LiteFold/DisProt huggingface dataset:
Protein: DP04372 (UniProt P0A367)
Region: residues 1064	to 1136
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Disordered regions indicating the location of cysteine residues are shown in gray font (Met1-Gly32, Gly780-Glu818, Glu1064-Pro1140).
The residues of Met1-Gly32, Ile369-Asn377, Gly442-Val444, Ser556-Asn559, Gly593, Thr609-Ala612, Gly780-Glu818, and Glu1064-Pro1140 could not be modelled because of missing of the corresponding electron density [25].
The disordered region described in the publication (Glu1064-Pro1140) corresponds to residues [1064–1136] in the UniProt sequence.
Cross-references: PDB:8W7N
Protein: DP04372 (UniProt P0A367)
Region: residues 1	to 32
Annotation: flexible N-terminal tail (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Disordered regions indicating the location of cysteine residues are shown in gray font (Met1-Gly32, Gly780-Glu818, Glu1064-Pro1140).
The residues of Met1-Gly32, Ile369-Asn377, Gly442-Val444, Ser556-Asn559, Gly593, Thr609-Ala612, Gly780-Glu818, and Glu1064-Pro1140 could not be modelled because of missing of the corresponding electron density [25].
Cross-references: PDB:8W7N
Protein: DP04373 (UniProt P9WI79)
Region: residues 403	to 413
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Two regions of the structure were disordered in all three independent monomers: a four amino acid loop (455–458) in blade 1 and the N-terminal 11 residues (403–413) that connect the sensor domain to the transmembrane domain.
In contrast, the 11 N-terminal residues were disordered in both crystal forms.
Cross-references: PDB:1RWI
PDB:1RWL
Protein: DP04373 (UniProt P9WI79)
Region: residues 403	to 413
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Two regions of the structure were disordered in all three independent monomers: a four amino acid loop (455–458) in blade 1 and the N-terminal 11 residues (403–413) that connect the sensor domain to the transmembrane domain.
Moreover, although the PknD sensor domain construct begins at the first residue following the predicted transmembrane helix, the first 11 residues of the sensor domain are disordered in all three independent monomers. This disorder suggests that the sensor domain is tethered flexibly to the transmembrane domain.
Cross-references: PDB:1RWI
PDB:1RWL
Protein: DP04375 (UniProt P71875)
Region: residues 211	to 224
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model of the complex contains residues 14–375 except for residues 216–222 of the mouth loop.
The 15-residue loop between strands β14 and β15, which partly seals off the pocket in the substrate-free structure, is disordered in the ADD-bound structure. It is possible that this loop has multiple conformations in the presence of ADD.
The exact residue numbers of the "mouth loop" were not explicitly provided in the publication. However, the authors describe it as a "15-residue loop between strands β14 and β15." Based on inspection of the referenced structure, this corresponds to residues 211–224, which span the loop connecting β14 and β15.
Cross-references: PDB:4QCK
Protein: DP04375 (UniProt P71875)
Region: residues 1	to 13
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region lacks electron density, indicating it is disordered.
Cross-references: PDB:4QCK
Protein: DP04375 (UniProt P71875)
Region: residues 1	to 13
Annotation: flexible N-terminal tail (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region lacks electron density, indicating it is disordered.
Cross-references: PDB:4QCK
Protein: DP04375 (UniProt P71875)
Region: residues 375	to 386
Annotation: flexible C-terminal tail (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region lacks electron density, indicating it is disordered.
Cross-references: PDB:4QCK
Protein: DP04375 (UniProt P71875)
Region: residues 375	to 386
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region lacks electron density, indicating it is disordered.
Cross-references: PDB:4QCK
Protein: DP04376 (UniProt Q9I0F4)
Region: residues 1	to 29
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The cryo-EM density map was of high quality, allowing the ab initio model building of the structure except for residues 1–29, 873–909 and 1196–1317, as a result of their structural flexibility or disorder (Fig. 1b, Supplementary Fig. 1).
Cross-references: PDB:8CP6
EMDB:16778
Protein: DP04376 (UniProt Q9I0F4)
Region: residues 873	to 909
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The cryo-EM density map was of high quality, allowing the ab initio model building of the structure except for residues 1–29, 873–909 and 1196–1317, as a result of their structural flexibility or disorder (Fig. 1b, Supplementary Fig. 1).
Cross-references: PDB:8CP6
EMDB:16778
Protein: DP04376 (UniProt Q9I0F4)
Region: residues 1196	to 1317
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The cryo-EM density map was of high quality, allowing the ab initio model building of the structure except for residues 1–29, 873–909 and 1196–1317, as a result of their structural flexibility or disorder (Fig. 1b, Supplementary Fig. 1).
For Tse5-CT (residues 1169–1317), we could only assign the first 27 N-terminal residues (residues 1169–1195) inside the Tse5-Shell cavity. The cryo-EM density inside the Tse5-Shell cavity for the remaining C-terminal 1196–1317 residues of Tse5-CT was too weak (Supplementary Fig. 3a). Such weak density is consistent with the encapsulated Tse5-CT remaining mostly flexible or disordered, in agreement with cryo-EM maps of Rhs11 and RhsA2 where only 10% and 23% of their encapsulated C-terminal toxin fragments could be resolved, respectively.
Cross-references: PDB:8CP6
EMDB:16778
Protein: DP04376 (UniProt Q9I0F4)
Region: residues 1196	to 1317
Annotation: flexible C-terminal tail (Disorder function)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The cryo-EM density map was of high quality, allowing the ab initio model building of the structure except for residues 1–29, 873–909 and 1196–1317, as a result of their structural flexibility or disorder (Fig. 1b, Supplementary Fig. 1).
For Tse5-CT (residues 1169–1317), we could only assign the first 27 N-terminal residues (residues 1169–1195) inside the Tse5-Shell cavity. The cryo-EM density inside the Tse5-Shell cavity for the remaining C-terminal 1196–1317 residues of Tse5-CT was too weak (Supplementary Fig. 3a). Such weak density is consistent with the encapsulated Tse5-CT remaining mostly flexible or disordered, in agreement with cryo-EM maps of Rhs11 and RhsA2 where only 10% and 23% of their encapsulated C-terminal toxin fragments could be resolved, respectively.
Cross-references: PDB:8CP6
EMDB:16778
Protein: DP04377 (UniProt Q51693)
Region: residues 336	to 351
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This crystal form contained two CapD molecules in the asymmetric unit, one with bound di-α-l-Glu and one unliganded (Table 2). Electron densities in both crystals were of high quality and generally continuous. Nevertheless, electron densities for residues 29–45 and 337–351, i.e. the first 17 and the last 15 residues of the L chain, and residue 528, the last residue of the S chain, were poorly defined, and these residues could not be modeled into the structure.
The P-segment, Cys336–Ser351, is disordered within the structure of CapD, as occurs with other Ntn hydrolases (36, 37).
Cross-references: PDB:3G9K
PDB:3GA9
Protein: DP04377 (UniProt Q51693)
Region: residues 29	to 45
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This crystal form contained two CapD molecules in the asymmetric unit, one with bound di-α-l-Glu and one unliganded (Table 2). Electron densities in both crystals were of high quality and generally continuous. Nevertheless, electron densities for residues 29–45 and 337–351, i.e. the first 17 and the last 15 residues of the L chain, and residue 528, the last residue of the S chain, were poorly defined, and these residues could not be modeled into the structure.
Cross-references: PDB:3G9K
PDB:3GA9
Protein: DP04378 (UniProt O82882)
Region: residues 138	to 247
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal domain IG adopts an immunoglobulin-like fold that consists of complementary segments spanning residues 57–122 and 257–287. Within domain IG, a sequence-variable region with weak electron density, which we designate as INS (insertion residues Lys150-Ser245), inserts between strands 5 and 6 of the immunoglobulin β sandwich (Figures 1A and 1B; Figure S2 sequence alignment).
Extending in opposite directions away from this axis are disordered structural elements, INS and D1, spanning Arg578-Arg676 (as judged by residual density and weak anomalous signals likely reflecting SeMet594, 598, and 608 in region D1).
The fact that we did not observe well-ordered density for INS in our model suggests this region may adopt multiple conformations that contribute to the ability of StcE to capture a variety of complex substrates at the cell surface.
This annotation of disorder in this region should be interpreted with caution: although the authors describe the region as disordered and it is not resolved in the full-length protein structure, the insertion domain (INS) adopts a well-defined, stable fold when expressed and crystallized independently at high resolution. The lack of electron density in the full-length structure may reflect flexibility introduced by the flanking linker regions, rather than intrinsic disorder of the INS domain itself.
Cross-references: PDB:3UJZ
Protein: DP04378 (UniProt O82882)
Region: residues 150	to 247
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The fact that we did not observe well-ordered density for INS in our model suggests this region may adopt multiple conformations that contribute to the ability of StcE to capture a variety of complex substrates at the cell surface. To explore this hypothesis further, we solved the structure of the isolated INS domain using an iodide soak SIRAS technique. Indeed, domain INS folds independently as a mixed, eight-stranded β sandwich with homology to the T4 bacteriophage structural protein gp9 (Z-score of 6.2) and contains an additional β strand followed by a perpendicular arrangement of two α helices in its N-terminal region.
Domain INS (H132-N251) was cloned using 5′-CCGCAGGCTAGCCATCTGGATGGTGTTCCGGAAG-3′ and 5′- CCGCAGCTCGAGTTAATTATTCTCCAGTTCACCGGAG-3′.
While this region has been annotated as a transition between disorder and order—based on its absence in the full-length protein structure and its well-defined, stable fold when expressed independently—this interpretation should be approached with caution. The apparent disorder in the context of the full-length protein may instead arise from conformational flexibility introduced by adjacent linker regions, rather than from intrinsic disorder within the domain itself.
Cross-references: PDB:4DNY
PDB:3UJZ
Protein: DP04378 (UniProt O82882)
Region: residues 578	to 676
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Extending in opposite directions away from this axis are disordered structural elements, INS and D1, spanning Arg578-Arg676 (as judged by residual density and weak anomalous signals likely reflecting SeMet594, 598, and 608 in region D1).
Cross-references: PDB:3UJZ
Protein: DP04378 (UniProt O82882)
Region: residues 150	to 247
Annotation: order (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
To explore this hypothesis further, we solved the structure of the isolated INS domain using an iodide soak SIRAS technique. Indeed, domain INS folds independently as a mixed, eight-stranded β sandwich with homology to the T4 bacteriophage structural protein gp9 (Z-score of 6.2) and contains an additional β strand followed by a perpendicular arrangement of two α helices in its N-terminal region. We then positioned the compact module in the context of the existing model to obtain a more complete description of the StcE structure and function (correct placement was confirmed by the anomalous signal of SeMet205). A long loop (His132-Lys150) links the N terminus of INS to domain IG and provides flexibility, placing the putative exosite domain ∼35 Å away from the catalytic center in our model (Figure 5A).
Cross-references: PDB:4DNY
Protein: DP04378 (UniProt O82882)
Region: residues 138	to 150
Annotation: flexible linker (Disorder function)
Evidence: combinatorial experimental and curator inference evidence used in manual assertion
Supporting statements:
To explore this hypothesis further, we solved the structure of the isolated INS domain using an iodide soak SIRAS technique. Indeed, domain INS folds independently as a mixed, eight-stranded β sandwich with homology to the T4 bacteriophage structural protein gp9 (Z-score of 6.2) and contains an additional β strand followed by a perpendicular arrangement of two α helices in its N-terminal region. We then positioned the compact module in the context of the existing model to obtain a more complete description of the StcE structure and function (correct placement was confirmed by the anomalous signal of SeMet205). A long loop (His132-Lys150) links the N terminus of INS to domain IG and provides flexibility, placing the putative exosite domain ∼35 Å away from the catalytic center in our model (Figure 5A).
Being flexibly linked, domain INS may exist in various conformations to present a potential protein-binding interface relative to its respective targets.
Protein: DP04378 (UniProt O82882)
Region: residues 140	to 243
Annotation: peptidase activity (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
Curiously, the poorly resolved density corresponding to the INS region (Lys150-Ser245) appears to approach the active site (Figure 1B). We generated a truncation mutant of this sequence-variable region (ΔINS) (Figure S2) to test its involvement in substrate binding. ΔINS exhibited decreased proteolytic activity toward C1-INH compared to WT StcE (Figure 4A) (circular dichroism spectrum confirmed no large perturbation to the overall structure due to the mutation, as shown in Figures 4B and 4C).
Protein: DP04378 (UniProt O82882)
Region: residues 140	to 243
Annotation: proteolysis (Biological process)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
Curiously, the poorly resolved density corresponding to the INS region (Lys150-Ser245) appears to approach the active site (Figure 1B). We generated a truncation mutant of this sequence-variable region (ΔINS) (Figure S2) to test its involvement in substrate binding. ΔINS exhibited decreased proteolytic activity toward C1-INH compared to WT StcE (Figure 4A) (circular dichroism spectrum confirmed no large perturbation to the overall structure due to the mutation, as shown in Figures 4B and 4C).
Protein: DP04378 (UniProt O82882)
Region: residues 719	to 753
Annotation: disorder (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
A partially resolved region, residues 679–798 (D2), docks against M on the opposite face of the active site.
This region lacks electron density, indicating it is disordered.
Cross-references: PDB:3UJZ
Protein: DP04379 (UniProt Q8DR55)
Region: residues 1	to 159
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H-15N correlation spectrum of this MapZcyto construct displays typical features of an unfolded protein, i.e. intense narrow peaks and very low chemical shift dispersion, especially in the proton dimension (Fig. 1b).
The cytoplasmic domain of MapZ therefore appears to be mostly an intrinsically disordered region (IDR) with moderate tendency to be structured for the amino acid region 22 to 86.
Cross-references: BMRB:28006
Protein: DP04379 (UniProt Q8DR55)
Region: residues 17	to 43
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The N-terminal residues 17 to 43 experienced an intensity decrease of up to 70% for the MapZcyto:FtsZa 1:4.7 ratio, whereas other residues of the cytoplasmic domain of MapZ remained largely unaffected. Similar results were obtained with the FtsZb construct in the presence of which the intensity of the same signals decreased stronger at higher MapZcyto:FtsZb protein ratios (Fig. S4a). These results suggest that the 17-to-43 N-terminal region of MapZcyto interacts with monomeric FtsZ, whereas the remainder of the cytosolic region stays completely flexible in the protein-protein complex.
Protein: DP04379 (UniProt Q8DR55)
Region: residues 11	to 110
Annotation: lipid binding (Molecular function)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
Altogether, monitoring of MapZcyto with liquid-state NMR and deuterated liposomes with 2H 1D ssNMR shows that the N-terminal portion of MapZcyto (up to residue 110) interacts with membrane lipids. On one hand, the unfolded and positively charged region of MapZcyto (residues 3 to 11) interacts with the negatively charged lipid heads. On the other hand, the two amphipathic helices (residues 45 to 68 and 79 to 95), which present hydrophobic spots surrounded by positively charged and hydrophilic residues, induce packing defects of the lipids by increasing the mobility of their acyl chains
This evidence was specifically created for the solid-state NMR experiments.
Protein: DP04379 (UniProt Q8DR55)
Region: residues 314	to 354
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The two MapZextra1 and MapZextra2 subdomains are linked by a long polypeptide containing a serine-rich region (serine-rich linker, SRL) from residues K314 to S354. Whereas the majority of the amide protons of this SRL were not detected in the 2D-[1H,15N] correlation spectrum recorded at pH 7.5, intense resonances appear at pH 4.5 with chemical shifts that were characteristic of a disordered structure (8.1–8.5 p.p.m.; Supplementary Fig. 3B).
Protein: DP04379 (UniProt Q8DR55)
Region: residues 314	to 354
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The two MapZextra1 and MapZextra2 subdomains are linked by a long polypeptide containing a serine-rich region (serine-rich linker, SRL) from residues K314 to S354. Whereas the majority of the amide protons of this SRL were not detected in the 2D-[1H,15N] correlation spectrum recorded at pH 7.5, intense resonances appear at pH 4.5 with chemical shifts that were characteristic of a disordered structure (8.1–8.5 p.p.m.; Supplementary Fig. 3B).
All these results point out a bi-modular organization of the extracellular domain of MapZ, with two independent subdomains connected by a highly dynamic SRL.
Protein: DP04379 (UniProt Q8DR55)
Region: residues 314	to 354
Annotation: flexible linker (Disorder function)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The independent mobility of the two domains conferred by the flexible SRL was confirmed by small-angle X-ray scattering (SAXS) data recorded on the full-length extracellular domain at two concentrations (Supplementary Fig. 5A). Indeed, the Kratky plot derived from the experimental I(s) scattering curves showed a behaviour for s>2 nm−1 in agreement with the presence of a large flexibility.
All these results point out a bi-modular organization of the extracellular domain of MapZ, with two independent subdomains connected by a highly dynamic SRL.
Protein: DP04379 (UniProt Q8DR55)
Region: residues 1	to 41
Annotation: protein binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
Co-immuno-precipitation revealed in vivo interaction between FtsZ and MapZ, which is mediated by the cytoplasmic domain of MapZ (Fig. 4a). The cytoplasmic domain of MapZ (MapZcyto) strongly interacts with FtsZ (KD= 8.76 nM), more precisely via its N-terminal peptide predicted as an alpha-helix (MapZ(1-41) from Met-1 to Gly-41) (KD= 20.4 nM) (Extended Data Fig. 7a-d).
Protein: DP04379 (UniProt Q8DR55)
Region: residues 1	to 41
Annotation: protein binding (Molecular function)
Evidence: deletion mutation phenotypic evidence used in manual assertion
Supporting statements:
In vivo deletion of MapZ N-terminal peptide (mapZΔ(1-41)) did not impaired MapZ septal localization (Extended Data Fig. 6e), but resulted in delocalization of FtsZ (Extended Data Fig. 6f-g), which subsequently leads to aberrant cell morphogenesis, asymmetric division or cell lysis (Extended Data Fig. 1a and Fig. 6h, Supplementary Video 8). This was also observed in mapZΔcyto strain (Extended Data Fig. 6i, Supplementary Video 9). Therefore, MapZ direct interaction with FtsZ is strictly required for FtsZ positioning.
Protein: DP04379 (UniProt Q8DR55)
Region: residues 65	to 69
Annotation: phosphorylation display site (Disorder function)
Evidence: protein mass spectrometry evidence used in manual assertion
Supporting statements:
Mass spectrometry analysis of MapZ further showed that MapZ is phosphorylated on Thr-67 and Thr-78 (Extended Data Fig. 8a-b).
Protein: DP04379 (UniProt Q8DR55)
Region: residues 76	to 80
Annotation: phosphorylation display site (Disorder function)
Evidence: protein mass spectrometry evidence used in manual assertion
Supporting statements:
Mass spectrometry analysis of MapZ further showed that MapZ is phosphorylated on Thr-67 and Thr-78 (Extended Data Fig. 8a-b).
Protein: DP04380 (UniProt P15917)
Region: residues 34	to 61
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal 26 residues are invisible in our electron density maps, and we presume that they are disordered.
Cross-references: PDB:1J7N