LiteFold/DisProt huggingface dataset:
Protein: DP03048 (UniProt Q9XWJ1)
Region: residues 150	to 176
Annotation: molecular sequestering activity (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
GDP binds SMG9c at a similar position as in Atlastin and GBP1, in particular with similarities at the phosphatebinding loops, e.g., at the motifs G1 (P loop), G2 (switch 1), and G3 (switch 2) (Fig. 2B,C). In SMG9c, the P loop residues Lys99SMG9 and Ser100SMG9 coordinate the phosphates of GDP. Although parts of the switch regions are disordered in our GDP-bound structure, the switch 2 residue Asp150SMG9 is at the position expected for coordinating the magnesium ion, while the switch 1 residue Thr135SMG9 is 10 Å away from the position expected upon γ -phosphate binding.
Cross-references: PDB:5NKK
Protein: DP03048 (UniProt Q9XWJ1)
Region: residues 150	to 176
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
GDP binds SMG9c at a similar position as in Atlastin and GBP1, in particular with similarities at the phosphatebinding loops, e.g., at the motifs G1 (P loop), G2 (switch 1), and G3 (switch 2) (Fig. 2B,C). In SMG9c, the P loop residues Lys99SMG9 and Ser100SMG9 coordinate the phosphates of GDP. Although parts of the switch regions are disordered in our GDP-bound structure, the switch 2 residue Asp150SMG9 is at the position expected for coordinating the magnesium ion, while the switch 1 residue Thr135SMG9 is 10 Å away from the position expected upon γ -phosphate binding.
Cross-references: PDB:5NKK
Protein: DP03048 (UniProt Q9XWJ1)
Region: residues 107	to 139
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
GDP binds SMG9c at a similar position as in Atlastin and GBP1, in particular with similarities at the phosphatebinding loops, e.g., at the motifs G1 (P loop), G2 (switch 1), and G3 (switch 2) (Fig. 2B,C). In SMG9c, the P loop residues Lys99SMG9 and Ser100SMG9 coordinate the phosphates of GDP. Although parts of the switch regions are disordered in our GDP-bound structure, the switch 2 residue Asp150SMG9 is at the position expected for coordinating the magnesium ion, while the switch 1 residue Thr135SMG9 is 10 Å away from the position expected upon γ -phosphate binding.
Cross-references: PDB:5NKK
Protein: DP03049 (UniProt Q18235)
Region: residues 193	to 244
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Securin, which forms an extended structure that interacts mainly with the  periphery of separase, was well resolved around the substrate-binding site but less well defined elsewhere (Supplementary Fig. 2 and Table 1).
Table 1. Disordered regions. Securin 1-117, 193-244
Cross-references: PDB:5MZ6
Protein: DP03049 (UniProt Q18235)
Region: residues 1	to 117
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Securin, which forms an extended structure that interacts mainly with the  periphery of separase, was well resolved around the substrate-binding site but less well defined elsewhere (Supplementary Fig. 2 and Table 1).
The N-terminal 116 residues, including the APC/C degron  recognition and ubiquitination sites are unstructured (Fig. 1a).
Table 1. Disordered regions. Securin 1-117, 193-244
Cross-references: PDB:5MZ6
Protein: DP03049 (UniProt Q18235)
Region: residues 118	to 192
Annotation: protein binding (Molecular function)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
Securin, which forms an extended structure that interacts mainly with the  periphery of separase, was well resolved around the substrate-binding site but less well defined elsewhere (Supplementary Fig. 2 and Table 1).
Our structure shows that bound to separase, securin forms an  extended conformation interacting along the entire length of separase in an anti-parallel  orientation (Fig. 1b, c). 
Cross-references: PDB:5MZ6
Protein: DP03049 (UniProt Q18235)
Region: residues 118	to 192
Annotation: disorder to order (Structural transition)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
Securin, which forms an extended structure that interacts mainly with the  periphery of separase, was well resolved around the substrate-binding site but less well defined elsewhere (Supplementary Fig. 2 and Table 1).
Our structure shows that bound to separase, securin forms an  extended conformation interacting along the entire length of separase in an anti-parallel  orientation (Fig. 1b, c). 
Cross-references: PDB:5MZ6
Protein: DP03050 (UniProt G5ED39)
Region: residues 391	to 446
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Table 1 shows that the region 391-446 based on the Cryo-EM experiments
The αsolenoid domain accommodates two disordered insertions. Insert-1 includes the site of
regulatory CDK-phosphorylation of human separase 17,28, whereas insert-2 incorporates
the auto-cleavage sites 2,29,30 and cyclin B1 (refs 15,18) and PP2A 31 binding sites of
vertebrate separase (Fig. 1 and Supplementary Fig. 4).
Cross-references: PDB:5MZ6
Protein: DP03050 (UniProt G5ED39)
Region: residues 590	to 628
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Table 1 shows that the region 590-628 based on the Cryo-EM experiments.
The αsolenoid domain accommodates two disordered insertions. Insert-1 includes the site of
regulatory CDK-phosphorylation of human separase 17,28, whereas insert-2 incorporates
the auto-cleavage sites 2,29,30 and cyclin B1 (refs 15,18) and PP2A 31 binding sites of
vertebrate separase (Fig. 1 and Supplementary Fig. 4).
Cross-references: PDB:5MZ6
Protein: DP03050 (UniProt G5ED39)
Region: residues 1	to 10
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Table 1 shows that the region 1-10 based on the Cryo-EM experiments
Cross-references: PDB:5MZ6
Protein: DP03050 (UniProt G5ED39)
Region: residues 1141	to 1262
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Table 1 shows that the region  1141-1262 based on the Cryo-EM experiments. 
Figure 1 A shows a scheme indicating region 1141-1262 as an IDR.
Cross-references: PDB:5MZ6
Protein: DP03051 (UniProt O54952)
Region: residues 1801	to 1817
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Five N-terminal residues (residues 1589–1593), a three-residue portion of the inter-repeat linker region (residues 1702–1704), and the C terminus (residues 1800–1817) do not have interpretable electron density, and we presume are disordered. 
On matching missing residues in PDB structure 1L0B with Uniprot sequence, the disordered region starts at 1801 and not 1800. 
Cross-references: PDB:1L0B
Protein: DP03052 (UniProt Q06486)
Region: residues 297	to 314
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The last 18 residues at the C terminus were disorderedin  both  molecules.
Cross-references: PDB:1CKJ
Protein: DP03054 (UniProt P91870)
Region: residues 11	to 44
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Far-UV circular dichroism and nuclear magnetic resonance confirmed that the CeSPD-2 AR is intrinsically disordered with a classical random-coil structure (Figure S2CE).
Far-UV circular dichroism (CD) spectra of recombinant acidic regions: CeSPD-2 (aa 11-44), DmAsl (aa 21-60), MmAsl (aa 1-47), and MmSPD-2 (aa 168-256). All acidic regions demonstrated a classical random coil structure with maximum below 0 and minimum at ~200 nm.
Protein: DP03054 (UniProt P91870)
Region: residues 1	to 46
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Far-UV circular dichroism and nuclear magnetic resonance confirmed that the CeSPD-2 AR is intrinsically disordered with a classical random-coil structure (Figure S2CE).
2D 1H-15N HSQC spectrum of the CeSPD-2 AR (aa 1-46) shows a very narrow chemical shift range of amide proton resonances (8.0 - 8.6 ppm), suggesting that the protein is either intrinsically disordered or composed of helical secondary structures.
Amide region of the 2D NOESY spectrum of the CeSPD-2 AR (aa 1-46) shows no helical HN-HN cross peaks (dashed-line encircled regions), suggesting that the protein does not have any helical content.
Protein: DP03054 (UniProt P91870)
Region: residues 1	to 46
Annotation: protein binding (Molecular function)
Evidence: bait-prey hybrid interaction evidence used in manual assertion
Supporting statements:
To find out whether the ZYG-1 CPB interacts with all or part of the CeSPD-2 acidic region (CeSPD-2 AR), we generated maltose binding protein (MBP)-tagged WT CeSPD-2 (aa 1-46) and three mutant versions (LEFT, CENTER and RIGHT; Figure 2C) that charge reversed negatively charged residues in the center or in the left or right flanking sides of the CeSPD-2 AR. All three mutants pulled down significantly less ZYG-1 CPB than the WT AR, suggesting that negatively charged residues across the entire CeSPD-2 AR interact with the ZYG-1 CPB (Figures 2D, S3A).
Interestingly, the CeSPD-2 AR has distal acidic patches on both sides (Figure 7E, F) that are functionally important in vitro and in vivo (Figures 2C, 2D, 3) and basic residues on the sides of the ZYG-1 CPB dimer are also important for SPD-2 AR binding, ZYG-1 targeting, and daughter centriole assembly (Figures 2E, 2F, 4).
Protein: DP03054 (UniProt P91870)
Region: residues 11	to 44
Annotation: protein binding (Molecular function)
Evidence: microscale thermophoresis evidence used in manual assertion
Supporting statements:
Microscale thermophoresis (MST; Seidel et al., 2013) using fluorescently labeled ZYG-1 CPB as reporter revealed that thioredoxin fusions with three CeSPD-2 N-terminal fragments (aa 1-147, 1-46 and 11-44) bound with nearly identical affinities (Kd ~ 0.5 μM; Figure 2B), indicating that residues 11-44 of CeSPD-2 are sufficient for interaction.
Interestingly, the CeSPD-2 AR has distal acidic patches on both sides (Figure 7E, F) that are functionally important in vitro and in vivo (Figures 2C, 2D, 3) and basic residues on the sides of the ZYG-1 CPB dimer are also important for SPD-2 AR binding, ZYG-1 targeting, and daughter centriole assembly (Figures 2E, 2F, 4).
Protein: DP03054 (UniProt P91870)
Region: residues 1	to 46
Annotation: localization (Biological process)
Evidence: confocal microscopy evidence used in manual assertion
Supporting statements:
A distributed array of negatively charged residues in the CeSPD-2 N-terminus recruits ZYG-1 to mother centrioles to initiate centriole duplication in vivo.
Interestingly, the CeSPD-2 AR has distal acidic patches on both sides (Figure 7E, F) that are functionally important in vitro and in vivo (Figures 2C, 2D, 3) and basic residues on the sides of the ZYG-1 CPB dimer are also important for SPD-2 AR binding, ZYG-1 targeting, and daughter centriole assembly (Figures 2E, 2F, 4).
Protein: DP03054 (UniProt P91870)
Region: residues 1	to 46
Annotation: molecular adaptor activity (Molecular function)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
We conclude that an array of negatively charged residues in the CeSPD-2 N-terminus recruits ZYG-1 to mother centrioles; selective alteration of charges in the beginning, middle or end of this region disrupts ZYG-1 docking and centriole duplication.
Graph plotting mean centrosomal ZYG-1 fluorescence. Values are percentage of the mean control value. n = number of centrosomes.
Interestingly, the CeSPD-2 AR has distal acidic patches on both sides (Figure 7E, F) that are functionally important in vitro and in vivo (Figures 2C, 2D, 3) and basic residues on the sides of the ZYG-1 CPB dimer are also important for SPD-2 AR binding, ZYG-1 targeting, and daughter centriole assembly (Figures 2E, 2F, 4).
Protein: DP03056 (UniProt P13199)
Region: residues 8	to 107
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In its free form the Nterminal region aa8–120 of ORF57 is flexible and mainly
unstructured, apart from the short a-helix aa108–118 which we
named R-b helix.
Our experimental NMR data,
namely dihedral angles derived from TALOS+ [42], 15N[1
H] NOE
experiments, and presence of characteristic i to i+3 NOEs for a
shorter peptide ORF57103–120 (see Fig. S2), also all demonstrate that
the ORF578–120 site aa107–118 exists in a-helical conformation;
therefore this region was named ‘‘R-b helix’’.
Protein: DP03056 (UniProt P13199)
Region: residues 64	to 107
Annotation: RNA binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In contrast, the ORF57-specific oligos caused substantial signal broadening in
all signals corresponding to the region aa64–120 (Fig. 1A).
Signal perturbation mapping therefore suggested a specific
RNA binding site encompassing aa64–120 within ORF578–120,
whilst also showing the ALYREF-binding region aa103–120
located within this site is not sufficient for the recognition of
specific viral RNA.
Protein: DP03056 (UniProt P13199)
Region: residues 64	to 79
Annotation: RNA binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Based on the results of saturation transfer
mapping, which are also in line with signal perturbation mapping,
we conclude that ORF578–120 contacts the specific RNA motifs
directly using primarily its regions aa107–120 and aa81–92, with
additional contribution from residues within aa94–105 and aa64–
79.
Protein: DP03056 (UniProt P13199)
Region: residues 81	to 92
Annotation: RNA binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Based on the results of saturation transfer
mapping, which are also in line with signal perturbation mapping,
we conclude that ORF578–120 contacts the specific RNA motifs
directly using primarily its regions aa107–120 and aa81–92, with
additional contribution from residues within aa94–105 and aa64–
79.
In the ternary complex
ORF57 aa106–120 directly interacts with the ALYREF RRM,
whereas flexible flanking regions of ALYREF (aa24–48) and
ORF57 (aa81–92), and to lesser extent, parts of helix 2 of the
ALYREF RRM, jointly keep hold of the viral RNA molecule.
Protein: DP03056 (UniProt P13199)
Region: residues 94	to 105
Annotation: RNA binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Based on the results of saturation transfer
mapping, which are also in line with signal perturbation mapping,
we conclude that ORF578–120 contacts the specific RNA motifs
directly using primarily its regions aa107–120 and aa81–92, with
additional contribution from residues within aa94–105 and aa64–
79.
Protein: DP03056 (UniProt P13199)
Region: residues 81	to 89
Annotation: RNA binding (Molecular function)
Evidence: mutant phenotype evidence used in manual assertion
Supporting statements:
The results of NMR mapping of RNA binding regions of
ORF578–120 were confirmed by UV cross-linking using purified
protein and radio-labeled RNA oligonucleotide, performed as
previously described [10]. The ORF57 mutants Y81A+R82A,
R88A+F89A and W108A+R111A+V112A all significantly reduced the efficiency of cross-linking with RNA 14merS (Fig. 7A).
Protein: DP03056 (UniProt P13199)
Region: residues 8	to 107
Annotation: RNA binding (Molecular function)
Evidence: cross-linking evidence used in manual assertion
Supporting statements:
To independently confirm the NMR observations in regard to
RNA oligonucleotide binding with ORF578–120, ALYREF1–155
and their complex, we performed in vitro reconstitution assays
followed by UV cross-linking experiments. ORF578–120 showed a
strong RNA-binding activity for 7merS and 14merS in sharp
contrast to GST-ALYREF which bound weakly with both RNAs
(Fig. 7B,C). When ORF578–120 was incubated with RNA prior to
mixing with GST-ALYREF, followed by GST affinity purification
of the resulting complexes and UV cross-linking, there was a
drastic reduction of the RNA cross-linked to ORF578–120 and a
concomitant increase in the RNA cross-linked onto GSTALYREF. Therefore the RNA-binding activity of ORF578–120 is
severely reduced upon interaction with ALYREF, whereas the
amount of RNA in contact with ALYREF increases in the ternary
complex. This independent data obtained at a molecular (i.e,
macroscopic) level concurs fully with the NMR data obtained at a
residue-specific level of detail.
Protein: DP03056 (UniProt P13199)
Region: residues 81	to 92
Annotation: molecular adaptor activity (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In this study we used solution state NMR to reveal molecular
details of the ternary complex assembly of functional fragments of
HVS ORF57, HVS RNA and ALYREF, and suggest a model for
the mechanism of RNA transfer between protein molecules in this
system.
The NMR experiments therefore all indicate that ALYREF
partially displaces the viral RNA initially bound specifically to
ORF57, but retains it within the complex. In the ternary complex
ORF57 aa106–120 directly interacts with the ALYREF RRM,
whereas flexible flanking regions of ALYREF (aa24–48) and
ORF57 (aa81–92), and to lesser extent, parts of helix 2 of the
ALYREF RRM, jointly keep hold of the viral RNA molecule.
Interestingly, amide signals from flexible protein regions which
become involved in direct contacts with RNA (as evidenced by
RNA-protein saturation transfer), are only partially broadened in
the complex. They had intensities higher than signals from the
folded regions, but lower than signals from the unfolded noninteracting regions (examples of this behavior can be seen in Fig. 5
and Fig. S5). This suggests that the interaction with RNA in these
conditions was somewhat transient and did not lead to the
formation of a rigid 3D structure.
Protein: DP03056 (UniProt P13199)
Region: residues 8	to 107
Annotation: molecular adaptor activity (Molecular function)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
The experimental fluorescence equilibrium binding data thus
reveal the overall cooperativity in the ternary complex formation
when the components are present at or near stoichiometric
amounts, and support a role of ORF57 as an adaptor introducing
RNA to ALYREF.
Protein: DP03056 (UniProt P13199)
Region: residues 8	to 107
Annotation: molecular adaptor activity (Molecular function)
Evidence: cross-linking evidence used in manual assertion
Supporting statements:
To independently confirm the NMR observations in regard to
RNA oligonucleotide binding with ORF578–120, ALYREF1–155
and their complex, we performed in vitro reconstitution assays
followed by UV cross-linking experiments. ORF578–120 showed a
strong RNA-binding activity for 7merS and 14merS in sharp
contrast to GST-ALYREF which bound weakly with both RNAs
(Fig. 7B,C). When ORF578–120 was incubated with RNA prior to
mixing with GST-ALYREF, followed by GST affinity purification
of the resulting complexes and UV cross-linking, there was a
drastic reduction of the RNA cross-linked to ORF578–120 and a
concomitant increase in the RNA cross-linked onto GSTALYREF. Therefore the RNA-binding activity of ORF578–120 is
severely reduced upon interaction with ALYREF, whereas the
amount of RNA in contact with ALYREF increases in the ternary
complex.
Protein: DP03056 (UniProt P13199)
Region: residues 8	to 107
Annotation: RNA binding (Molecular function)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
As the measured Kd values
for the formation of binary complexes are significantly higher than
for the ternary complexes (e.g., Kd
O+R= 7.57 mM.
Kd
OA+R= 1.55 mM), the assembly shows clear-cut cooperative behavior [44].
Protein: DP03057 (UniProt Q20728)
Region: residues 91	to 120
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Because no long range NOEs were observed for residues 91–120, and 15N-1H heteronuclear NOEvalues (Fig. 2A) confirmed that those C-terminal residues are dynamically disordered on the picosecond to nanosecond timescale (23), the final structure calculations included only CoB residues 1–90. 
Values for residues 91–120 (not shown) ranged from -0.4 to +0.2 consistent with an absence of defined tertiary structure beyond the extent of the β-grasp domain.
Cross-references: PDB:1T0Y
Protein: DP03057 (UniProt Q20728)
Region: residues 91	to 120
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Disordered C-terminal residues of the construct used in this analysis may serve as a flexible linker between the N-terminal Ubl domain and the C-terminal CAP-Gly domain (12) of CoB.
Cross-references: PDB:1T0Y
Protein: DP03058 (UniProt Q58F21)
Region: residues 144	to 257
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
 New resonances, which appeared in the BRDT
(1–2) 1H, 15N HSQC spectrum (Supplementary Fig. 3c), were
attributed to the linker; these resonances were predominantly
grouped in the middle of the spectrum and have significantly higher intensities, suggesting that the linker is unstructured.
Protein: DP03058 (UniProt Q58F21)
Region: residues 144	to 257
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The radius of gyration (Rg) = 49 +/- 9 Å and Dmax of > 160 Å derived from the
SAXS data of BRDT(1-2) indicate a large average distance between the two bromodomains. In
structures with random linker conformations and a corresponding Rg, the distance between the
center of mass of the two bromodomains is > 80 Å. The Kratky plot shows a clear bell-shaped
curve indicative of structured proteins; however, the curve increases asymptotically as expected
for a non-structured protein. Thus the data confirm the existence of an unstructured linker
connecting the two bromodomains.