipticity at 222 nm, less positive ellipticity at 190 nm, and a shift to lower wavelengths of the Nt minimum at 208 nm and the PHD minimum at 202 nm. These results suggest that NLS behaves as a disordered random coil.
Protein: DP01351 (UniProt P12302)
Region: residues 171	to 188
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Although purified spinach PsbP protein shows no degradation products by analytical SDS gel electrophoresis and full-length protein is recovered from dissolved crystals as reported already [35], the electron density is not resolved in the N-terminal region (residues 1–15) and in two internal regions (residues 90–107 and 135–139), as in the structure of tobacco PsbP (PDB ID 1V2B [33]; Figure 1).
Unresolved residues (90-107) correspond to residues 171-188 in Uniprot
Cross-references: PDB:2VU4
Protein: DP01351 (UniProt P12302)
Region: residues 82	to 92
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
 Except for the N-terminal 11 residues, we constructed the structure of spinach PsbP in its entirety for the first time (P12 to A186) (Figure 1A).
Cross-references: PDB:4RTI
Protein: DP01351 (UniProt P12302)
Region: residues 171	to 188
Annotation: manganese ion binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Our structures add crucial structural information for PsbP, with two Mn ions identified inside PsbP for the first time. We propose that one of the ions is responsible for a dramatic conformational change (with a maximum move of 20 Å) that is revealed here within the long region (aa 90–107).
We propose that the observed conformational change in the loop90–107 region is induced by binding of Mn2.
Cross-references: PDB:4RTI
Protein: DP01351 (UniProt P12302)
Region: residues 82	to 96
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Although purified spinach PsbP protein shows no degradation products by analytical SDS gel electrophoresis and full-length protein is recovered from dissolved crystals as reported already [35], the electron density is not resolved in the N-terminal region (residues 1–15) and in two internal regions (residues 90–107 and 135–139), as in the structure of tobacco PsbP (PDB ID 1V2B [33]; Figure 1).
Unresolved residues (1-15) correspond to residues 82-96 in Uniprot.
Cross-references: PDB:2VU4
Protein: DP01351 (UniProt P12302)
Region: residues 117	to 188
Annotation: order (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The two internal segments (aa 90–107 and aa 134–139), unresolved in the previous structures, were unambiguously defined in our structure based on their electron density maps (Supplemental Figure 2), with both segments exhibiting a loop conformation.
We propose that the observed conformational change in the loop90–107 region is induced by binding of Mn2.
Cross-references: PDB:4RTI
Protein: DP01351 (UniProt P12302)
Region: residues 117	to 188
Annotation: disorder to order (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The two internal segments (aa 90–107 and aa 134–139), unresolved in the previous structures, were unambiguously defined in our structure based on their electron density maps (Supplemental Figure 2), with both segments exhibiting a loop conformation.
We propose that the observed conformational change in the loop90–107 region is induced by binding of Mn2.
Cross-references: PDB:4RTI
Protein: DP01351 (UniProt P12302)
Region: residues 1	to 95
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the Cryo-EM structure of spinach PSII-LHCII supercomplex portrayed in the PDB this region lacks electron density, indicating it is disordered.
Cross-references: PDB:3JCU
EMDB:EMD-6617
Protein: DP01355 (UniProt P46014)
Region: residues 299	to 313
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
C-terminal residues 299–313 appear to be unstructured
Cross-references: PDB:1MZK
Protein: DP01356 (UniProt Q49492)
Region: residues 116	to 144
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
MycF WT crystal contents Mg-disordered lid. The active site of MycF becomes progressively more ordered as the cosubstrate and substrate bind. SAM/SAH binding to MycF closes the helical lid domain over the cosubstrate, partially orders the lid loop, and forms the binding site for the substrate mycinamicin III, which orders the remainder of the lid loop.
Cross-references: PDB:4XVZ
Protein: DP01366 (UniProt Q24139)
Region: residues 227	to 237
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
"Interactions between the WW domains of Drosophila Nedd4 (dNedd4) and Commissureless (Comm) PY motifs promote axon crossing at the CNS midline and muscle synaptogenesis. Here we report the solution structure of the dNedd4 WW3* domain complexed to the second PY motif (227'TGLPSYDEALH237') of Comm. ... Residues Y232'-L236' form a helical turn, following the PPII helical PY motif."
Protein: DP01368 (UniProt Q8WXE9)
Region: residues 301	to 340
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
This article and the region was mentioned to be an IDR in the article with Pubmed ID 23874186. In this article Figure 4 shows the IDR and cites the PDB: 2JXC structure article as: "In panel D, a relatively long disordered segment of human stonin-2 interacts with one folded EF-hand domain of human EPS15 (PDB: 2JXC)."
Cross-references: PDB:2JXC
Protein: DP01368 (UniProt Q8WXE9)
Region: residues 301	to 340
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Stonin-2 NMR structure in complex with Eps15 (UniProt ID: P42566 "EPS15_HUMAN")
Protein: DP01368 (UniProt Q8WXE9)
Region: residues 301	to 331
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
"Figure 2b: Secondary chemical shifts Δδ(Cα–Cβ) of the stonin 2 peptide bound to Eps15 EH2."
Protein: DP01377 (UniProt J7M799)
Region: residues 1	to 237
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In contrast, the CD spectrum of CAHS1 had a single deep minimum around 200 nm, similar to that of hydrated LEA proteins [31], suggesting that these proteins are unstructured in hydrated conditions (Fig. 4B).
Protein: DP01378 (UniProt P0CU43)
Region: residues 1	to 224
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
IDPs lack persistent secondary structure (Theillet et al., 2014; Yamaguchi et al., 2012), which we confirmed for CAHS proteins using nuclear magnetic resonance spectroscopy (NMR).
For α-synuclein, a known disordered protein, and for CAHS proteins, the crosspeaks occur over a narrower window (Figure 2, top), from ~8.0 to ~8.6 ppm, which coincides with the range for amide protons in the central residue of unstructured tripeptides (Schwarzinger et al., 2000).
Protein: DP01378 (UniProt P0CU43)
Region: residues 1	to 224
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence used in manual assertion
Supporting statements:
For the disordered proteins tested (α-synuclein and CAHS proteins), nearly all the amide protons were exchanged for deuterons within 20 min, as shown by the decrease in intensity of the one-dimensional proton spectrum (Figure 2).
Protein: DP01378 (UniProt P0CU43)
Region: residues 3	to 222
Annotation: response to desiccation (Biological process)
Evidence: small interfering RNA knockdown evidence used in manual assertion
Supporting statements:
Tardigrades Use Intrinsically Disordered Proteins to Survive Desiccation.
Tardigrade-Specific IDPs Are Required for Desiccation Tolerance
However, targeting two of four highly induced (13- to 22-fold) CAHS genes significantly (p < 0.01) reduced survival after desiccation compared with a control treatment, GFP RNAi (Figure 4B).
Protein: DP01379 (UniProt P0CU44)
Region: residues 1	to 224
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
IDPs lack persistent secondary structure (Theillet et al., 2014; Yamaguchi et al., 2012), which we confirmed for CAHS proteins using nuclear magnetic resonance spectroscopy (NMR).
For α-synuclein, a known disordered protein, and for CAHS proteins, the crosspeaks occur over a narrower window (Figure 2, top), from ~8.0 to ~8.6 ppm, which coincides with the range for amide protons in the central residue of unstructured tripeptides (Schwarzinger et al., 2000).