LiteFold/DisProt huggingface dataset:
Protein: DP00939 (UniProt P04859)
Region: residues 504	to 508
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The two alanines A-504 and A-507 both have high negative normalized order parameters. They are located in the stretch (504–508), which from the backbone 15N relaxation data was identified as a very flexible linker between the unstructured and structured domain; and this highly flexible character is clearly also sensed by the alanine Cα-Cβ axis. All other normalized order parameters in the unstructured part are also negative, meaning that the methyl groups are more flexible than on average in structured proteins.
Protein: DP00939 (UniProt P04859)
Region: residues 505	to 515
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We show that this small protein presents two subdomains linked by an 11-residue linker, with the N-subdomain lacking a well-defined conformation.
To supplement the structural characterisation of PX, we measured heteronuclear relaxation at 600 MHz. Of the 95 amino acid residues (474–568), 68 {1H}-15N nOes (Fig. 3), 68 R1 and 68 R2 (data not shown) could be measured. The resulting data confirm that residues 474–515 indeed present differential dynamic behaviour compared to residues 516–568. In particular, the {1H}-15N nOe reveals a rigid domain (516–568) linked to a flexible domain (474–504) by an even more flexible linker (505–515).
Cross-references: PDB:1R4G
Protein: DP00939 (UniProt P04859)
Region: residues 474	to 515
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
This model is validated by experimental RDCs and SAXS data measured from PX from Sendai virus, a molecule containing folded and unfolded domains, confirming both local conformational sampling and the average size and shape of the ensemble. Despite the highly disperse ensemble, regions of preferential structuring along the flexible chain of PX are detected.
In this study, experimental RDCs and SAXS data are combined with a conformational sampling algorithm to develop a structural model of the 57-aa unfolded domain of PX. Although they cover a smaller range than the RDCs measured in the folded domain, the N-NH and C′-NH RDC measured for PX aligned in 5% of C12E6/hexanol nevertheless present identifiable fine structure and values that are non-negligible compared with the folded domain.
57-aa including the 15 residues of the His-tag.
Protein: DP00941 (UniProt Q93009)
Region: residues 54	to 64
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The amino terminus and four loops are completely disordered.
Cross-references: PDB:1YZE
Protein: DP00941 (UniProt Q93009)
Region: residues 174	to 187
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The amino terminus and four loops are completely disordered.
Cross-references: PDB:1YZE
Protein: DP00941 (UniProt Q93009)
Region: residues 105	to 114
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The amino terminus and four loops are completely disordered.
Cross-references: PDB:1YZE
Protein: DP00941 (UniProt Q93009)
Region: residues 174	to 187
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
In crystals generated by the USP7-EBNA1 complex, lattice contacts were not observed in the peptide binding region but were confined to the loops connecting the β strands (amino acids 77, 80, and 82 interacted with residues 178, 180, and 181).
Upon USP7-EBNA1 complex formation this region becomes structures, as shown in the PDB 1YY6.
Cross-references: PDB:1YZE
PDB:1YY6
Protein: DP00941 (UniProt Q93009)
Region: residues 500	to 509
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
PDB structure shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:2F1Z
Protein: DP00941 (UniProt Q93009)
Region: residues 1084	to 1102
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
PDB structure of USP7/HAUSP in complex with ICP0 shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:5C56
Protein: DP00944 (UniProt P12736)
Region: residues 1	to 95
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB structure of the Haloarcula marismortui 50S complexed with a pretranslocational intermediate in protein synthesis shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:1KQS
Protein: DP00944 (UniProt P12736)
Region: residues 1	to 95
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The fully refined crystal structure of the Haloarcula marismortui Large Ribosomal Subunit shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:1JJ2
Protein: DP00944 (UniProt P12736)
Region: residues 1	to 95
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB structure of the 50S ribosomal subunit of Haloarcula marismortui bound to Spiramycinazi, thromycin, Carbomycin or A tylosin; shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:1K8A
PDB:1M1K
PDB:1KD1
PDB:1K9M
Protein: DP00944 (UniProt P12736)
Region: residues 1	to 95
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB structure of CC-Puromycin bound to the A-site of the 50S ribosomal subunit shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:1Q82
Protein: DP00948 (UniProt P59595)
Region: residues 1	to 44
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
SARS-CoV N protein contains three intrinsically disordered regions
In conjunction with the observation that all additional resonances are observed in between 8.3±0.5 ppm in the proton dimension and PONDR results, we conclude that aminoacids 1–44, 182–247 and 366–422 are disordered.
The spectrum of N1-181 is a superposition of well-dispersed resonances and a cluster of overlapping resonances   around 8.3±0.4 ppm (Figure 2b).
Protein: DP00948 (UniProt P59595)
Region: residues 182	to 247
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
SARS-CoV N protein contains three intrinsically disordered regions
 In conjunction with the observation that all additional resonances are observed in between 8.3±0.5 ppm in the proton dimension and PONDR results, we conclude that amino acids 1–44, 182–247 and 366–422 are disordered.
Protein: DP00948 (UniProt P59595)
Region: residues 366	to 422
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
SARS-CoV N protein contains three intrinsically disordered regions
In conjunction with the observation that all additional resonances are observed in between 8.3±0.5 ppm in the proton dimension and PONDR results, we conclude that amino acids 1–44, 182–247 and 366–422 are disordered.
Protein: DP00948 (UniProt P59595)
Region: residues 182	to 247
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Furthermore, size exclusion chromatography of NP45-247 shows that the protein elutes out of the column with a Stokes radius corresponding to a globular protein of 41 kDa (Fig.5B). The theoretical molecular mass of the construct is 22.9 kDa, suggesting that the NP45-247 construct has an elongated shape. This is in contrast to the NTD, which is mainly globular (13). We attribute this to residues 182 to 247 forming an extraneous “tail” that affects the hydrodynamic properties of the molecule. 
Taken together, our results are compatible with previous reports from this lab where the didomain construct NP45-365 was shown to have resonances in the disordered region of the spectrum without affecting resonances belonging to either structural domain (2). We conclude that the flexible linker (residues 182 to 247) forms a bona fide ID domain not affected by either structural domain in the context of the whole protein.
Protein: DP00948 (UniProt P59595)
Region: residues 182	to 247
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
Small-angle X-ray scattering data show that the protein is in an extended conformation and that the two structural domains of the SARS-CoV N protein are far apart. Both the NTD and the CTD have been shown to bind RNA. Here we show that all disordered regions are also capable of binding to RNA.
Data analysis showed that the radius of gyration of the NP45-365 dimer is 61 Å, much larger than expected for a 72-kDa globular protein ​(Fig.7B). This is consistent with the model that the NTD and CTD do not interact, and the two NTDs in the dimer are likely to float freely in solution
Protein: DP00948 (UniProt P59595)
Region: residues 248	to 259
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Second, the two N-termini (residues 248–259) protruding from the dimer core are disordered in the NMR structure, whereas, in the crystal structure, they are involved in a number of intramonomer and intradimer contacts and are more rigid (Fig. 4a). The disorder of the N-termini in solution was further supported by the analysis of backbone amide-exchange rates (data not shown). 
Cross-references: PDB:2JW8
Protein: DP00948 (UniProt P59595)
Region: residues 248	to 259
Annotation: molecular adaptor activity (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
To identify these residues, we conducted chemical shift displacement (CSD) studies by titrating 10-mer (dT10) or 20-mer (dT20) poly-deoxythymine (poly-dT) single-stranded DNA (ssDNA) into the protein samples. ssDNA were used throughout this study as surrogates of single-stranded RNA. Titration of dT10 or dT20 into the protein sample caused a concentration-dependent gradual shift of some resonances, instead of the appearance of a new set of resonances, suggesting that the binding occurs in the fast-exchange regime, which is indicative of a low-affinity nucleic-acid-binding protein.13 For dT10, significant chemical shift changes were localized primarily in the N-terminal region, particularly K250, E253, A254, S256, K257, and K258 (Fig. 6a and b), while the majority of the other resonances were scarcely affected. This result suggests that dT10 binds to the SARS-CoV NP at the N-terminal flexible segment, without affecting the overall structure of the protein (Fig. 4). The binding constant estimated from the CSD studies at various dT10 concentrations is Kd ∼ 30 μM.
Protein: DP00948 (UniProt P59595)
Region: residues 248	to 259
Annotation: DNA binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
To identify these residues, we conducted chemical shift displacement (CSD) studies by titrating 10-mer (dT10) or 20-mer (dT20) poly-deoxythymine (poly-dT) single-stranded DNA (ssDNA) into the protein samples. ssDNA were used throughout this study as surrogates of single-stranded RNA. Titration of dT10 or dT20 into the protein sample caused a concentration-dependent gradual shift of some resonances, instead of the appearance of a new set of resonances, suggesting that the binding occurs in the fast-exchange regime, which is indicative of a low-affinity nucleic-acid-binding protein.13 For dT10, significant chemical shift changes were localized primarily in the N-terminal region, particularly K250, E253, A254, S256, K257, and K258 (Fig. 6a and b), while the majority of the other resonances were scarcely affected. This result suggests that dT10 binds to the SARS-CoV NP at the N-terminal flexible segment, without affecting the overall structure of the protein (Fig. 4). The binding constant estimated from the CSD studies at various dT10 concentrations is Kd ∼ 30 μM.
Protein: DP00948 (UniProt P59595)
Region: residues 182	to 247
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The  long  disordered  linker  between  the  two structural domains is consistent with the observation that there is little interaction between the two domains.
The two structural domains are connected by a disordered linker and capped by disordered N-terminal head and C-terminal tail.
The lack of resonance perturbation when the two domains are linked together suggests that interaction between these two domains is weak, if they interact at all. Our results conclude that SARS-CoV N protein contains two independent structural domains located at a.a. 45–181 and 248–365.
The flexible linker between the two structural domains is largely disordered. This disordered region may enable transient interactions with several structurally distinct partners. It has been shown that the M protein of SARS-CoV binds to this region between a.a. 168–208 [16]. Interestingly, human cellular hnRNP A1 has also been shown to bind to almost the same region between a.a. 161–210 [17]. The disordered state of this region potentially allows it to interact with different partners depending on context, e.g. with the M protein during virus assembly and with hnRNP A1 during host cell infection.
Flexible linker connecting the N-terminal RNA-binding domain (RBD) (residues 45–181) and the C-terminal dimerization domain (residues 248–365) (DD) of SARS-CoV Nucleoprotein.
Protein: DP00948 (UniProt P59595)
Region: residues 184	to 196
Annotation: self-assembly (Disorder function)
Evidence: bait-prey hybrid interaction evidence used in manual assertion
Supporting statements:
Furthermore, mutational analyses characterized that a serine/arginine-rich motif (SSRSSSRSRGNSR) between amino acids 184 and 196 is crucial for N protein oligomerization, since deletion of this region completely abolished the N protein self-multimerization.
As shown in Fig. 4C, deletion of the serine/arginine-rich region (aa 184–196) resulted in a complete loss of SEAP activities, suggesting these amino acids are required for N self-interaction. Finally, consistent with results in Fig. 2, no self-interaction was observed in the viral M proteins. Taken together, these results suggest that amino acids 184–196 are indispensable for multimerization of SARS-CoV nucleocapsid protein.
Protein: DP00948 (UniProt P59595)
Region: residues 182	to 247
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Comparing the HSQC spectrum of NP45-247 with that of the NTD (NP45-181) in Fig.5A, we observed additional resonances in the spectrum of NP45-247 clustered in the 7.5- to 8.5-ppm range on the proton chemical shift. This strongly suggests that the additional residues from aa 182 to 247 of NP45-247 are disordered. 
Taken together, our results are compatible with previous reports from this lab where the didomain construct NP45-365 was shown to have resonances in the disordered region of the spectrum without affecting resonances belonging to either structural domain (2). We conclude that the flexible linker (residues 182 to 247) forms a bona fide ID domain not affected by either structural domain in the context of the whole protein.
Protein: DP00948 (UniProt P59595)
Region: residues 1	to 44
Annotation: RNA binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
Both the NTD and the CTD have been shown to bind RNA. Here we show that all disordered regions are also capable of binding to RNA. Constructs containing multiple RNA-binding regions showed Hill coefficients greater than 1, suggesting that the N protein binds to RNA cooperatively. The current results underscore the important roles of multisite nucleic acid binding and intrinsic disorder in N protein function and RNP packaging.
Here we tested all three disordered regions of the SARS-CoV N protein and found that they are all involved in RNA binding. The central region, in particular, had a large impact on binding behavior as monitored by electrophoretic mobility shift assays (EMSA).
Figure 3 shows that inclusion of either the first 44 residues (aa 1 to 44) or the central flexible linker (residues 182 to 247) of the SARS-CoV N protein increases the apparent binding affinity for 20-mer poly(U) ssRNA three- to fourfold over that of the NTD (residues 45 to 181) alone. Inclusion of the flexible linker not only increases the apparent affinity; it also has a large effect on the apparent Hill coefficient. Similar results are obtained when either the central flexible linker or the C-terminal 54 residues (residues 366 to 422) are included in the construct of the CTD (residues 248 to 365), as shown in ​Fig.4. The increase in apparent binding affinity is even more pronounced (six- to eightfold), probably due to the dimeric nature of the CTD, which has two attached disordered regions, whereas the NTD has one.
Taken together, a common trend is quickly apparent: inclusion of the disordered regions enhances the binding affinity of any particular construct. Of particular interest is the central flexible linker, which not only increases the binding affinity but also greatly enhances the Hill coefficients of the constructs.
Protein: DP00948 (UniProt P59595)
Region: residues 182	to 247
Annotation: RNA binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
Both the NTD and the CTD have been shown to bind RNA. Here we show that all disordered regions are also capable of binding to RNA. Constructs containing multiple RNA-binding regions showed Hill coefficients greater than 1, suggesting that the N protein binds to RNA cooperatively. The current results underscore the important roles of multisite nucleic acid binding and intrinsic disorder in N protein function and RNP packaging.
Here we tested all three disordered regions of the SARS-CoV N protein and found that they are all involved in RNA binding. The central region, in particular, had a large impact on binding behavior as monitored by electrophoretic mobility shift assays (EMSA).
Figure 3 shows that inclusion of either the first 44 residues (aa 1 to 44) or the central flexible linker (residues 182 to 247) of the SARS-CoV N protein increases the apparent binding affinity for 20-mer poly(U) ssRNA three- to fourfold over that of the NTD (residues 45 to 181) alone. Inclusion of the flexible linker not only increases the apparent affinity; it also has a large effect on the apparent Hill coefficient. Similar results are obtained when either the central flexible linker or the C-terminal 54 residues (residues 366 to 422) are included in the construct of the CTD (residues 248 to 365), as shown in ​Fig.4. The increase in apparent binding affinity is even more pronounced (six- to eightfold), probably due to the dimeric nature of the CTD, which has two attached disordered regions, whereas the NTD has one.
Taken together, a common trend is quickly apparent: inclusion of the disordered regions enhances the binding affinity of any particular construct. Of particular interest is the central flexible linker, which not only increases the binding affinity but also greatly enhances the Hill coefficients of the constructs.
Protein: DP00948 (UniProt P59595)
Region: residues 366	to 422
Annotation: RNA binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
Both the NTD and the CTD have been shown to bind RNA. Here we show that all disordered regions are also capable of binding to RNA. Constructs containing multiple RNA-binding regions showed Hill coefficients greater than 1, suggesting that the N protein binds to RNA cooperatively. The current results underscore the important roles of multisite nucleic acid binding and intrinsic disorder in N protein function and RNP packaging.
Here we tested all three disordered regions of the SARS-CoV N protein and found that they are all involved in RNA binding. The central region, in particular, had a large impact on binding behavior as monitored by electrophoretic mobility shift assays (EMSA)
Figure 3 shows that inclusion of either the first 44 residues (aa 1 to 44) or the central flexible linker (residues 182 to 247) of the SARS-CoV N protein increases the apparent binding affinity for 20-mer poly(U) ssRNA three- to fourfold over that of the NTD (residues 45 to 181) alone. Inclusion of the flexible linker not only increases the apparent affinity; it also has a large effect on the apparent Hill coefficient. Similar results are obtained when either the central flexible linker or the C-terminal 54 residues (residues 366 to 422) are included in the construct of the CTD (residues 248 to 365), as shown in ​Fig.4. The increase in apparent binding affinity is even more pronounced (six- to eightfold), probably due to the dimeric nature of the CTD, which has two attached disordered regions, whereas the NTD has one. 
Taken together, a common trend is quickly apparent: inclusion of the disordered regions enhances the binding affinity of any particular construct. Of particular interest is the central flexible linker, which not only increases the binding affinity but also greatly enhances the Hill coefficients of the constructs.
Protein: DP00948 (UniProt P59595)
Region: residues 1	to 46
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Multiple constructs were designed covering different regions of ORF9a from Tor2 strain of SARS-CoV as part of the structural and functional proteomics of SARS-CoV (FSPS) project. Domain boundaries were arrived at based on secondary structure predictions, earlier observations made in the literature regarding proteolytic susceptibility, and sequence conservation characteristics.