LiteFold/DisProt huggingface dataset:
Protein: DP04199 (UniProt Q9C7W1)
Region: residues 165	to 178
Annotation: RNA folding (Biological process)
Evidence: fluorescence resonance energy transfer evidence used in manual assertion
Supporting statements:
In contrast to RNA alone (Kann = 0.0051 s−1), PARCL increased the 21R+ and 21R- RNA annealing activity about 4-fold (Kann = 0.019 s−1), a similar activity as measured with StpA that is known to facilitate RNA strand displacement and annealing (56, 57). The annealing activity was concentration dependent and decreased with RNA protein ratios lower than 1:100. Larger ratios led to a saturating effect with a Kann up to 0.02 s−1 (Fig. 3B). 
RNA chaperone effects and solution structure of AtPARCL.
Protein: DP04200 (UniProt A0A078IB52)
Region: residues 1	to 150
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The purified AtPARCL and BnPARCL proteins were further subjected to CD measurements including diverse potential ligands like divalent ions, tRNA, and detergents for an initial structural characterization. The measurements showed that both proteins are highly unstructured with no detectable β-sheets and an α-helix content below 5% (Table 1 and Fig. S9). Although approximately 19% shorter than the Arabidopsis protein, BnPARCL showed the same level of disorder. Addition of tRNA had no effect on secondary structure (Table 1).
Protein: DP04200 (UniProt A0A078IB52)
Region: residues 1	to 5
Annotation: acetylation display site (Disorder function)
Evidence: mass spectrometry evidence used in manual assertion
Supporting statements:
Additionally, an N-terminal acetylation site was identified by MS (Fig. S2).
Protein: DP04200 (UniProt A0A078IB52)
Region: residues 1	to 150
Annotation: RNA binding (Molecular function)
Evidence: microscale thermophoresis evidence used in manual assertion
Supporting statements:
To verify this, different long and short RNAs and DNAs were used for in vitro Microscale thermophoresis (MST) assays: the phloem-abundant 21 nucleotide long miRNAs 398, 164, and 396 (2, 3) as RNA and complementary DNA, full-length folded transfer tRNAMet, PARCL mRNA, and a 21-nucleotide long RNA probe (21R-) that does not form any secondary structures was used to confirm RNA chaperone activity (56, 57).
While the dissociation constants (Kd) for RNAs were in the low μM range, the Kd for DNA could not be determined (>500 μM), showing that PARCL has a strong preference for RNA (Fig. S3A and Table S3). PARCL showed similar binding affinities towards phloem RNAs of different lengths (miRNAs, tRNA, mRNA), with equilibrium dissociation constants (Kd) ranging between 1.3 and 2.9 μM (Fig. 2B and Table S3).
Protein: DP04201 (UniProt Q9LYG9)
Region: residues 1	to 164
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
We purified recombinant C-terminally His-tagged MSL10N (Figure 2a) and performed far-UV circular dichroism (CD) spectroscopy. Measured spectra at 20°C presented a minimum near 200 nm (202 nm), which is typical of disordered proteins (Na et al., 2018) (Figure 2b). The slight shoulder visible at 222 nm is indicative of residual helical structure (Greenfield, 2006).
Protein: DP04201 (UniProt Q9LYG9)
Region: residues 1	to 165
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
However, the N-terminal ‘death’ domain (residues 1–165), part of the cytoplasmic domain between TM4 and TM5, including residues 335–386, 397–431, and 469–480, and the C-terminal end (residues 732–734), were not resolved in the reconstruction, and thus were absent in the final refined atomic model.
Cross-references: EMDB:41164
PDB:8TDJ
Protein: DP04201 (UniProt Q9LYG9)
Region: residues 335	to 386
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
However, the N-terminal ‘death’ domain (residues 1–165), part of the cytoplasmic domain between TM4 and TM5, including residues 335–386, 397–431, and 469–480, and the C-terminal end (residues 732–734), were not resolved in the reconstruction, and thus were absent in the final refined atomic model.
Cross-references: EMDB:41164
PDB:8TDJ
Protein: DP04201 (UniProt Q9LYG9)
Region: residues 397	to 431
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
However, the N-terminal ‘death’ domain (residues 1–165), part of the cytoplasmic domain between TM4 and TM5, including residues 335–386, 397–431, and 469–480, and the C-terminal end (residues 732–734), were not resolved in the reconstruction, and thus were absent in the final refined atomic model.
Cross-references: EMDB:41164
PDB:8TDJ
Protein: DP04201 (UniProt Q9LYG9)
Region: residues 469	to 480
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
However, the N-terminal ‘death’ domain (residues 1–165), part of the cytoplasmic domain between TM4 and TM5, including residues 335–386, 397–431, and 469–480, and the C-terminal end (residues 732–734), were not resolved in the reconstruction, and thus were absent in the final refined atomic model.
Cross-references: EMDB:41164
PDB:8TDJ
Protein: DP04201 (UniProt Q9LYG9)
Region: residues 313	to 506
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Owing to the limited dimension of lipid nanodiscs generated by membrane scaffold proteins38, we decided to reconstitute AtMSL10 in a lipid environment using saposin lipid nanoparticles39 and determined the cryo-EM structure at an overall resolution of ~3.6 Å (Fig. 3d, Supplementary Fig. 4), which is similar to the structure of AtMSL10 in detergents (root-mean-square deviation (r.m.s.d) of ~1.6 Å for all Cα atoms).
Interestingly, the CLD between TM4 and TM5 was completely disordered in the lipid environment, further indicating structural flexibility of this peripheral domain.
Cross-references: EMDB:41166
PDB:8TDL
Protein: DP04201 (UniProt Q9LYG9)
Region: residues 1	to 164
Annotation: self-assembly (Disorder function)
Evidence: yeast 2-hybrid evidence used in manual assertion
Supporting statements:
Furthermore, the soluble N-terminus (MSL101–164) and the C-terminal half of MSL10 (MSL10461–734) interacted, as did the N-terminal half of MSL10 (MSL101–460) and the soluble C-terminus (MSL10553–734). This result showed that the middle part of the protein—which contains all the TM helices—is not required for self-association.
Here we present several lines of evidence in support of a direct interaction between the soluble N-terminus and the soluble C-terminus of the plant mechanosensitive ion channel AtMSL10.
Protein: DP04202 (UniProt P0A567)
Region: residues 86	to 100
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
A striking feature of the complex is the disordered N- and particularly C-termini of both proteins (residues 2–5 and 86–100 in CFP-10 and 1–3 and 86–95 in ESAT-6), which form long flexible arms at both ends of the four-helix bundle core.
Cross-references: PDB:1WA8
Protein: DP04202 (UniProt P0A567)
Region: residues 86	to 100
Annotation: flexible C-terminal tail (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
A striking feature of the complex is the disordered N- and particularly C-termini of both proteins (residues 2–5 and 86–100 in CFP-10 and 1–3 and 86–95 in ESAT-6), which form long flexible arms at both ends of the four-helix bundle core.
Cross-references: PDB:1WA8
Protein: DP04203 (UniProt P9WNK7)
Region: residues 86	to 95
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
A striking feature of the complex is the disordered N- and particularly C-termini of both proteins (residues 2–5 and 86–100 in CFP-10 and 1–3 and 86–95 in ESAT-6), which form long flexible arms at both ends of the four-helix bundle core.
Cross-references: PDB:1WA8
Protein: DP04203 (UniProt P9WNK7)
Region: residues 86	to 95
Annotation: flexible C-terminal tail (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
A striking feature of the complex is the disordered N- and particularly C-termini of both proteins (residues 2–5 and 86–100 in CFP-10 and 1–3 and 86–95 in ESAT-6), which form long flexible arms at both ends of the four-helix bundle core.
Cross-references: PDB:1WA8
Protein: DP04208 (UniProt T2B9R0)
Region: residues 1	to 30
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The first 30 residues of the N-terminal region of MERS-CoV NTD+, corresponding to a disordered region, could not be resolved. This region was previously scarcely resolved in all structures obtained using X-ray diffraction techniques, while it was resolved as far as amino acid 24 in the 1ssk structure measured in solution by NMR.
Cross-references: PDB:4UD1
Protein: DP04208 (UniProt T2B9R0)
Region: residues 1	to 30
Annotation: flexible N-terminal tail (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The first 30 residues of the N-terminal region of MERS-CoV NTD+, corresponding to a disordered region, could not be resolved. This region was previously scarcely resolved in all structures obtained using X-ray diffraction techniques, while it was resolved as far as amino acid 24 in the 1ssk structure measured in solution by NMR
Cross-references: PDB:4UD1
Protein: DP04210 (UniProt Q9FN03)
Region: residues 397	to 423
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Our measurements showed characteristic intrinsically disordered protein (IDP)-like features for the UVR8C27 peptide, with a strong negative peak at 198 nm and a negative shoulder around 220 nm (Fig. 1A)
Protein: DP04210 (UniProt Q9FN03)
Region: residues 397	to 423
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The naturally abundant 1H-15N HSQC NMR spectrum for UVR8C27 recorded at 25  °C in 10% D2O at pH6 is shown in Fig. 1E. From this spectrum it is obvious that all 24 backbone NH-groups (not counting prolines and the N-terminal residue) can be found within the same narrow spectral window (8.6 ppm-7.7 ppm) in the 1H-dimension. The indicated spectral range is typical for intrinsically disordered proteins reflecting the dynamic nature of the peptide24,25.
Protein: DP04211 (UniProt Q9BZV1)
Region: residues 1	to 133
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
Although the positive values correlated with most of the defined partially transient secondary structural elements and point toward restricted backbone motility, the overall hetNOE values were below 0.5, indicating that UBXD1-N is a flexible region lacking a rigid three-dimensional folding topology.
Protein: DP04211 (UniProt Q9BZV1)
Region: residues 1	to 133
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
CD spectrum of UBXD1-N showing an unstructured protein with α-helical character. deg, degrees. C, analysis of Hα chemical shift differences with respect to random coil values (30).
Protein: DP04211 (UniProt Q9BZV1)
Region: residues 1	to 133
Annotation: flexible N-terminal tail (Disorder function)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
The flexible N-terminal region of UBXD1 contains the well defined α-helical VIM, which is known to bind the groove between the two subdomains of p97-N (23, 32). This interaction was also confirmed by our NMR spectroscopic studies at the atomic level.
Protein: DP04211 (UniProt Q9BZV1)
Region: residues 1	to 154
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
The 1H-15N HSQC NMR spectrum of UBXD1-N(1–133) (Fig. 2A) showed 109 NH signals, most of which were dispersed over less than 1 ppm along the 1H dimension (∼7.8–8.6 ppm). Neither extension of the N terminus of UBXD1 to Val154 nor reduction to Arg80 had any apparent effect on signal dispersion, indicating that all three constructs share a common core structure.
Protein: DP04211 (UniProt Q9BZV1)
Region: residues 52	to 63
Annotation: ATPase binding (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
The mutation (R62A/L63A) of the VIM in UBXD1-N leads to a loss of binding of UBXD1-N to p97-N throughout the VIM, whereas binding still occurs through amino acids of the N terminus of UBXD1 (Gly20, Gln21, Lys22, and Lys30).
Protein: DP04214 (UniProt P40399)
Region: residues 85	to 112
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron density map does not reveal the conformation of residues 85–112, and these amino acids are missing from the final structure; we assume them to be disordered.
Cross-references: PDB:1W53
Protein: DP04215 (UniProt Q9JK62)
Region: residues 261	to 335
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The distal intracellular C-terminal region was not resolved, suggesting it is conformationally heterogenous or unstructured as observed in previous K2P crystal structures18-21.
Cross-references: PDB:6WM0
PDB:6WLV
Protein: DP04216 (UniProt P0CAV4)
Region: residues 139	to 255
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Although full-length SkgA (residues 1–255) protein was used for crystallization, only residues 1–138 were observed in the final structure. The established structure consists of the N-terminal MerR-type HTH motif, coiled-coil region, and the initial two α-helices of the C-terminal TipAS domain (Fig. 1B and Fig. S1B), whereas the rest of the TipAS domain was still invisible in the current model, probably because of structural flexibility or diffraction damage.
Cross-references: PDB:7CLA
Protein: DP04217 (UniProt Q2KHT3)
Region: residues 892	to 1050
Annotation: mitophagy (Biological process)
Evidence: flow cytometry evidence used in manual assertion
Supporting statements:
To determine whether loss of the CLEC16A C-terminal IDPR impairs mitophagy, we used several complementary approaches in primary islets and in MEFs. We examined key steps of mitophagy following mitochondrial damage, including turnover of outer mitochondrial membrane proteins, such as MFN2 (mitofusin 2), and clearance of damaged mitochondria by targeting to the lysosome [43]. We observed impaired MFN2 turnover in isolated Clec16acurt/curt islets following exposure to the mitochondrial ionophore valinomycin, which is suggestive of impaired mitophagy flux (Figure 3D and S4E). Next, we intercrossed the mt-Keima mitophagy reporter model with Clec16acurt/curt mice. Mt-Keima mice express a fluorescently labeled pH-sensitive mitochondrial biosensor that shifts excitation spectra based on pH [44]. Mt-Keima allows for detection of mitophagy as mitochondria are targeted to acidic autophagosomes/lysosomes for degradation. Flow cytometry of dissociated islets revealed that mt-Keima;Clec16acurt/curt β-cells had an increase in cells with mitochondria in acidic compartments (Figure 3E). This suggests that Clec16acurt/curt β-cells accumulate mitochondria in acidic autophagosomes or lysosomes that may be incompletely cleared, consistent with previous observations following CLEC16A deficiency in β-cells [6].
Protein: DP04217 (UniProt Q2KHT3)
Region: residues 892	to 1052
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We next investigated CLEC16A C-terminal structure using nuclear magnetic resonance (NMR). In an IDPR, backbone hydrogen atoms do not participate in hydrogen bonds that generate secondary structure, and instead are found in a flexible extended conformation. Thus, all backbone hydrogen atoms in an IDPR are in a similar chemical environment and are tightly clustered in the hydrogen dimension of an 1H-15N heteronuclear single quantum coherence/HSQC-NMR spectrum [35]. The heteronuclear single quantum coherence-NMR spectrum of the CLEC16A C terminus was tightly clustered in the hydrogen dimension between 8–8.5 ppm, which strongly suggests that the CLEC16A C terminus is an IDPR (Figure 1F).
1H-15N HSQC spectra of recombinant CLEC16A C terminus (AA 892–1050). Spectra clusters near 1H 8ppm, consistent with being an IDPR.
Protein: DP04217 (UniProt Q2KHT3)
Region: residues 892	to 1052
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
While Flag epitope-tagged full-length CLEC16A and a C-terminal deficient CLEC16A mutant (CLEC16A ∆C) migrated at their expected molecular mass, a CLEC16A construct encoding only the C terminus migrated more slowly, at nearly double its expected molecular mass (Figure 1E).
Protein: DP04218 (UniProt Q9V9N4)
Region: residues 41	to 86
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence used in manual assertion
Supporting statements:
All HN chemical shifts of the 1–86 region are plotted into the interval from 7.6 to 8.6 ppm. These chemical shift values correspond to the unstructured protein chain [49] (Figure 3a).
To ensure that CLAMP41−86 is unstructured, we obtained 15N-labeled CLAMP41−153 and compared its HSQC spectrum with CLAMP87−153. As most signals in 87–153 are still present at their places in the spectrum of CLAMP40−153, we can assign the rest of the signals to the 41–86 region (Figure S5). In total, 38 peaks were found corresponding to that region (most probably several of them represent more than one signal because of peak overlapping). All HN chemical shifts of the 41–86 region also fall into the interval from 7.6 to 8.6 ppm, suggesting a lack of the secondary structure [49]. Additionally, we measured transverse relaxation rates (R2) to assess the protein chain mobility in different regions. R2 reflects protein chain mobility and can be used to measure disordered state of the protein [50]
he averaged R2 value for 41–86 is 2.2 ± 1.3 s, whereas for 89–119 (unfolded region preceding the zinc-finger) it is 2.9 ± 0.8 s, and 4.6 ± 0.8 s for 122–151 (zinc-finger domain). Thus, we conclude that according to NMR data the CLAMP41−86 region is unstructured.
Protein: DP04218 (UniProt Q9V9N4)
Region: residues 41	to 86
Annotation: protein homodimerization activity (Molecular function)
Evidence: yeast 2-hybrid evidence used in manual assertion
Supporting statements:
Results of the Y2H assay of dimerization activity of the CLAMP N-terminal region shown for the domain structure of the CLAMP protein. AD stands for GAL4 activation domain and BD stands for GAL4 DNA-binding domain. Positive interaction indicates the ability of yeast to grow on assay plates without histidine
Protein: DP04218 (UniProt Q9V9N4)
Region: residues 1	to 86
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
All HN chemical shifts of the 1–86 region are plotted into the interval from 7.6 to 8.6 ppm. These chemical shift values correspond to the unstructured protein chain [49] (Figure 3a).
Protein: DP04218 (UniProt Q9V9N4)
Region: residues 89	to 119
Annotation: disorder (Structural state)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
The averaged R2 value for 41–86 is 2.2 ± 1.3 s, whereas for 89–119 (unfolded region preceding the zinc-finger) it is 2.9 ± 0.8 s, and 4.6 ± 0.8 s for 122–151 (zinc-finger domain).
Protein: DP04218 (UniProt Q9V9N4)
Region: residues 1	to 113
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The same plot of CLAMP1–113 only revealed the presence of a small bell-shaped area, suggesting that it does not represent a completely unfolded polypeptide chain but rather lacks a stable spatial structure (Figure 3c).
Thus, the NMR and SAXS data suggest that the N-terminal domain of CLAMP preceding the zinc-finger has the features of an IDR.
This experiment shows this region lacks a fixed 3D structure.
Protein: DP04218 (UniProt Q9V9N4)
Region: residues 41	to 86
Annotation: protein homodimerization activity (Molecular function)
Evidence: cross-linking evidence used in manual assertion
Supporting statements:
Using chemical cross-linking (Figure 2a,c) and size-exclusion chromatography (Figure 2b) experiments, we demonstrated that the CLAMP1–127 can form multimers (presumably dimers) similar to CLAMP1–153. Shortening of the region to 1–113 amino acids and deleting the first 40 residues only weakly reduced the efficiency of cross-linking, supporting the data of Y2H (Figure 2a). Further shortening of the region decreased the cross-linking efficiency (Figure 2a and Figure S3), likely because cross-linking is dependent on the presence of neighbor lysines; thus, it is not suitable for the precise mapping of the dimerization motif and was not used on smaller fragments.
Protein: DP04218 (UniProt Q9V9N4)
Region: residues 41	to 86
Annotation: protein homodimerization activity (Molecular function)
Evidence: glutathione S-transferase pull-down assay evidence used in manual assertion
Supporting statements:
Interactions between 6xHis thioredoxin- or glutathione S-transferase (GST)-tagged CLAMP deletion derivatives were further studied with a pull-down assay after co-expression in bacteria cells (Figure 2c and Figure S4). Because CLAMP1–113 binds non-specifically to Ni-NTA resin, 6xHis pull-down was used only as protein expression control. CLAMP41–113 interacts efficiently with the larger GST-tagged CLAMP1–113 polypeptide; however, the interaction between CLAMP1–91 and CLAMP1–113 polypeptides was slightly impaired. The 87–153 fragment lacking most of the dimerization sequences did not interact with CLAMP1–113. Taken together, these results suggest that the 46–86 amino acids are sufficient for dimerization and include two modules that can both form dimers.
Protein: DP04218 (UniProt Q9V9N4)
Region: residues 1	to 86
Annotation: protein homodimerization activity (Molecular function)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
SAXS provides precise information about the size of macromolecules in solution that is almost independent of their shape [48].
By contrast, the molecular weight estimation for CLAMP87–153 resulted in values in the range 5.1–6.8 kDa, which corresponds to the monomer. The estimated molecular weight CLAMP1–113 falls into the range of 20–24 kDa, which confirms that it exists as a dimer in solution.