LiteFold/DisProt huggingface dataset:
Protein: DP04243 (UniProt A0A0H2UWN8)
Region: residues 1	to 60
Annotation: disorder to order (Structural transition)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
"It can be clearly seen that in the absence of high‐salt or crowding agents, the 1H‐15N HSQC dispersion pattern of Prx at pH 7 is similar to that measured under denaturing conditions. Specifically, all backbone chemical shifts show low dispersion and are clustered between 8.0 and 8.6 ppm in the hydrogen dimension. This 1H‐15N HSQC pattern is diagnostic of a protein that lacks secondary structure and is disordered (Pandey et al., 2023; Prehna et al., 2014).
In contrast, the addition of unlabeled ComR DNA‐binding domain (DBD) to 15N‐labeled Prx results in a well resolved 1H‐15N HSQC indicative of an ordered and globular protein fold (Figure 3c).
Protein: DP04243 (UniProt A0A0H2UWN8)
Region: residues 1	to 60
Annotation: protein binding (Molecular function)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
In contrast, the addition of unlabeled ComR DNA‐binding domain (DBD) to 15N‐labeled Prx results in a well resolved 1H‐15N HSQC indicative of an ordered and globular protein fold (Figure 3c).
Additionally, the data shows that Prx ultimately adopts a well‐ordered globular domain when bound to its biological interaction partner ComR.
Protein: DP04243 (UniProt A0A0H2UWN8)
Region: residues 5	to 10
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
This binding network is extended across the full face of the DBD:Prx interaction by Prx E6 making a hydrogen bond with the invariable ComR residue K49 and Prx E9 providing a mainchain hydrogen bond with ComR T44 (Fig. 3A).
Cross-references: PDB:7N1N
PDB:7N10
Protein: DP04243 (UniProt A0A0H2UWN8)
Region: residues 32	to 44
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Specifically, Prx utilizes D32 to make hydrogen bonds with both the essential arginine residues R33 and R37 in ComR that are responsible for DNA recognition (22) (Fig. 3A). Furthermore, residue D32 is the focal point for a stabilized hydrogen bonding network that positions Prx E44 to make a salt-bridge with ComR R33, Prx D38 to salt-bridge with ComR R37 and for the arginine side chains to be further stabilized by hydrogen bond interactions with the Prx mainchain. This binding network is extended across the full face of the DBD:Prx interaction by Prx E6 making a hydrogen bond with the invariable ComR residue K49 and Prx E9 providing a mainchain hydrogen bond with ComR T44 (Fig. 3A).
Cross-references: PDB:7N1N
PDB:7N10
Protein: DP04243 (UniProt A0A0H2UWN8)
Region: residues 30	to 35
Annotation: protein binding (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
Multiple Prx protein variants were assessed for their ability to bind to full-length ComR using SEC. Prx variants of the three residues highlighted in Figure 3A (PrxE6A, PrxE9A, PrxD32A) were unable to form a complex with ComR, while Prx D12A, which is not at the DBD interface, was still able to form a complex (Fig. 4, A and B, and Fig. S5).
Cross-references: PDB:7N1N
PDB:7N10
Protein: DP04243 (UniProt A0A0H2UWN8)
Region: residues 5	to 10
Annotation: protein binding (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
Multiple Prx protein variants were assessed for their ability to bind to full-length ComR using SEC. Prx variants of the three residues highlighted in Figure 3A (PrxE6A, PrxE9A, PrxD32A) were unable to form a complex with ComR, while Prx D12A, which is not at the DBD interface, was still able to form a complex (Fig. 4, A and B, and Fig. S5).
Cross-references: PDB:7N1N
PDB:7N10
Protein: DP04243 (UniProt A0A0H2UWN8)
Region: residues 1	to 60
Annotation: negative regulation of DNA binding (Biological process)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
When ComR, XIP, and were Prx added together, Prx completely prevented ComR from binding DNA in a dose-dependent manner (Fig. 7A left).
When ComR and Prx were incubated together first followed by the addition of XIP and DNA, similar results were observed to when all components were added together (Fig. 7A middle).
Additionally, when Prx was added after the ComR:XIP:DNA complex was allowed to form Prx could still block the interaction of ComR with DNA (Fig. 7A right).
Protein: DP04243 (UniProt A0A0H2UWN8)
Region: residues 1	to 60
Annotation: negative regulation of establishment of competence for transformation (Biological process)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
When ComR, XIP, and were Prx added together, Prx completely prevented ComR from binding DNA in a dose-dependent manner (Fig. 7A left).
When ComR and Prx were incubated together first followed by the addition of XIP and DNA, similar results were observed to when all components were added together (Fig. 7A middle).
Additionally, when Prx was added after the ComR:XIP:DNA complex was allowed to form Prx could still block the interaction of ComR with DNA (Fig. 7A right).
While the biological role of Prx relative to its genetically paired toxin remains to be determined, Prx has been shown to function as a negative regulator of natural competence in Streptococcus. Specifically, Prx binds directly to the apo-form of ComR preventing DNA binding in vitro and acts as a repressor of the S. pyogenes competence regulon in vivo (18).
Protein: DP04244 (UniProt P40205)
Region: residues 1	to 109
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H-15N HSQC spectrum of NCYM is shown in Fig. 1: the poor dispersion observed for the amide proton resonances, centered at ≈ 8.4 ppm, strongly suggests the absence of a well-defined 3D structure for NYCM that behaves as an Intrinsically Disordered Protein (IDP).
 The values obtained for the difference (SCS Cα—SCS Cβ) are indicative of an overall highly-disordered structure, but the predominance of positive values for successive residues in the central part of the peptide (segment 45–70) suggests their propensity to adopt an alpha-helical structure (Fig. 2A).
Nevertheless, TALOS-N Q-ratios calculated for the helix (Fig. 2B) on the residues belonging to this region are low (< 0.5), as well as the RCI-S2 order parameters (< 0.6) (Fig. 2D), indicating a highly dynamic region, where the alpha-helix can be formed only transiently. This conclusion is further supported by the absence of medium-range NOEs specific to helical secondary structure in the 3D NOESY-HSQC experiment.
Protein: DP04244 (UniProt P40205)
Region: residues 1	to 109
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The Kratky plot (Q2･I(Q) vs Q) (42) shows that the Q2･I(Q) value reaches a peak at around Q = 0.1 [Å-1] and decreases slightly, followed by the increase, suggesting that NCYM is not a completely unfolded protein, but a partially folded protein. This interpretation is further supported by the Q3 plot (Q3･I(Q) vs Q3), where the Q3･I(Q) value reaches a plateau, which is a hallmark of partially folded proteins (43). In contrast, no plateau was observed in the Porod-Debye plot (43), suggesting that NCYM is not a well-folded protein.
Protein: DP04244 (UniProt P40205)
Region: residues 1	to 109
Annotation: protein stabilization (Biological process)
Evidence: genetic transformation evidence used in manual assertion
Supporting statements:
In addition, knockdown of NCYM decreased the stability of the MYCN protein (Figure S11B). This NCYM knockdown-mediated destabilization of MYCN could be inhibited using the proteasome inhibitor MG132 (Figure S11C).
Protein: DP04244 (UniProt P40205)
Region: residues 1	to 109
Annotation: protein binding (Molecular function)
Evidence: immunoprecipitation evidence used in manual assertion
Supporting statements:
Therefore, using immunoprecipitation, we next searched for factors interacting with NCYM that are able to induce MYCN stabilization, and found that NCYM forms a complex with MYCN and GSK3β in CHP134 cells (Figure 3F and G).
Protein: DP04244 (UniProt P40205)
Region: residues 1	to 109
Annotation: protein binding (Molecular function)
Evidence: glutathione S-transferase pull-down assay evidence used in manual assertion
Supporting statements:
In addition, purified NCYM was capable of interacting with purified GSK3β and MYCN in vitro (Figure 3H).
Protein: DP04244 (UniProt P40205)
Region: residues 1	to 109
Annotation: negative regulation of protein kinase activity (Biological process)
Evidence: in vitro protein kinase assay evidence used in manual assertion
Supporting statements:
To examine the effect of NCYM on GSK3β-mediated phosphorylation of MYCN, we performed an in vitro kinase assay (Figure 3I). NCYM protein inhibited the phosphorylation of MYCN. Because the purified NCYM protein is not a substrate of GSK3β (Figure S12), it is unlikely that NCYM competes with MYCN for GSK3β as a substrate. Taken together these results suggest that the NCYM protein inhibits GSK3β-mediated MYCN phosphorylation and stabilizes the MYCN protein in vitro.
Protein: DP04244 (UniProt P40205)
Region: residues 1	to 109
Annotation: negative regulation of apoptotic process (Biological process)
Evidence: small interfering RNA knockdown evidence used in manual assertion
Supporting statements:
We performed NCYM knockdown in BE (2)-C, CHP134, SK-N-AS and SH-SY5Y human neuroblastoma cells. SK-N-AS and SH-SY5Y cells are MYCN-single copy but have a high expression of MYC, while BE (2)-C and CHP134 are cell lines with MYCN-amplification and hence have a high expression of MYCN and NCYM (Figure S13A). NCYM knockdown did not affect the survival of the MYCN-single neuroblastoma cell lines, but promoted massive apoptosis of the MYCN-amplified neuroblastoma cells (Figure S13B and C). In addition, in BE (2)-C cells, NCYM knockdown was found to inhibit cell proliferation and invasion (Figure S14B and D). These results suggest that NCYM promotes the survival and aggressiveness of MYCN-amplified neuroblastoma cells.
Protein: DP04244 (UniProt P40205)
Region: residues 1	to 109
Annotation: positive regulation of cell migration (Biological process)
Evidence: small interfering RNA knockdown evidence used in manual assertion
Supporting statements:
We performed NCYM knockdown in BE (2)-C, CHP134, SK-N-AS and SH-SY5Y human neuroblastoma cells. SK-N-AS and SH-SY5Y cells are MYCN-single copy but have a high expression of MYC, while BE (2)-C and CHP134 are cell lines with MYCN-amplification and hence have a high expression of MYCN and NCYM (Figure S13A). NCYM knockdown did not affect the survival of the MYCN-single neuroblastoma cell lines, but promoted massive apoptosis of the MYCN-amplified neuroblastoma cells (Figure S13B and C). In addition, in BE (2)-C cells, NCYM knockdown was found to inhibit cell proliferation and invasion (Figure S14B and D). These results suggest that NCYM promotes the survival and aggressiveness of MYCN-amplified neuroblastoma cells.
Protein: DP04244 (UniProt P40205)
Region: residues 1	to 109
Annotation: negative regulation of apoptotic process (Biological process)
Evidence: transgenic organism evidence used in manual assertion
Supporting statements:
We next examined the number of apoptotic cells in neuroblastomas from MYCN transgenic mice and MYCN/NCYM double transgenic mice by staining for cleaved caspase-3 (Figure S17). The number of apoptotic tumor cells was significantly decreased in the primary tumors of MYCN/NCYM double transgenic mice, suggesting that NCYM promotes the survival of neuroblastoma cells in vivo.
Protein: DP04244 (UniProt P40205)
Region: residues 1	to 109
Annotation: positive regulation of cell migration (Biological process)
Evidence: transgenic organism evidence used in manual assertion
Supporting statements:
Although tumor formation was not accelerated in the MYCN/NCYM double transgenic mice (Figure S15E), the incidence of neuroblastomas with distant metastases was significantly increased in the MYCN/NCYM double transgenic mice (Figure 4, Figure S16, Table S3).
Protein: DP04246 (UniProt Q4KL64)
Region: residues 1	to 73
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N terminal region of mALYREF2 (residues 1 to 73) does not show traceable density and is possibly disordered.
Cross-references: PDB:8SRR
EMDB:40739
Protein: DP04247 (UniProt Q8QL46)
Region: residues 1	to 12
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The protein forms a dimer in solution. The NMR solution structure of the protein consists of a ribbon-helix-helix (RHH) fold between residues 13 and 56 and a disordered N-terminal region (residues 1-12).
The structural ensemble of SvtR showed a well ordered region between residues 13 and 56 and an N-terminal non-convergent region between residues 1 and 12 (Fig. 1A).
Cross-references: PDB:2KEL
Protein: DP04247 (UniProt Q8QL46)
Region: residues 1	to 12
Annotation: flexible N-terminal tail (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The protein forms a dimer in solution. The NMR solution structure of the protein consists of a ribbon-helix-helix (RHH) fold between residues 13 and 56 and a disordered N-terminal region (residues 1-12).
The structural ensemble of SvtR showed a well ordered region between residues 13 and 56 and an N-terminal non-convergent region between residues 1 and 12 (Fig. 1A).
Cross-references: PDB:2KEL
Protein: DP04248 (UniProt C8ZKB3)
Region: residues 1	to 17
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal residues 1–17 of Drc and five amino acids that remained from the tag could not be resolved from the electron density maps. This region is predicted by ESpritz to be disordered (Supplementary Figure S3), which could explain the weak electron density (37).
Cross-references: PDB:6QLC
Protein: DP04248 (UniProt C8ZKB3)
Region: residues 1	to 17
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 N-terminal residues 1–17 of Drc and five amino acids that remained from the tag could not be resolved from the electron density maps. This region is predicted by ESpritz to be disordered (Supplementary Figure S3), which could explain the weak electron density (37).
Cross-references: PDB:6QLC
Protein: DP04249 (UniProt Q1D3H3)
Region: residues 422	to 489
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The C-terminal region (aa 422–489) was not resolved in the crystal structure, suggesting that it is flexible.
Cross-references: PDB:6RYK
Protein: DP04249 (UniProt Q1D3H3)
Region: residues 422	to 489
Annotation: flexible C-terminal tail (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The C-terminal region (aa 422–489) was not resolved in the crystal structure, suggesting that it is flexible.
Cross-references: PDB:6RYK
Protein: DP04250 (UniProt P0DJL7)
Region: residues 130	to 146
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The solution structure of the C-terminal domain, consisting of residues N130-L226 plus a 13-residue N-terminal extension, has been determined by using NMR spectroscopy. Residues before A147 are highly mobile and adopt a random coil conformation, but residues A147-L226 form a single structured domain consisting of five beta-strands and three helices arranged into a partially orthogonal, two-sheet beta-barrel, similar to the structure observed in the crystalline Co2+ complex of full-length DtxR.
The structure of DtxR(130–226) consists of a disordered N-terminal region (residues N130-A146) followed by a folded domain (residues A147-L226) (Fig. 3).
Residues preceding A147 have negative heteronuclear NOEs (Fig. 1b), indicating high mobility (25).
Cross-references: PDB:1BYM
Protein: DP04250 (UniProt P0DJL7)
Region: residues 130	to 144
Annotation: protein binding (Molecular function)
Evidence: gel electrophoresis evidence used in manual assertion
Supporting statements:
During purification and characterization of DtxR(130–226), it was observed that highly purified protein ran as a series of bands in nondenaturing polyacrylamide gels that correlated in mass to multiples of the monomeric protein molecular weight (Fig. 4).
However, in contrast to DtxR(130–226), DtxR(144–226) migrated as a single band corresponding to monomer molecular weight in nondenaturing polyacrylamide gels (Fig. 4).
Protein: DP04251 (UniProt O60832)
Region: residues 1	to 22
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
While the most N-terminal parts of dyskerin (residues 1-22 and 1-42 for the 5’ and 3’ dyskerin, respectively) are not visible in our structure, several disease mutations are located at our newly resolved inter-dyskerin interface (Fig. 2g)16.
The PDB structures show this region lacks electron density, indicating it is disordered. 
Cross-references: EMDB:17191
EMDB:17190
PDB:8OUF
PDB:8OUE
Protein: DP04251 (UniProt O60832)
Region: residues 1	to 22
Annotation: flexible N-terminal tail (Disorder function)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
While the most N-terminal parts of dyskerin (residues 1-22 and 1-42 for the 5’ and 3’ dyskerin, respectively) are not visible in our structure, several disease mutations are located at our newly resolved inter-dyskerin interface (Fig. 2g)16.
The PDB structures show this region lacks electron density, indicating it is disordered. 
Cross-references: EMDB:17191
EMDB:17190
PDB:8OUF
PDB:8OUE
Protein: DP04251 (UniProt O60832)
Region: residues 422	to 514
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Dyskerin consists of four domains: an N-terminal extension (NTE), a pseudouridine synthase and achaeosine transglycosylase (PUA), a tRNA pseudouridine synthase B-like (TruB) and a C-terminal extension (CTE) domain (Fig. 2a).
The PDB structures show this region lacks electron density, indicating it is disordered.
Cross-references: EMDB:17191
EMDB:17190
PDB:8OUF
PDB:8OUE
Protein: DP04251 (UniProt O60832)
Region: residues 422	to 514
Annotation: flexible C-terminal tail (Disorder function)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Dyskerin consists of four domains: an N-terminal extension (NTE), a pseudouridine synthase and achaeosine transglycosylase (PUA), a tRNA pseudouridine synthase B-like (TruB) and a C-terminal extension (CTE) domain (Fig. 2a).
The PDB structures show this region lacks electron density, indicating it is disordered.
Cross-references: EMDB:17191
EMDB:17190
PDB:8OUF
PDB:8OUE
Protein: DP04252 (UniProt Q9NX24)
Region: residues 1	to 22
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Secondary structures of dyskerin, GAR1, NHP2, NOP10 and
TCAB1 obtained from our structure are shown at the top of each sequence.
Supplementary Table 2 shows this region couldn't be modelled. The PDB structures show this region lacks electron density, indicating it is disordered.
Cross-references: EMDB:17191
PDB:8OUF
PDB:8OUE
EMDB:17190
Protein: DP04252 (UniProt Q9NX24)
Region: residues 1	to 22
Annotation: flexible N-terminal tail (Disorder function)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Secondary structures of dyskerin, GAR1, NHP2, NOP10 and
TCAB1 obtained from our structure are shown at the top of each sequence.
Supplementary Table 2 shows this region couldn't be modelled. The PDB structures show this region lacks electron density, indicating it is disordered.
Cross-references: EMDB:17191
PDB:8OUF
PDB:8OUE
EMDB:17190
Protein: DP04253 (UniProt Q9NY12)
Region: residues 162	to 217
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Secondary structures of dyskerin, GAR1, NHP2, NOP10 and TCAB1 obtained from our structure are shown at the top of each sequence.
Although the rest of the 3’ GAR1 CTE remains unresolved, our structure suggests that GAR1 helix 1 likely serves a similar role in substrate turnover in human H/ACA RNPs32.
Supplementary Table 2 shows this region couldn't be modelled. The PDB structures show this region lacks electron density, indicating it is disordered.
Cross-references: EMDB:17191
PDB:8OUE
PDB:8OUF
EMDB:17190
Protein: DP04253 (UniProt Q9NY12)
Region: residues 162	to 217
Annotation: flexible C-terminal tail (Disorder function)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Secondary structures of dyskerin, GAR1, NHP2, NOP10 and TCAB1 obtained from our structure are shown at the top of each sequence.
Although the rest of the 3’ GAR1 CTE remains unresolved, our structure suggests that GAR1 helix 1 likely serves a similar role in substrate turnover in human H/ACA RNPs32.
Supplementary Table 2 shows this region couldn't be modelled. The PDB structures show this region lacks electron density, indicating it is disordered.
Cross-references: EMDB:17191
PDB:8OUE
PDB:8OUF
EMDB:17190
Protein: DP04253 (UniProt Q9NY12)
Region: residues 1	to 64
Annotation: flexible N-terminal tail (Disorder function)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Secondary structures of dyskerin, GAR1, NHP2, NOP10 and TCAB1 obtained from our structure are shown at the top of each sequence.
Supplementary Table 2 shows this region couldn't be modelled. The PDB structures show this region lacks electron density, indicating it is disordered.
Cross-references: EMDB:17191
PDB:8OUE
PDB:8OUF
EMDB:17190
Protein: DP04253 (UniProt Q9NY12)
Region: residues 1	to 64
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Secondary structures of dyskerin, GAR1, NHP2, NOP10 and TCAB1 obtained from our structure are shown at the top of each sequence.
Supplementary Table 2 shows this region couldn't be modelled. The PDB structures show this region lacks electron density, indicating it is disordered.
Cross-references: EMDB:17191
PDB:8OUE
PDB:8OUF
EMDB:17190