LiteFold/DisProt huggingface dataset:
Protein: DP01467 (UniProt Q9SP32)
Region: residues 1732	to 1811
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
NOESY-15N-HSQC spectra of the protein show few NOE crosspeaks, corresponding to intra and i-1 correlations, further supporting the absence of a stable structure.
Protein: DP01467 (UniProt Q9SP32)
Region: residues 1732	to 1811
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
We employed SAXS data to obtain information on global shape of the ensemble. The Kratky plot shows the typical features of disordered proteins.
Protein: DP01467 (UniProt Q9SP32)
Region: residues 1	to 249
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The cryo-EM structures of  Arabidopsis DCL1 in complex with pre-miRNA and pri-miRNA show this region lacks electron density, indicating it is disordered.
Cross-references: PDB:7ELE
PDB:7ELD
EMDB:31181
EMDB:31182
Protein: DP01467 (UniProt Q9SP32)
Region: residues 494	to 525
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The cryo-EM structures of  Arabidopsis DCL1 in complex with pre-miRNA and pri-miRNA show this region lacks electron density, indicating it is disordered.
Cross-references: PDB:7ELE
PDB:7ELD
EMDB:31181
EMDB:31182
Protein: DP01467 (UniProt Q9SP32)
Region: residues 595	to 650
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The cryo-EM structures of  Arabidopsis DCL1 in complex with pre-miRNA and pri-miRNA show this region lacks electron density, indicating it is disordered.
Cross-references: PDB:7ELE
PDB:7ELD
EMDB:31181
EMDB:31182
Protein: DP01467 (UniProt Q9SP32)
Region: residues 921	to 974
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Linkers between the DUF283 and the Platform (residues 921–974), between the Platform and the PAZ (residues 1,114–1,198) and between two RNase III domains (residues 1,532–1,557) are not modelled because of the high flexibility of these fragments.
Cross-references: PDB:7ELE
PDB:7ELD
EMDB:31181
EMDB:31182
Protein: DP01467 (UniProt Q9SP32)
Region: residues 921	to 974
Annotation: flexible linker (Disorder function)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Linkers between the DUF283 and the Platform (residues 921–974), between the Platform and the PAZ (residues 1,114–1,198) and between two RNase III domains (residues 1,532–1,557) are not modelled because of the high flexibility of these fragments.
Cross-references: PDB:7ELE
PDB:7ELD
EMDB:31181
EMDB:31182
Protein: DP01467 (UniProt Q9SP32)
Region: residues 985	to 1006
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The cryo-EM structures of Arabidopsis DCL1 in complex with pre-miRNA and pri-miRNA show this region lacks electron density, indicating it is disordered.
Cross-references: PDB:7ELE
PDB:7ELD
EMDB:31181
EMDB:31182
Protein: DP01467 (UniProt Q9SP32)
Region: residues 1070	to 1100
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The cryo-EM structures of Arabidopsis DCL1 in complex with pre-miRNA and pri-miRNA show the regions 1070-1084 and 1092-1100 lack electron density. Even though the residue 1085-1091 are present in the structure, the region is too short to be considered as structured, therefore the whole region 1070-1100 is considered as disordered.
Cross-references: PDB:7ELE
PDB:7ELD
EMDB:31181
EMDB:31182
Protein: DP01467 (UniProt Q9SP32)
Region: residues 1114	to 1198
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Linkers between the DUF283 and the Platform (residues 921–974), between the Platform and the PAZ (residues 1,114–1,198) and between two RNase III domains (residues 1,532–1,557) are not modelled because of the high flexibility of these fragments.
Cross-references: PDB:7ELE
PDB:7ELD
EMDB:31181
EMDB:31182
Protein: DP01467 (UniProt Q9SP32)
Region: residues 1114	to 1198
Annotation: flexible linker (Disorder function)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Linkers between the DUF283 and the Platform (residues 921–974), between the Platform and the PAZ (residues 1,114–1,198) and between two RNase III domains (residues 1,532–1,557) are not modelled because of the high flexibility of these fragments.
Cross-references: PDB:7ELE
PDB:7ELD
EMDB:31181
EMDB:31182
Protein: DP01467 (UniProt Q9SP32)
Region: residues 1283	to 1299
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The cryo-EM structures of Arabidopsis DCL1 in complex with pre-miRNA and pri-miRNA show this region lacks electron density, indicating it is disordered.
Cross-references: PDB:7ELE
PDB:7ELD
EMDB:31181
EMDB:31182
Protein: DP01467 (UniProt Q9SP32)
Region: residues 1431	to 1494
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The cryo-EM structures of Arabidopsis DCL1 in complex with pre-miRNA and pri-miRNA show this region lacks electron density, indicating it is disordered.
Cross-references: PDB:7ELE
PDB:7ELD
EMDB:31181
EMDB:31182
Protein: DP01467 (UniProt Q9SP32)
Region: residues 1532	to 1557
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Linkers between the DUF283 and the Platform (residues 921–974), between the Platform and the PAZ (residues 1,114–1,198) and between two RNase III domains (residues 1,532–1,557) are not modelled because of the high flexibility of these fragments.
Cross-references: PDB:7ELE
PDB:7ELD
EMDB:31181
EMDB:31182
Protein: DP01467 (UniProt Q9SP32)
Region: residues 1532	to 1557
Annotation: flexible linker (Disorder function)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Linkers between the DUF283 and the Platform (residues 921–974), between the Platform and the PAZ (residues 1,114–1,198) and between two RNase III domains (residues 1,532–1,557) are not modelled because of the high flexibility of these fragments.
Cross-references: PDB:7ELE
PDB:7ELD
EMDB:31181
EMDB:31182
Protein: DP01467 (UniProt Q9SP32)
Region: residues 1670	to 1688
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The cryo-EM structures of Arabidopsis DCL1 in complex with pre-miRNA and pri-miRNA show this region lacks electron density, indicating it is disordered.
Cross-references: PDB:7ELE
PDB:7ELD
EMDB:31181
EMDB:31182
Protein: DP01467 (UniProt Q9SP32)
Region: residues 1795	to 1909
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The cryo-EM structures of Arabidopsis DCL1 in complex with pre-miRNA and pri-miRNA show this region lacks electron density, indicating it is disordered.
Cross-references: PDB:7ELE
PDB:7ELD
EMDB:31181
EMDB:31182
Protein: DP01467 (UniProt Q9SP32)
Region: residues 1732	to 1909
Annotation: double-stranded RNA binding (Molecular function)
Evidence: fluorescence polarization evidence used in manual assertion
Supporting statements:
The affinity of the isolated DCL1-A construct for pri-miR172a fragments is similar to the one determined previously for DCL1-B (13). DCL1-A RNA binding affinity is somewhat higher for the pri-miR172a-ls construct than for the miR172a stem loop. The secondary structure of the former is less regular than that of the latter, including one mismatch and three G•U wobble base pairs, thus suggesting that DCL1-A may have some preference for imperfect dsRNA segments. In contrast, the double domain DCL1-AB shows an affinity one order of magnitude higher for the miR172a stem-loop and threefold higher for the primiR172a-ls construct, indicating that both domains participate jointly in the recognition of the substrate.
Protein: DP01467 (UniProt Q9SP32)
Region: residues 1732	to 1811
Annotation: DNA binding (Molecular function)
Evidence: fluorescence anisotropy evidence used in manual assertion
Supporting statements:
We found that both constructs do bind dsDNA, showing that DCL1-A is also peculiar in terms of nucleic acid recognition with respect to other dsRBDs. The affinity of the double domain for dsDNA is similar to that for both isolated domains, indicating that in this case the domains behave as independent binding units.
Protein: DP01467 (UniProt Q9SP32)
Region: residues 1826	to 1909
Annotation: DNA binding (Molecular function)
Evidence: fluorescence anisotropy evidence used in manual assertion
Supporting statements:
We found that both constructs do bind dsDNA, showing that DCL1-A is also peculiar in terms of nucleic acid recognition with respect to other dsRBDs. The affinity of the double domain for dsDNA is similar to that for both isolated domains, indicating that in this case the domains behave as independent binding units.
Protein: DP01467 (UniProt Q9SP32)
Region: residues 1732	to 1811
Annotation: double-stranded RNA binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
We first tested this by following the formation of DCL1-A:RNA complex by CD spectroscopy ​(Figure 3A) using the pri-miR172a-ls construct. The free protein shows the characteristic spectrum of unfolded polypeptides, with a negative minimum at ca. 200 nm. Addition of RNA immediately changes the spectrum in the far UV region, but due to the intense negative band of dsRNA at 210 nm it is hard to determine if the protein develops secondary structure.
Protein: DP01467 (UniProt Q9SP32)
Region: residues 1732	to 1811
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
We first tested this by following the formation of DCL1-A:RNA complex by CD spectroscopy ​(Figure 3A) using the pri-miR172a-ls construct. The free protein shows the characteristic spectrum of unfolded polypeptides, with a negative minimum at ca. 200 nm. Addition of RNA immediately changes the spectrum in the far UV region, but due to the intense negative band of dsRNA at 210 nm it is hard to determine if the protein develops secondary structure.
Two of the basis spectra correspond well with the spectra of the free protein and of the free RNA, whereas the third component closely matches the spectrum of canonical dsRBDs (Supplementary Figure S6), suggesting that DCL1-A acquires the same secondary structure as other stably folded homologs.
However, the contribution of the folded protein component to the spectra can clearly be noticed at 10 equivalents added protein.
Protein: DP01467 (UniProt Q9SP32)
Region: residues 1732	to 1811
Annotation: DNA binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectra of DCL1-A:DNA complexes show a slight shift in the minimum from 200 to 202 nm, and a small variation in the CD200nm/CD220nm ratio, demonstrating that binding to DNA induces a variation in the conformational sampling of the protein, but this still remains disordered (Supplementary Figure S9).
Protein: DP01468 (UniProt A3RMR8)
Region: residues 1658	to 1856
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
It exhibits a reduced chemical shift dispersion, especially in the 1H dimension between 8.5 and 7.5 ppm (Fig. 1C), which is a characteristic of the intrinsically disordered proteins (42).
We carried out detailed characterization of a 199-aa-long CHIKV HVD by NMR spectroscopy at atomic resolution. The results revealed the absence of stable secondary structures in this domain and clearly demonstrated that CHIKV HVD was present in solution in a disordered conformation.
IDR in the publication is 100% identical to this Uniprot sequence.
Protein: DP01468 (UniProt A3RMR8)
Region: residues 1761	to 1856
Annotation: protein binding (Molecular function)
Evidence: qualitative western immunoblotting evidence used in manual assertion
Supporting statements:
Western blot analysis with NAP1L1-specific Abs also definitively detected the latter protein in the co-IP samples generated on the cells infected with VEErep/Flag-GFP-ABCD but not with any other constructs, including VEErep/Flag-GFP-ABC and VEErep/Flag-GFP-123D (Fig. 8B). The most plausible explanation for the lack of NAP1L1 binding to CHIKV HVD deletion mutant constructs was that NAP1L1 binding requires the presence of intact aa sequences of both fragments C and D. Indeed, two isoforms of NAP1L1 were readily detectable in the samples generated from the cells infected with replicons expressing Flag-GFP-12CD and Flag-GFP-12(C3)D fusions (Fig. 8C). This was an indication that NAP1L1 interacts with HVD on the border between C and D fragments (see Fig. 11).
IDR in the publication is 100% identical to this Uniprot sequence.
Protein: DP01468 (UniProt A3RMR8)
Region: residues 1658	to 1856
Annotation: viral life cycle (Biological process)
Evidence: green fluorescent protein reporter gene assay evidence used in manual assertion
Supporting statements:
These experimental data strongly suggested that HVDs play critical roles in the adaptation of CHIKV and EILV to replication in particular cell types. Despite having very similar G3BP-binding repeating peptides, heterologous HVDs changed cell specificities of replication for both viruses. This was a strong support for the hypothesis that HVD fragments located upstream of the carboxy-terminal G3BP/Rin-binding repeat play an indispensable role in CHIKV replication.
In the case of CHIKV, G3BP binding is particularly critical. In contrast to the results of the studies performed on SINV and SFV, deletion of even a single element of the G3BP-binding HVD repeat had a strong negative effect on CHIKV replication in both vertebrate and mosquito cells (Fig. 2) (34). Deletion of both elements, in turn, completely abrogated virus replication.
IDR in the publication is 100% identical to this Uniprot sequence.
Protein: DP01468 (UniProt A3RMR8)
Region: residues 1658	to 1856
Annotation: molecular adaptor activity (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
In vertebrate cells, CHIKV HVD also coimmunoprecipitated cellular SH3-binding proteins BIN1, CD2AP, and SH3KBP1. In mosquito C7/10 cells, it interacted with A0A182G3T6, the mosquito BIN1 homolog (Fig. 6B). Interestingly, isolation of CD2AP/SH3KBP1 and BIN1 was strongly dependent on the cell type. In human Huh7 and mouse NIH 3T3 cells (35), BIN1, but not CD2AP or SH3KBP1, efficiently interacted with CHIKV HVD. However, in another human cell line, HEK 293 cells, CHIKV HVD preferentially interacted with CD2AP and SH3KBP1, but not with BIN1.
IDR in the publication is 100% identical to this Uniprot sequence.
Protein: DP01468 (UniProt A3RMR8)
Region: residues 1658	to 1856
Annotation: protein binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
In vertebrate cells, CHIKV HVD also coimmunoprecipitated cellular SH3-binding proteins BIN1, CD2AP, and SH3KBP1. In mosquito C7/10 cells, it interacted with A0A182G3T6, the mosquito BIN1 homolog (Fig. 6B). Interestingly, isolation of CD2AP/SH3KBP1 and BIN1 was strongly dependent on the cell type. In human Huh7 and mouse NIH 3T3 cells (35), BIN1, but not CD2AP or SH3KBP1, efficiently interacted with CHIKV HVD. However, in another human cell line, HEK 293 cells, CHIKV HVD preferentially interacted with CD2AP and SH3KBP1, but not with BIN1.
In the case of CHIKV, G3BP binding is particularly critical. In contrast to the results of the studies performed on SINV and SFV, deletion of even a single element of the G3BP-binding HVD repeat had a strong negative effect on CHIKV replication in both vertebrate and mosquito cells (Fig. 2) (34). Deletion of both elements, in turn, completely abrogated virus replication.
IDR in the publication is 100% identical to this Uniprot sequence.
Protein: DP01469 (UniProt A4L7I4)
Region: residues 1658	to 1856
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
It exhibits a reduced chemical shift dispersion, especially in the 1H dimension between 8.5 and 7.5 ppm (Fig. 1C), which is a characteristic of the intrinsically disordered proteins (42).
We carried out detailed characterization of a 199-aa-long CHIKV HVD by NMR spectroscopy at atomic resolution. The results revealed the absence of stable secondary structures in this domain and clearly demonstrated that CHIKV HVD was present in solution in a disordered conformation.
IDR in the publication is 100% identical to this Uniprot sequence.
Protein: DP01469 (UniProt A4L7I4)
Region: residues 1761	to 1856
Annotation: protein binding (Molecular function)
Evidence: qualitative western immunoblotting evidence used in manual assertion
Supporting statements:
Western blot analysis with NAP1L1-specific Abs also definitively detected the latter protein in the co-IP samples generated on the cells infected with VEErep/Flag-GFP-ABCD but not with any other constructs, including VEErep/Flag-GFP-ABC and VEErep/Flag-GFP-123D (Fig. 8B). The most plausible explanation for the lack of NAP1L1 binding to CHIKV HVD deletion mutant constructs was that NAP1L1 binding requires the presence of intact aa sequences of both fragments C and D. Indeed, two isoforms of NAP1L1 were readily detectable in the samples generated from the cells infected with replicons expressing Flag-GFP-12CD and Flag-GFP-12(C3)D fusions (Fig. 8C). This was an indication that NAP1L1 interacts with HVD on the border between C and D fragments (see Fig. 11).
IDR in the publication is 100% identical to this Uniprot sequence.
Protein: DP01469 (UniProt A4L7I4)
Region: residues 1658	to 1856
Annotation: protein binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
In vertebrate cells, CHIKV HVD also coimmunoprecipitated cellular SH3-binding proteins BIN1, CD2AP, and SH3KBP1. In mosquito C7/10 cells, it interacted with A0A182G3T6, the mosquito BIN1 homolog (Fig. 6B). Interestingly, isolation of CD2AP/SH3KBP1 and BIN1 was strongly dependent on the cell type. In human Huh7 and mouse NIH 3T3 cells (35), BIN1, but not CD2AP or SH3KBP1, efficiently interacted with CHIKV HVD. However, in another human cell line, HEK 293 cells, CHIKV HVD preferentially interacted with CD2AP and SH3KBP1, but not with BIN1.
In the case of CHIKV, G3BP binding is particularly critical. In contrast to the results of the studies performed on SINV and SFV, deletion of even a single element of the G3BP-binding HVD repeat had a strong negative effect on CHIKV replication in both vertebrate and mosquito cells (Fig. 2) (34). Deletion of both elements, in turn, completely abrogated virus replication.
IDR in the publication is 100% identical to this Uniprot sequence.
Protein: DP01469 (UniProt A4L7I4)
Region: residues 1658	to 1856
Annotation: molecular adaptor activity (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
In vertebrate cells, CHIKV HVD also coimmunoprecipitated cellular SH3-binding proteins BIN1, CD2AP, and SH3KBP1. In mosquito C7/10 cells, it interacted with A0A182G3T6, the mosquito BIN1 homolog (Fig. 6B). Interestingly, isolation of CD2AP/SH3KBP1 and BIN1 was strongly dependent on the cell type. In human Huh7 and mouse NIH 3T3 cells (35), BIN1, but not CD2AP or SH3KBP1, efficiently interacted with CHIKV HVD. However, in another human cell line, HEK 293 cells, CHIKV HVD preferentially interacted with CD2AP and SH3KBP1, but not with BIN1.
IDR in the publication is 100% identical to this Uniprot sequence.
Protein: DP01469 (UniProt A4L7I4)
Region: residues 1658	to 1856
Annotation: viral life cycle (Biological process)
Evidence: green fluorescent protein reporter gene assay evidence used in manual assertion
Supporting statements:
These experimental data strongly suggested that HVDs play critical roles in the adaptation of CHIKV and EILV to replication in particular cell types. Despite having very similar G3BP-binding repeating peptides, heterologous HVDs changed cell specificities of replication for both viruses. This was a strong support for the hypothesis that HVD fragments located upstream of the carboxy-terminal G3BP/Rin-binding repeat play an indispensable role in CHIKV replication.
In the case of CHIKV, G3BP binding is particularly critical. In contrast to the results of the studies performed on SINV and SFV, deletion of even a single element of the G3BP-binding HVD repeat had a strong negative effect on CHIKV replication in both vertebrate and mosquito cells (Fig. 2) (34). Deletion of both elements, in turn, completely abrogated virus replication.
IDR in the publication is 100% identical to this Uniprot sequence.
Protein: DP01471 (UniProt P36118)
Region: residues 1	to 322
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Intrinsic disorder
of full-length Ntr2 was also reflected in its 1H-15NHSQC
NMR spectrum
Protein: DP01471 (UniProt P36118)
Region: residues 1	to 322
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Together
with the peptide SPOT analysis, the results presented above
show that the N-terminal half of Ntr2 encompasses three
Brr2-binding regions, of which the first two regions (within
residues 1–75) are necessary and sufficient for stable Brr2
binding in SEC.
Protein: DP01471 (UniProt P36118)
Region: residues 1	to 322
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
CD spectra of
both Ntr2FL and the N-terminal half of the protein (residues
1–162: Ntr21–162) at 20  C showed a global minimum at
around 200 nm, lacked a CD signal at 190 nm, and exhibited
a flat region in the 210–230 nm range (Fig. 1 B), which are
typical signatures of intrinsically disordered proteins (IDPs)
Protein: DP01471 (UniProt P36118)
Region: residues 1	to 322
Annotation: disorder (Structural state)
Evidence: dynamic light scattering assay evidence used in manual assertion
Supporting statements:
The hydrodynamic
radii of Ntr2FL, Ntr21–162, and Ntr21–75 derived from
quasi-elastic light scattering were in excellent agreement
with the expected values for IDPs