LiteFold/DisProt huggingface dataset:
Protein: DP04392 (UniProt Q83RJ4)
Region: residues 562	to 571
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model contains residues 25–561 and misses the N-terminal 24 residues, the C-terminal 10 residues and some residues in the disordered linking loops (broken lines in Fig. 2a) owing to the lack of electron density.
Cross-references: PDB:3CVR
Protein: DP04392 (UniProt Q83RJ4)
Region: residues 269	to 278
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model contains residues 25–561 and misses the N-terminal 24 residues, the C-terminal 10 residues and some residues in the disordered linking loops (broken lines in Fig. 2a) owing to the lack of electron density.
The two domains are linked by a long disordered loop (residues 269–278).
Cross-references: PDB:3CVR
Protein: DP04392 (UniProt Q83RJ4)
Region: residues 269	to 278
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model contains residues 25–561 and misses the N-terminal 24 residues, the C-terminal 10 residues and some residues in the disordered linking loops (broken lines in Fig. 2a) owing to the lack of electron density.
The two domains are linked by a long disordered loop (residues 269–278).
In solution, the long flexible loop should allow for changes of distance and relative orientation between the catalytic domain and the putative substrate binding LRR domain (see below).
In IpaH3, the two domains are linked together by a long flexible loop. During elongation of polyubiquitin chains on the substrate, the distance between the last-added ubiquitin and the active site cysteine in E3 would increase and impede further ubiquitin transfer for a rigid structure. Thus, the linking loop probably provides an ideal structural flexibility that could help to shorten the distance between the catalytic cysteine in IpaH and ubiquitin at the end of the elongating chain, and therefore allows for ubiquitin transfer during chain elongation.
Cross-references: PDB:3CVR
Protein: DP04392 (UniProt Q83RJ4)
Region: residues 507	to 540
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model contains residues 25–561 and misses the N-terminal 24 residues, the C-terminal 10 residues and some residues in the disordered linking loops (broken lines in Fig. 2a) owing to the lack of electron density.
Notably, the C-terminal two helices, α14 and α15, connected by a long disordered loop of 35 residues, project outward from the core structure, which, together with parts of α8-α10, α12 and α13, generates a concave surface on the molecule.
Although the paper does not specify residue numbers, the disordered loop described as "a long disordered loop of 35 residues" connecting helices α14 and α15 can be mapped to residues 507–540 based on the analysis of the PDB structure.
Cross-references: PDB:3CVR
Protein: DP04392 (UniProt Q83RJ4)
Region: residues 1	to 24
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 final model contains residues 25–561 and misses the N-terminal 24 residues, the C-terminal 10 residues and some residues in the disordered linking loops (broken lines in Fig. 2a) owing to the lack of electron density.
Cross-references: PDB:3CVR
Protein: DP04392 (UniProt Q83RJ4)
Region: residues 562	to 571
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 final model contains residues 25–561 and misses the N-terminal 24 residues, the C-terminal 10 residues and some residues in the disordered linking loops (broken lines in Fig. 2a) owing to the lack of electron density.
Cross-references: PDB:3CVR
Protein: DP04393 (UniProt P31489)
Region: residues 52	to 61
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron density quality was good throughout the structure (Figure 1), but 37 residues were disordered in the final model (see below).
Amino (N)‐terminal residues 26–31 and loop 52–61 are missing in the final model, as well as the start of the stalk domain (221–241). The head region is composed almost solely of β‐sheets making a novel nine coiled left‐handed parallel β‐roll (LPBR), surrounded by a partly disordered (N)‐terminal random coil and a C‐terminal neck region, which consists of a random coil and a short helix at the start of the stalk domain.
The rest of the proline‐rich loop (52‐PVRPPVPGAG‐61) is disordered, but one possibility is that the chain reverses direction at Y51, forming another IS and then loops around clockwise to connect to G62 (see Supplementary data, Figure 2).
Cross-references: PDB:1P9H
Protein: DP04393 (UniProt P31489)
Region: residues 221	to 241
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron density quality was good throughout the structure (Figure 1), but 37 residues were disordered in the final model (see below).
Amino (N)‐terminal residues 26–31 and loop 52–61 are missing in the final model, as well as the start of the stalk domain (221–241). The head region is composed almost solely of β‐sheets making a novel nine coiled left‐handed parallel β‐roll (LPBR), surrounded by a partly disordered (N)‐terminal random coil and a C‐terminal neck region, which consists of a random coil and a short helix at the start of the stalk domain.
Cross-references: PDB:1P9H
Protein: DP04394 (UniProt P0C7U7)
Region: residues 261	to 279
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues Lys261–Pro279 could not be fitted to the electron density owing to disorder.
Similarly, in our model the residues Lys261–Pro279 could not be modeled owing to disorder.
Cross-references: PDB:4JBU
Protein: DP04394 (UniProt P0C7U7)
Region: residues 49	to 63
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N- and C termini of the protein (residues 23–27 and 323–326) are not visible in the electron density maps, nor is Tyr90 or the residues in two internal loops (49–63 and 260–275). The inherent flexibility of these regions may have impeded efforts to crystallize the wild-type protein.
Cross-references: PDB:1R6F
Protein: DP04394 (UniProt P0C7U7)
Region: residues 260	to 275
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N- and C termini of the protein (residues 23–27 and 323–326) are not visible in the electron density maps, nor is Tyr90 or the residues in two internal loops (49–63 and 260–275). The inherent flexibility of these regions may have impeded efforts to crystallize the wild-type protein.
Cross-references: PDB:1R6F
Protein: DP04395 (UniProt P9WNI7)
Region: residues 1	to 12
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Additional regions of disorder are found at the N- and C-termini of the complexes with the EsxFma and EsxOmt subunits having a substantial number of disordered residues at their C-termini.
Although the original publication does not explicitly define the boundaries of the disordered regions, manual inspection of the structure indicates that the N-terminal residues 1–12 are not resolved in the electron density map, suggesting intrinsic disorder in this segment. The structured regions observed in the model correspond to residues A13–A39, A49–A69, and C13–C68, as listed in Table 2. Based on this analysis, the disordered region was annotated accordingly.
Cross-references: PDB:3OGI
Protein: DP04395 (UniProt P9WNI7)
Region: residues 70	to 94
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Additional regions of disorder are found at the N- and C-termini of the complexes with the EsxFma and EsxOmt subunits having a substantial number of disordered residues at their C-termini.
Although the original publication does not explicitly define the boundaries of the disordered regions, manual inspection of the structure indicates that the C-terminal residues 70–94 are not resolved in the electron density map, suggesting intrinsic disorder in this segment. The structured regions observed in the model correspond to residues A13–A39, A49–A69, and C13–C68 in the case of 3OGI, and residues A12–A69; C9-C69 in 4GZR, as listed in Table 2. Based on this analysis, the disordered region was annotated accordingly.
Cross-references: PDB:3OGI
PDB:4GZR
Protein: DP04396 (UniProt P9WGU1)
Region: residues 25	to 41
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
N-terminal residues 2–18 are disordered, as electron densities for these residues were essentially absent in all three structures, consistent with high flexibility.
The recombinant PstS-1 lacks the first residue (Cys), and residues 2–18 (Figure 2) in the three independent structures show no interpretable densities.
As indicated in Figure 1, residues 2–18 (GSKPPSGSPETGAGAGT) of the PstS-1 crystal structure are disordered.
This tether is apparently highly flexible, since no interpretable electron density was observed for residues 2–18 in all three independent structures of PstS-1 in the asymmetric unit. (The recombinant PstS-1 lacks the Cys1 residue [see Experimental Procedures].)
The N-terminal segment that tethers PstS-1 on the cell surface is highly flexible.
The disordered region from residues 2 to 18 mentioned in the paper corresponds to residues 25 to 41 of the UniProt sequence.
Cross-references: PDB:1PC3
Protein: DP04396 (UniProt P9WGU1)
Region: residues 25	to 41
Annotation: flexible N-terminal tail (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
 As indicated in Figure 1, residues 2–18 (GSKPPSGSPETGAGAGT) of the PstS-1 crystal structure are disordered. The first 26 residues of the mature PstS-1 do not exist in PBP (Andersen, 1994; Chang et al., 1994; Lefevre et al., 1997).
After processing, this region acts as the N-terminal tail of the mature protein.
Protein: DP04397 (UniProt Q5ZTK6)
Region: residues 492	to 501
Annotation: order to disorder (Structural transition)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Interestingly, post-glutamylation, the SidJ loop (residues 492–501) making up the migrated pocket becomes disordered in the structure, while the canonical pocket architecture remains intact (Fig. 4C, D).
Structural comparison between SidJ E565A (Yellow)/CaM + SdeA (Green) in its pre-glutamylation and post-catalytic states. Highlighted is a loop of SidJ (Red) located in the migrated pocket that undergoes structural change post-catalysis.
Cross-references: PDB:7PQE
PDB:7PPO
Protein: DP04397 (UniProt Q5ZTK6)
Region: residues 497	to 501
Annotation: protein adenylylation (Biological process)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
Since there is a cluster of glutamates (E497, E499, E501, and E565) concentrated in and around the bridging peptide of SidJ (Supplementary Fig. 9), we decided to mutagenize all these glutamates individually and combined. Mutating single glutamates in the bridging peptide did not result in the decrease of autoAMPylation, but mutating the cluster of glutamates resulted in a marked reduction in SidJ autoAMPylation (Fig. 5D)."
Protein: DP04397 (UniProt Q5ZTK6)
Region: residues 492	to 501
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Interestingly, post-glutamylation, the SidJ loop (residues 492–501) making up the migrated pocket becomes disordered in the structure, while the canonical pocket architecture remains intact (Fig. 4C, D).
Cross-references: PDB:7PQE
Protein: DP04398 (UniProt Q5ZTK4)
Region: residues 590	to 759
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Interestingly, after 3D classification of the particles, we observed two well-resolved particle classes, Class I (15% of total particles) contained both SidJ/CaM and SdeA well resolved and Class II (17% of total particles) represented only SidJ/CaM with discernible density while SdeA was found to be disordered, presumably dissociated from SidJ but still tethered to it due to GraFix (Supplementary Fig. 5).
After manual inspection of the PDB structure, the disordered regions in SdeA mentioned by the authors in the post-catalytic state correspond to residues 590–759 and 903–1190.
Cross-references: PDB:7PQE
Protein: DP04398 (UniProt Q5ZTK4)
Region: residues 903	to 1190
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Interestingly, after 3D classification of the particles, we observed two well-resolved particle classes, Class I (15% of total particles) contained both SidJ/CaM and SdeA well resolved and Class II (17% of total particles) represented only SidJ/CaM with discernible density while SdeA was found to be disordered, presumably dissociated from SidJ but still tethered to it due to GraFix (Supplementary Fig. 5).
After manual inspection of the PDB structure, the disordered regions in SdeA mentioned by the authors in the post-catalytic state correspond to residues 590–759 and 903–1190.
Cross-references: PDB:7PQE
Protein: DP04399 (UniProt P08062)
Region: residues 518	to 556
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Two large portions of the VirE2 molecule are not observed in the crystal structure. The experimental maps contained no electron density at the C terminus (last 39 residues), which suggests a flexible and possibly unstructured form.
No electron density was observed for these regions in a second crystal form that was obtained under different conditions and crystallized in a different space group (P21) (data not shown).
These findings suggest that the terminal regions of VirE2 are flexible or intrinsically unstructured, although partial proteolysis may also have occurred during crystallization.
The final model includes residues 112–179, 183–342, 345–356, 364–439, 445–473, and 476–517 of VirE2 and residues 30–57 of VirE1, 68 water molecules and one molecule of PEG.
Cross-references: PDB:3BTP
Protein: DP04399 (UniProt P08062)
Region: residues 1	to 111
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
A larger segment at the N terminus (111 residues) also lacks electron density. No electron density was observed for these regions in a second crystal form that was obtained under different conditions and crystallized in a different space group (P21) (data not shown).
These findings suggest that the terminal regions of VirE2 are flexible or intrinsically unstructured, although partial proteolysis may also have occurred during crystallization.
The final model includes residues 112–179, 183–342, 345–356, 364–439, 445–473, and 476–517 of VirE2 and residues 30–57 of VirE1, 68 water molecules and one molecule of PEG.
Cross-references: PDB:3BTP
Protein: DP04399 (UniProt P08062)
Region: residues 1	to 111
Annotation: flexible N-terminal tail (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
A larger segment at the N terminus (111 residues) also lacks electron density. No electron density was observed for these regions in a second crystal form that was obtained under different conditions and crystallized in a different space group (P21) (data not shown).
These findings suggest that the terminal regions of VirE2 are flexible or intrinsically unstructured, although partial proteolysis may also have occurred during crystallization.
The final model includes residues 112–179, 183–342, 345–356, 364–439, 445–473, and 476–517 of VirE2 and residues 30–57 of VirE1, 68 water molecules and one molecule of PEG.
Cross-references: PDB:3BTP
Protein: DP04399 (UniProt P08062)
Region: residues 518	to 556
Annotation: flexible C-terminal tail (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Two large portions of the VirE2 molecule are not observed in the crystal structure. The experimental maps contained no electron density at the C terminus (last 39 residues), which suggests a flexible and possibly unstructured form.
No electron density was observed for these regions in a second crystal form that was obtained under different conditions and crystallized in a different space group (P21) (data not shown).
These findings suggest that the terminal regions of VirE2 are flexible or intrinsically unstructured, although partial proteolysis may also have occurred during crystallization.
The final model includes residues 112–179, 183–342, 345–356, 364–439, 445–473, and 476–517 of VirE2 and residues 30–57 of VirE1, 68 water molecules and one molecule of PEG.
Cross-references: PDB:3BTP
Protein: DP04401 (UniProt A0AAI8ESY0)
Region: residues 154	to 255
Annotation: molten globule (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In agreement with previous observations (Souza et al., 2011), the 1H-15N heteronuclear single quantum coherence (HSQC) spectrum of VirB9CT recorded at 37°C displays fewer cross peaks than expected and a broad distribution of line widths, characteristic of a domain with significant conformational freedom (Figure 1B).
Protein: DP04401 (UniProt A0AAI8ESY0)
Region: residues 154	to 255
Annotation: order (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In contrast, the 1H-15N HSQC spectrum of 15N labeled VirB9CT in the presence of the unlabeled VirB7NT peptide displays the expected number of cross peaks and a narrower distribution of line widths (Figures 1B and S1), indicating that complex formation stabilizes a single VirB9CT conformation.
The profile of 15N order parameters along the backbone of VirB9CT in complex with VirB7NT is shown in Figures 4A and S6A and color-coded on the backbone of the complex (Figure 4B). VirB9CT displays S2 typical of a rigid protein with an average S2 value of 0.8.
Protein: DP04401 (UniProt A0AAI8ESY0)
Region: residues 154	to 255
Annotation: molten globule to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In agreement with previous observations (Souza et al., 2011), the 1H-15N heteronuclear single quantum coherence (HSQC) spectrum of VirB9CT recorded at 37°C displays fewer cross peaks than expected and a broad distribution of line widths, characteristic of a domain with significant conformational freedom (Figure 1B). In contrast, the 1H-15N HSQC spectrum of 15N labeled VirB9CT in the presence of the unlabeled VirB7NT peptide displays the expected number of cross peaks and a narrower distribution of line widths (Figures 1B and S1), indicating that complex formation stabilizes a single VirB9CT conformation.
VirB9CT is only partially folded in solution but forms a tight and rigid complex upon binding to VirB7.
Here, we show that VirB7NT forms a short β strand upon binding to VirB9 and stabilizes it.
Protein: DP04401 (UniProt A0AAI8ESY0)
Region: residues 154	to 255
Annotation: molten globule (Structural state)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
The greater ANS fluorescence change observed upon addition of the free protein relative to the complex indicates that the unbound VirB9Ct exposes a greater amount of hydrophobic surface area than the complex.
Protein: DP04401 (UniProt A0AAI8ESY0)
Region: residues 154	to 255
Annotation: order (Structural state)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
The greater ANS fluorescence change observed upon addition of the free protein relative to the complex indicates that the unbound VirB9Ct exposes a greater amount of hydrophobic surface area than the complex.
Protein: DP04401 (UniProt A0AAI8ESY0)
Region: residues 154	to 255
Annotation: molten globule to order (Structural transition)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
The greater ANS fluorescence change observed upon addition of the free protein relative to the complex indicates that the unbound VirB9Ct exposes a greater amount of hydrophobic surface area than the complex.
Protein: DP04401 (UniProt A0AAI8ESY0)
Region: residues 154	to 255
Annotation: protein binding (Molecular function)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
The greater ANS fluorescence change observed upon addition of the free protein relative to the complex indicates that the unbound VirB9Ct exposes a greater amount of hydrophobic surface area than the complex.
Protein: DP04401 (UniProt A0AAI8ESY0)
Region: residues 154	to 255
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In contrast, the 1H-15N HSQC spectrum of 15N labeled VirB9CT in the presence of the unlabeled VirB7NT peptide displays the expected number of cross peaks and a narrower distribution of line widths (Figures 1B and S1), indicating that complex formation stabilizes a single VirB9CT conformation.
Protein: DP04401 (UniProt A0AAI8ESY0)
Region: residues 154	to 255
Annotation: protein binding (Molecular function)
Evidence: protein thermal shift assay evidence used in manual assertion
Supporting statements:
Notably, the thermal denaturation experiment showed that the complex has significantly higher unfolding enthalpy (29.57 kcal/mol) than the unbound VirB9Ct (10.42 kcal/mol; Figure 2C). This observation may be explained considering that VirB9Ct−VirB7Nt unfolding and dissociation
occur within a single transition as a consequence of the coupling between these two processes.
Protein: DP04401 (UniProt A0AAI8ESY0)
Region: residues 154	to 255
Annotation: molten globule (Structural state)
Evidence: protein thermal shift assay evidence used in manual assertion
Supporting statements:
Notably, the thermal denaturation experiment showed that the complex has significantly higher unfolding enthalpy (29.57 kcal/mol) than the unbound VirB9Ct (10.42 kcal/mol; Figure 2C). This observation may be explained considering that VirB9Ct−VirB7Nt unfolding and dissociation
occur within a single transition as a consequence of the coupling between these two processes.