LiteFold/DisProt huggingface dataset:
Protein: DP02312 (UniProt Q8T9B6)
Region: residues 19	to 91
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
We used limited proteolysis to map the domain structure of the mature proteins from three family members: Mus musculus (mm) Mesd; Drosophila melanogaster (dm) Boca; and Caenorhabditis elegans (ce) BMY-1. Each of these proteins reveals a similar proteolytic profile (Figure S1). The variable sequences from the N- and C-termini of the mature protein are removed at low protease concentrations. At higher protease concentrations, the rapid removal of an additional ~50 residues from the N-terminus generates a ~10 kDa protease-resistant fragment.
Protein: DP02312 (UniProt Q8T9B6)
Region: residues 31	to 91
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Nearly all the dispersed peaks within the CC spectra overlap with those of the SD spectra, implying that SD includes all of the well structured regions of the CC. The extra ~50 residues in the N-terminal region of dmBocaCC have resonance frequencies corresponding to those of an unstructured peptide, typified by limited dispersion centered at 1H resonance frequencies of ~8.2 ppm.
Protein: DP02313 (UniProt Q8IG33)
Region: residues 18	to 88
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
We used limited proteolysis to map the domain structure of the mature proteins from three family members: Mus musculus (mm) Mesd; Drosophila melanogaster (dm) Boca; and Caenorhabditis elegans (ce) BMY-1. Each of these proteins reveals a similar proteolytic profile (Figure S1). The variable sequences from the N- and C-termini of the mature protein are removed at low protease concentrations. At higher protease concentrations, the rapid removal of an additional ~50 residues from the N-terminus generates a ~10 kDa protease-resistant fragment.
Protein: DP02314 (UniProt Q9ERE7)
Region: residues 30	to 102
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
We used limited proteolysis to map the domain structure of the mature proteins from three family members: Mus musculus (mm) Mesd; Drosophila melanogaster (dm) Boca; and Caenorhabditis elegans (ce) BMY-1. Each of these proteins reveals a similar proteolytic profile (Figure S1). The variable sequences from the N- and C-termini of the mature protein are removed at low protease concentrations. At higher protease concentrations, the rapid removal of an additional ~50 residues from the N-terminus generates a ~10 kDa protease-resistant fragment.
Protein: DP02314 (UniProt Q9ERE7)
Region: residues 29	to 92
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
The majority of potential trypsin and V8 protease cleavage sites are highly protected within a core region spanning residues 64-150, indicating that this part of the protein represents a core, folded domain.

Note: residue numbers correspond to the mature form of the protein and have been amended in this entry.
Protein: DP02316 (UniProt O43663)
Region: residues 467	to 620
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
As we do not observe any additional density past the C terminus of the spectrin domain that is close to the microtubule lattice, we favor the possibility that the Lys/Arg-rich domain is disordered even when PRC1 is bound to a microtubule.
Cross-references: PDB:3NRY
Protein: DP02316 (UniProt O43663)
Region: residues 467	to 620
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
We were unable to detect microtubule associations of single molecules of GFP-PRC1-NS at the concentrations needed to resolve single molecules using TIRF microscopy (<10 nM; data not shown), suggesting that residues in the C terminus domain contribute to microtubule binding
Cross-references: PDB:3NRX
PDB:3NRY
Protein: DP02316 (UniProt O43663)
Region: residues 451	to 486
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The main chain atoms of most of the N-terminal 486 residues in PRC1-NSΔC could be assigned, except the C-terminal 36 residues that were disordered in the crystal and not included in the final model.
Cross-references: PDB:4L3I
Protein: DP02317 (UniProt Q03689)
Region: residues 228	to 289
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
[..] the per-residue chemical shift deviation of HET-S shows that it is composed of an N-terminal mostly helical structured domain comprising at least residues 13–222 followed by an unstructured and flexible C-terminal tail.
Note: Evidence also found in Supplementary Figures S2b and S3.

Note: In constructs roughly corresponding to this region (e.g. PDB:2RNM; Pubmed: 18339938) it forms a left-handed beta solenoid.
Protein: DP02318 (UniProt O14672)
Region: residues 697	to 748
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Consistent with the assessment by SPINE-D, recombinant cytoplasmic domain of human ADAM10 (A10Cp-6H, containing residues Lys697–Arg748 and a C-terminal hexahistidine tag) in the dodecylphosphocholine (DPC) micellar solution (10 mM DPC, 20 mM Tris·HCl, 100 mM NaCl, and 1 mM DTT, pH 8.0) contained little stable secondary structure as indicated by its circular dichroism (CD) spectrum (Fig. 2A and Fig. S1).
Protein: DP02318 (UniProt O14672)
Region: residues 697	to 748
Annotation: order (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
However, recombinant transmembrane-cytoplasmic domains of human ADAM10 (A10TmCp-6H, containing residues Leu666–Arg748 and a C-terminal hexahistidine tag) reconstituted in the same DPC micelles contained significant amount of α-helical structure (Fig. 2A and Fig. S1). Deconvolution of its CD spectrum (α helix: 87%, β strand: 1%, coil: 12%) suggested that most residues in A10TmCp-6H adopt the α-helical conformation (19). Because the transmembrane domain constitutes only 30% of the residues in A10TmCp-6H, significant amount of helical structure should be present in the cytoplasmic domain.
Protein: DP02318 (UniProt O14672)
Region: residues 697	to 748
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Consistent with the assessment by SPINE-D, recombinant cytoplasmic domain of human ADAM10 (A10Cp-6H, containing residues Lys697–Arg748 and a C-terminal hexahistidine tag) in the dodecylphosphocholine (DPC) micellar solution (10 mM DPC, 20 mM Tris·HCl, 100 mM NaCl, and 1 mM DTT, pH 8.0) contained little stable secondary structure as indicated by its circular dichroism (CD) spectrum (Fig. 2A and Fig. S1).
However, recombinant transmembrane-cytoplasmic domains of human ADAM10 (A10TmCp-6H, containing residues Leu666–Arg748 and a C-terminal hexahistidine tag) reconstituted in the same DPC micelles contained significant amount of α-helical structure (Fig. 2A and Fig. S1). Deconvolution of its CD spectrum (α helix: 87%, β strand: 1%, coil: 12%) suggested that most residues in A10TmCp-6H adopt the α-helical conformation (19). Because the transmembrane domain constitutes only 30% of the residues in A10TmCp-6H, significant amount of helical structure should be present in the cytoplasmic domain.
In other words, the cytoplasmic domain of ADAM10 is intrinsically disordered, but in the presence of its neighboring transmembrane domain, it takes on an ordered conformation.
Protein: DP02318 (UniProt O14672)
Region: residues 697	to 748
Annotation: protein homodimerization activity (Molecular function)
Evidence: fluorescence resonance energy transfer evidence used in manual assertion
Supporting statements:
These results indicate that A10TmCp-6H, but not A10Cp-6H, forms homo-oligomers in DPC micelles. It is noteworthy that the protein/detergent molar ratio in this experiment was 1/50,000 (200 nM protein/10 mM DPC). It is much lower than 1/200–1/1,000, a range typically used in the studies of homo-association of transmembrane helical peptides (23–26), suggesting that homo-association of A10TmCp-6H is not mediated by its transmembrane domain.
Overall, these results indicate that the dimerization of A10TmCp is mediated by its cytoplasmic domain.
What is unique and intriguing about our finding is that dimerization of the cytoplasmic domain of ADAM10 requires attachment to a transmembrane domain, yet the attached transmembrane domain does not directly mediate dimerization.
Protein: DP02318 (UniProt O14672)
Region: residues 697	to 748
Annotation: protein homodimerization activity (Molecular function)
Evidence: green fluorescent protein reporter gene assay evidence used in manual assertion
Supporting statements:
Comparison of the GFP fluorescence intensities indicated that, although MBP-a10Tm-AraC exhibited little dimerization in the membrane, MBP-a10TmCp-AraC dimerized as strongly as the positive control (Fig. 5C and Fig. S7).
Consistent with recent reports that the transmembrane and cytoplasmic domains of l-selectin or full-length l-selectin are monomeric in membrane conditions (30, 31), expression of MBP-lselTmCp-AraC induced little GFP fluorescence in the AraTM assay (Fig. 5C). In comparison, expression of MBP-lselTm-a10Cp-AraC produced as strong a GFP fluorescence as the positive control or MBP-A10TmCp-AraC. These results indicate that the cytoplasmic domain of ADAM10, when placed next to an unrelated transmembrane domain, can mediate strong dimerization of the host protein.
Protein: DP02320 (UniProt P0C8E0)
Region: residues 1	to 19
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Conantokins-Pr1 and -Pr2 adopt alpha-helical conformations in the presence of divalent cations (Mg2+ and Ca2+) but are generally unstructured in the absence of divalent cations.
Because con-Pr1, -Pr2, and -Pr3 all shared common characteristics of conantokins, we hypothesized that they would be structurally related to con-G, which adopts an α-helical conformation in solution in the presence of divalent cations. However, it is nearly structureless in the absence of divalent cations (22). To estimate the α-helical content of the C. parius conantokins, circular dichroism spectroscopy was employed. The α-helical content of con-Pr1 and -Pr2 was estimated to be much greater in the presence of Mg2+ or Ca2+ than in the absence of divalent cations, like con-G (Fig. 3).
con-Pr1 is unstructured in the absence of divalent cations, i.e. Mg2+ and Ca2+.
Protein: DP02321 (UniProt P0C8E1)
Region: residues 1	to 19
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Conantokins-Pr1 and -Pr2 adopt alpha-helical conformations in the presence of divalent cations (Mg2+ and Ca2+) but are generally unstructured in the absence of divalent cations.
Because con-Pr1, -Pr2, and -Pr3 all shared common characteristics of conantokins, we hypothesized that they would be structurally related to con-G, which adopts an α-helical conformation in solution in the presence of divalent cations. However, it is nearly structureless in the absence of divalent cations (22). To estimate the α-helical content of the C. parius conantokins, circular dichroism spectroscopy was employed. The α-helical content of con-Pr1 and -Pr2 was estimated to be much greater in the presence of Mg2+ or Ca2+ than in the absence of divalent cations, like con-G (Fig. 3).
con-Pr2 is unstructured in the absence of divalent cations, i.e. Mg2+ and Ca2+.
Protein: DP02322 (UniProt A0LU48)
Region: residues 36	to 80
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final electron density map showed continuous density except for a disordered region between residues 36 to 80.
Although it is disordered in our structure, this region could become more ordered in the presence of substrates or could play a role in the interaction with other potential binding partners.
Cross-references: PDB:4B0R
Protein: DP02323 (UniProt Q5L0X5)
Region: residues 231	to 261
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Fig. 2B shows the fragments obtained when Gste-ecDivIB was proteolyzed with trypsin for 3 h by using a DivIB:protease ratio of 100:1 at ambient temperature (fragment 1, Fig. 2B Left) or by using a DivIB:protease ratio of 200:1 at 37°C (fragment 2, Fig. 2B Right). Five cycles of N-terminal sequencing indicated that fragment 1 had an intact N terminus (i.e., G47SPLG), whereas the N terminus of fragment 2 (E117WRRI) corresponded to a trypsin cleavage after Arg-116 (Fig. 2C). Mass spectrometry indicated that the C terminus of both fragments was Arg-230.
Protein: DP02324 (UniProt P53865)
Region: residues 572	to 581
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
the electron density for the C-terminal residues of Cnm67 (residues His-574—Lys-581) is largely missing. Lys-581 is the C-terminal residue in Cnm67. [Note: they are afterwards demonstrated as disordered residues]
Protein: DP02324 (UniProt P53865)
Region: residues 572	to 581
Annotation: flexible C-terminal tail (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Collectively, the experimental evidence suggests that without its hydrophobic terminus, the seemingly very tight Cnm67 globular dimer (with >4000 Å2 buried!) unfolds and aggregates. The likeliest explanation for this is that the C-terminal residues function as a cover or clamp for a large hydrophobic patch that is evident at the tip of the globular domain adjacent to the dimer interface (Fig. 7A).
Protein: DP02325 (UniProt O60200)
Region: residues 67	to 81
Annotation: disorder (Structural state)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
Residues 67–81 did not exhibit defined electron density, suggesting that the C-terminal segment is disordered in solution.
Cross-references: PDB:4YTV
Protein: DP02326 (UniProt Q05776)
Region: residues 62	to 71
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The crystallographic B-factors of loop Ω1 are high as compared with those for the other regions, suggesting its flexible nature (Fig. 3d). As having been speculated for other START domains with such a flexible Ω loop, the loop Ω1 of Ups1 may function as a lid that regulates lipid binding to the pocket (see below).
Cross-references: PDB:4YTW
Protein: DP02326 (UniProt Q05776)
Region: residues 62	to 71
Annotation: molecular function regulator (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The crystallographic B-factors of loop Ω1 are high as compared with those for the other regions, suggesting its flexible nature (Fig. 3d). As having been speculated for other START domains with such a flexible Ω loop, the loop Ω1 of Ups1 may function as a lid that regulates lipid binding to the pocket (see below).
Protein: DP02326 (UniProt Q05776)
Region: residues 62	to 71
Annotation: lipid binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Deletion of the Ω1 loop (ΔLid) also completely impaired the PA transfer activity of Ups1–Mdm35. These results indicate that conserved basic residues at the bottom and near the entrance of the pocket and the Ω1 lid play essential roles in the PA transfer activity of Ups1–Mdm35.
Protein: DP02327 (UniProt Q00169)
Region: residues 1	to 12
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Electron density for the first 12 or 13 residues was not observed in all cases, because of disorder.
Protein: DP02327 (UniProt Q00169)
Region: residues 119	to 190
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Consistent with their proposed functions, both the regulatory loop and the C-terminal region were predicted to exhibit significant polypeptide backbone flexibility, a structural feature corroborated by specific B factors from the x-ray data.
Protein: DP02327 (UniProt Q00169)
Region: residues 119	to 190
Annotation: molecular recognition display site (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Examination of the PITP structure reveals that the intervening residues 119–190 form an extensive loop region between strands 7 and 8. Postulating that this loop is likely required for the association of PITP with a wide variety of lipid- and protein-modifying enzymes, we refer to this region as the regulatory loop.
Protein: DP02327 (UniProt Q00169)
Region: residues 119	to 190
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
two distinct forms of PITP exist: (1) a “closed” loaded PITP. form in which the PC lipid is buried within the structure and (2) an “open” lipid-free form in which the phosphoIntroduction lipid-binding cavity is opened up and the lipid-exchange loop is swung away from the body of the structure. [The mostly disordered loop acts as a lid]
Cross-references: PDB:1uw5
Protein: DP02327 (UniProt Q00169)
Region: residues 233	to 270
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Consistent with their proposed functions, both the regulatory loop and the C-terminal region were predicted to exhibit significant polypeptide backbone flexibility, a structural feature corroborated by specific B factors from the x-ray data. The relative instability of portions of this helix is supported by the high B-factors calculated for residues 243–250
Protein: DP02327 (UniProt Q00169)
Region: residues 233	to 270
Annotation: order to pre-molten globule (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
It seems that the interaction with lipid vesicles induce a conformational change of the C-terminus domain (helix), which adopts flexible conformation (not described, maybe a partial unfolding). This conformation allows the cleavage by trypsin in arg 253 and 259. This process is needed to extract the lipid from the vesicle.
Protein: DP02330 (UniProt C4PB33)
Region: residues 361	to 395
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The polyserine region in Bombus ignitus and Pimpla nipponica vitellogenin is a random coil.
Protein: DP02331 (UniProt O17428)
Region: residues 356	to 397
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The polyserine region in Bombus ignitus and Pimpla nipponica vitellogenin is a random coil.
Protein: DP02332 (UniProt Q9BUQ8)
Region: residues 1	to 257
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
A) Domain organization of hPrp28. The 100 kDa hPrp28 contains three domains: disordered domain (residues 1–257, green), DEAD box domain (residues 410–642, orange), and HELICc domain (residues 678–759, red). Residues 1–138 comprise the RS domain of hPrp28.
Although full-length hPrp28 has an additional 563 residues, the number of NMR signals in a 15N-1H HSQC spectrum was only slightly increased when compared to hPrp(1–257) (Figure 9A). Thus, the globular parts of hPrp28(1–820) tumble to slowly to be detected by solution-state NMR. Nevertheless, the close match of peak positions for the two proteins demonstrates that conformations of the isolated RS domain are retained in the intact protein.
The poor dispersion in 1H-NMR spectra, with signals clustered around the 8.0-8.5 ppm region, shows this region is disordered.
Protein: DP02332 (UniProt Q9BUQ8)
Region: residues 1	to 138
Annotation: phosphorylation display site (Disorder function)
Evidence: mass spectrometry evidence used in manual assertion
Supporting statements:
(B) Mass spectrometric (MS) determination of phosphorylation sites within the
N-terminal RS domain of hPrp28 in native U5 snRNP (square) and functional
spliceosomal B complex (circle).
Here, we analyzed the phosphorylation sites of hPrp28 in U5 snRNPs and assembled B complexes by mass spectrometry. The analysis identified serine residues at positions 14, 23, 38, 39, 41, 65, 67, 106, 107, 109, as well as T25, to be phosphorylated in both complexes (Figure 8B; Table S3). Phosphorylation at S16
and S63 was found only in U5 snRNP.
Table S3, related to Figure 8 | Phosphorylation sites (marked in red) in the RS domain of hPrP28 as identified by mass spectrometry in native U5 snRNP and spliceosomal B complex.
Protein: DP02332 (UniProt Q9BUQ8)
Region: residues 807	to 820
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final hPrp28ΔN model consists of residues 352–806, five sulfate
ions, two glycerol molecules, 3-cyclohexyl-1-propylsulfonic acid, one disordered Hg atom and 220 solvent molecules. Missing residues, namely the N-terminal residues 338–351, loops 695–702 and 724–727 and the C-terminal residues 807–820, resulted from non-interpretable electron density and are most likely to be disordered.
Two loop regions (residues 695–702 and 724–727) as well as the N-terminal residues 338–351 and the C-terminal residues 807–820 are not defined in the electron-density map and are most likely to be disordered.
Cross-references: PDB:4NHO
Protein: DP02332 (UniProt Q9BUQ8)
Region: residues 791	to 820
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The Electron Microscopy structure of the Precusor of Human Pre-catalytic Spliceosome (pre-B complex), shows this region of the Probable ATP-dependent RNA helicase DDX23 (alternative name Prp28) lacks electron density, indicating it is disordered.
Cross-references: PDB:6AH0
EMDB:EMD-9621
Protein: DP02332 (UniProt Q9BUQ8)
Region: residues 1	to 157
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The Electron Microscopy structure of the human U5.U4/U6 tri-snRNP and human fully-assembled precatalytic spliceosome (pre-B complex), shows this region of the Probable ATP-dependent RNA helicase DDX23 (alternative name Prp28) lacks electron density, indicating it is disordered.
Cross-references: PDB:6QX9
PDB:6QW6
EMDB:EMD-4665
EMDB:EMD-4658