LiteFold/DisProt huggingface dataset:
Protein: DP04380 (UniProt P15917)
Region: residues 379	to 400
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Noteworthy, the 2β2-2β3 loop region (residues 300–323) which is implicated in pore formation was not resolved in our map. This indicates a high flexibility of this loop, which is in line with previous MD simulations [38].
Cross-references: PDB:6ZXL
PDB:6ZXK
PDB:6ZXJ
Protein: DP04381 (UniProt P0CL43)
Region: residues 27	to 69
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 15N HSQC spectrum from InvH27-147 also showed increased dispersion upon binding InvG520-562 (Figures S4A and S4B). Furthermore, additional amides not present in the InvH70-147 complex have 1NH chemical shifts in the narrow range of 8.0–8.5 ppm. Consistent with sequence-based predictions (Cheng et al., 2005; Jones and Cozzetto, 2015; Kelley et al., 2015), these chemical shifts indicate that the InvH linker is conformationally disordered (Konrat, 2014).
Protein: DP04381 (UniProt P0CL43)
Region: residues 27	to 69
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 15N HSQC spectrum from InvH27-147 also showed increased dispersion upon binding InvG520-562 (Figures S4A and S4B). Furthermore, additional amides not present in the InvH70-147 complex have 1NH chemical shifts in the narrow range of 8.0–8.5 ppm. Consistent with sequence-based predictions (Cheng et al., 2005; Jones and Cozzetto, 2015; Kelley et al., 2015), these chemical shifts indicate that the InvH linker is conformationally disordered (Konrat, 2014).
Secondary structure analysis by Phyre2 for InvH predicted an α-helical C-terminal domain, joined by a long (∼50 residue) disordered linker region to the signature (L-A/S-G/A-C) N-terminal lipobox (Kelley et al., 2015).
Protein: DP04381 (UniProt P0CL43)
Region: residues 27	to 69
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
In the case of the InvH27-147 construct, which includes the predicted disordered linker region, fitting of the SAXS data produced an envelope with additional scattering density extending from both poles of the InvH70-147 structure (Figure 2B). These poles correspond to the locations of the N termini of the InvH70-147 crystal structure where the linker residues would be joined. Collectively, the SEC-MALS and SAXS data confirm the formation of an InvH homodimer in solution, with the SAXS data additionally supporting the position of the InvH27-147 N-terminal linker region.
Cross-references: SASBDB:SASDJR4
Protein: DP04381 (UniProt P0CL43)
Region: residues 70	to 82
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
However, whereas the crystallized homodimer has two helices, α1a and α1b (residues 73–88 and 90–101, respectively), the heterodimer in solution has one extended helix spanning residues 83–101, and residues 70–82 are disordered.
Cross-references: BMRB:30765
PDB:6XFL
Protein: DP04383 (UniProt D0ZRB2)
Region: residues 709	to 728
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In both copies of the NEL domain there was no visible electron density for loop αM–αN (residues 709–728) of the C-terminal helix bundle. In contrast, the loop linking the LRR and NEL domains that was disordered in the published apo structures of IpaH3 [21] and SspH2 [22] is clearly defined in the Trx1-bound SlrP structure.
Cross-references: PDB:4PUF
Protein: DP04384 (UniProt Q7BCK4)
Region: residues 741	to 758
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 591 to 740, in addition to six residues from the linker region of the N-terminal His tag (Fig. 1C). The last 18 residues of IcsA-AC are disordered.
Cross-references: PDB:3ML3
Protein: DP04384 (UniProt Q7BCK4)
Region: residues 741	to 758
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Furthermore, the chain can only be traced to residue 740, indicating that the last 18 amino acids are flexible in a manner consistent with it forming a linker connecting the extracellular α-domain to the β-barrel membrane anchor.
Cross-references: PDB:5KE1
Protein: DP04384 (UniProt Q7BCK4)
Region: residues 741	to 758
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Furthermore, the chain can only be traced to residue 740, indicating that the last 18 amino acids are flexible in a manner consistent with it forming a linker connecting the extracellular α-domain to the β-barrel membrane anchor.
Cross-references: PDB:5KE1
Protein: DP04385 (UniProt Q9ZKJ5)
Region: residues 41	to 50
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Two flexible loop regions (Lys14−Gly22 and Lys41−Tyr50 in chain A; Lys14−Lys24 and Pro40−Ser49 in chain B), as well as the C-terminal region containing the eight-residue affinity tag (LEHHHHHH) (13 residues in chain A; 12 residues in chain B) have no electron density and are missing from the model.
Cross-references: PDB:3AKJ
Protein: DP04385 (UniProt Q9ZKJ5)
Region: residues 14	to 23
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Two flexible loop regions (Lys14−Gly22 and Lys41−Tyr50 in chain A; Lys14−Lys24 and Pro40−Ser49 in chain B), as well as the C-terminal region containing the eight-residue affinity tag (LEHHHHHH) (13 residues in chain A; 12 residues in chain B) have no electron density and are missing from the model.
Cross-references: PDB:3AKJ
Protein: DP04385 (UniProt Q9ZKJ5)
Region: residues 14	to 23
Annotation: disorder to order (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
However, the nucleotide binding induces ordering in one of the two flexible loops that are disordered in the apo structure. That is, the glycine-rich loop (Lys14–Gly22) is disordered in the apo structure, whereas it becomes ordered upon binding ADP or AMP-PNP.
Cross-references: PDB:3AKJ
PDB:3AKK
PDB:3AKL
Protein: DP04385 (UniProt Q9ZKJ5)
Region: residues 41	to 50
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
As shown in the PDB crystal structures, in the presence of ADP, this disordered loop also gains structure.
Cross-references: PDB:3AKK
Protein: DP04386 (UniProt Q45914)
Region: residues 114	to 148
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
NTNHA-A has a large insert in nLC (nGly116 to nAla148, termed the nLoop) that is not present in LC.
The crystal structure reveals that the nLoop is fully exposed on the M-PTC surface and has no visible electron density, presumably because of its high flexibility (Fig. 1C).
Cross-references: PDB:3V0A
PDB:3V0B
Protein: DP04387 (UniProt A0A0H2XCS3)
Region: residues 457	to 469
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 456 to 470 from the β-hairpin loop were not visible in the electron density map, indicating a high flexibility for this region.
The disordered region of the β-hairpin loop in the Pr structure is represented by a curved dashed line.
The 2mFo-DFc electron density maps allowed for a fairly complete trace of the protein backbones with the exception for the initial 8 to 10 N-terminal residues and the regions comprising the residues 457 to 469 for the wild-type protein; 393 to 398, 527 to 528, 601 to 606, and 616 to 623 for G454E; and 333 to 340 and 389 to 401 for ΔPAS9(1–511), which correspond to exposed loops.
Cross-references: PDB:6PL0
Protein: DP04387 (UniProt A0A0H2XCS3)
Region: residues 457	to 469
Annotation: disorder to order (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 456 to 470 from the β-hairpin loop were not visible in the electron density map, indicating a high flexibility for this region.
The disordered region of the β-hairpin loop in the Pr structure is represented by a curved dashed line.
On the contrary, in the Pfr state, the tongue undergoes a conformational change interconverting the entrance and exit β strands in a loop and an α helix, respectively (Figs. 4B and 5A, middle).
The authors report that this region is disordered in the Pr (red light–absorbing) photostate and adopts an ordered conformation in the Pfr (far-red light–absorbing) photostate. To compare the structural differences between photostates, they analyzed wild-type protein crystals in the Pr state and two variants that favor the Pfr state: a deletion mutant lacking the PAS9 domain [ΔPAS9(1–511)] and a point mutant carrying the G454E substitution.
Cross-references: PDB:6PL0
PDB:7L5A
PDB:7L59
Protein: DP04388 (UniProt Q86VY4)
Region: residues 1	to 195
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Circular dichroism (CD) and nano differential scanning fluorimetry (nanoDSF) analysis revealed TSPYL5 FL exhibits at least partial folding, with an α-helical and β-sheet content (two minima near 208 nm and 222 nm) (Figure 2e) and a melting temperature of 63.2C (Figure 2f). In contrast, TSPYL5 TR showed profiles typical of unfolded proteins, consistent with structural predictions (Figure 2g,h).
Protein: DP04388 (UniProt Q86VY4)
Region: residues 1	to 195
Annotation: disorder (Structural state)
Evidence: differential scanning fluorimetry evidence
Supporting statements:
Circular dichroism (CD) and nano differential scanning fluorimetry (nanoDSF) analysis revealed TSPYL5 FL exhibits at least partial folding, with an α-helical and β-sheet content (two minima near 208 nm and 222 nm) (Figure 2e) and a melting temperature of 63.2C (Figure 2f). In contrast, TSPYL5 TR showed profiles typical of unfolded proteins, consistent with structural predictions (Figure 2g,h).
Protein: DP04388 (UniProt Q86VY4)
Region: residues 1	to 242
Annotation: disorder (Structural state)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
The HDx-MS data (Figure 2i) revealed that most of TSPYL5 exchanges deuterium rapidly, suggesting a predominantly flexible and disordered
conformation. 
Examining Figure 1 (b) as well as  Figure 2 (d) and (i) panels clearly supports that not only the region 1-195 corresponding to the TSPYL5 TR construct (pink in panel (d)) has experienced very high H-D exchange in 60 seconds, but also the following log alpha helix. So the full region corresponding to previously used constructs TSPYL5 #1 and #2 (region 1-242) experiences very high H-D exchage rates that is a hallmark of the disodered state.
Protein: DP04388 (UniProt Q86VY4)
Region: residues 1	to 195
Annotation: protein binding (Molecular function)
Evidence: microscale thermophoresis evidence used in manual assertion
Supporting statements:
In line with the cellular data, TSPYL5 TR also demonstrated strong binding to USP7 with a Kd of 102.4 nM (Figure 3b)
Protein: DP04388 (UniProt Q86VY4)
Region: residues 1	to 195
Annotation: protein binding (Molecular function)
Evidence: physical interaction evidence used in manual assertion
Supporting statements:
Similarly, the MATH domain exhibited comparable affinity for TSPYL5 TR, with a mean Kd of 2.1 nM.
This Kd was measured in a BLI experiment.
Protein: DP04388 (UniProt Q86VY4)
Region: residues 65	to 97
Annotation: protein binding (Molecular function)
Evidence: microscale thermophoresis evidence used in manual assertion
Supporting statements:
MST screening identified three overlapping peptides (peptides 9, 10, and 11) in the N-terminal region of TSPYL5 that bound to USP7, with dissociation constants (Kd) ranging from 12.6 to 500 μM (Figure 4d–e and Table S2). These peptides map to amino acids 65–97 of TSPYL5, suggesting this region forms a key interaction hotspot.
Protein: DP04388 (UniProt Q86VY4)
Region: residues 1	to 195
Annotation: protein homooligomerization (Biological process)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
To gain deeper insights into the oligomerization process of TSPYL5, we examined its truncated form (TSPYL5 TR, residues 1–195). Mass spectrometry determined its molecular weight (MW) to be 21 kDa, but size exclusion chromatography (SEC) analysis indicated a MW of ~65 kDa, suggesting trimer formation (Figure 2a).
These findings imply that the N-terminal region of TSPYL5 plays a crucial role in trimer formation, while the C-terminal region likely mediates the interaction of two trimers, leading to hexamer formation.
Protein: DP04388 (UniProt Q86VY4)
Region: residues 1	to 123
Annotation: protein binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
As expected, FlagTSPYL5 FL efficiently co-immunoprecipitated USP7, confirming their interaction. Flag-TSPYL5 #1 also pulled down USP7, indicating that this part of TSPYL5 mediates the interaction.
TSPYL5 #1 corresponds to the region 1-123.
Protein: DP04388 (UniProt Q86VY4)
Region: residues 124	to 242
Annotation: protein binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
Additionally, Flag-TSPYL5 #2, which includes the predicted α-helix, also recovered USP7, indicating an additional interaction site within this region. 
TSPYL5 #2 corresponds to the region 124-242.
Protein: DP04390 (UniProt A1C3L3)
Region: residues 201	to 212
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 15N relaxation rates at pH 8 for backbone amides between Glu-128 and Leu-208 reveal a well ordered structure with no flexible loops or residues in chemical exchange, although the termini (residues 116–127 and 209–231) are highly flexible.
The highly flexible regions reported by the authors in the paper correspond to residues 201-212 and 294-316 in the UniProt sequence.
Cross-references: PDB:2KUB
Protein: DP04390 (UniProt A1C3L3)
Region: residues 294	to 316
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 15N relaxation rates at pH 8 for backbone amides between Glu-128 and Leu-208 reveal a well ordered structure with no flexible loops or residues in chemical exchange, although the termini (residues 116–127 and 209–231) are highly flexible.
The highly flexible regions reported by the authors in the paper correspond to residues 201-212 and 294-316 in the UniProt sequence.
Cross-references: PDB:2KUB
Protein: DP04391 (UniProt A0AAI7ZGD2)
Region: residues 24	to 46
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum of VirB7Nt is typical of a random coil, as expected for a short peptide in aqueous solution (Figure 2A). The VirB7Nt peptide is a good model for the N-terminal tail within VirB7, which shows fast
backbone motions, as revealed by measurements of 15N relaxation rates.
Protein: DP04391 (UniProt A0AAI7ZGD2)
Region: residues 24	to 51
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The solution structure of VirB7XAC2622_24–139 consists of a globular domain (residues 52–133), flanked by a long disordered N-terminus (amino acids 24–51) and a short flexible C-terminus (residues 134–139) (Figure 1A).
The relaxation data are consistent with the presence of a flexible N-terminal tail and a more rigid globular domain (Figure 5).
Cross-references: PDB:2L4W
BMRB:17257
Protein: DP04391 (UniProt A0AAI7ZGD2)
Region: residues 24	to 50
Annotation: identical protein binding (Molecular function)
Evidence: cross-linking evidence used in manual assertion
Supporting statements:
To investigate whether VirB7XAC2622_24–139 forms dimers or higher-order oligomers, glutaraldehyde cross-linking experiments were performed. These assays showed that VirB7XAC2622_24–139 forms dimers, trimers and higher order oligomers (Figure S4A). When the cross-linking experiment was performed in the presence of 1% SDS, no covalently cross-linked oligomers were observed, indicating that oligomerization requires the presence of a correctly folded protein (Figure S4A). As expected, no cross-links were observed when the experiment was performed using VirB7XAC2622_51–134 which lacks the disordered N-terminal region (Figure S4B).
Protein: DP04391 (UniProt A0AAI7ZGD2)
Region: residues 27	to 41
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In order to map the VirB9 binding site on the structure of VirB7, we assigned the backbone resonances of VirB7XAC2622_24–139 in complex with VirB9XAC2620_154–255 and analyzed the chemical shift differences (Figure 3A and B). This analysis showed that only residues 27–41, within the disordered VirB7 N-terminus, undergo significant chemical shift perturbations (Figure 3C and D).
Indeed, the perturbations observed in the 15N-HSQC spectra of VirB9XAC2620_154–255 in the presence of the full-length VirB7XAC2622_24–139 or the VirB7XAC2622_24–46 peptide are essentially the same (Figure 4 and Figure S8), demonstrating that the VirB7 N-terminal region is sufficient to interact with the VirB9XAC2620 C-terminal domain.
Protein: DP04391 (UniProt A0AAI7ZGD2)
Region: residues 24	to 46
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
VirB7NT binds to VirB9CT in slow exchange at the NMR chemical shift timescale (Souza et al., 2011), with an apparent dissociation constant of 1 μM as estimated by isothermal titration calorimetry (ITC) at 37°C (Table 1).
Authors previously defined that the VirB7NT construct used covers residues 24-46 of VirB7.
Protein: DP04391 (UniProt A0AAI7ZGD2)
Region: residues 29	to 38
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
While the segment between VirB7NT D29 and N38 of VirB7NT is well defined, the NMR structure displays lower precision at its N- and C-terminal tails (residues 24–28 and 39–46).
The authors list shifts/contacts of the different residues from which it is apparent that the region 29-38 of VirB7 is mainly responsible for VirB9CT binding. There is also foldig up on binding of a very short segment (residues 35-36) forming a short beta strand in the complex that augments a beta sheet of VirB9CT.
Protein: DP04391 (UniProt A0AAI7ZGD2)
Region: residues 42	to 49
Annotation: identical protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Chemical shift perturbation data showed that two regions are involved in VirB7XAC2622 self-interactions: a region in the unfolded N-terminus (residues 42–49) and a patch on the surface of the globular domain made up of residues 63–65, 85–93, 111–119 and 131 (Figure 2B and C).
Protein: DP04391 (UniProt A0AAI7ZGD2)
Region: residues 24	to 46
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
Binding of VirB9Ct to VirB7Nt is enthalpically driven as indicated by isothermal titration calorimetry (ITC) experiments carried out at 10, 25, and 35 °C (Figure 3A,B). The VirB9Ct−VirB7Nt Kd app (see Experimental Section) is 0.70 μM at 35 °C, similar to the value reported before.
Protein: DP04391 (UniProt A0AAI7ZGD2)
Region: residues 24	to 46
Annotation: protein binding (Molecular function)
Evidence: stopped-flow fluorescence spectroscopy evidence
Supporting statements:
The presence of tryptophan residues at positions 177 and 34 in VirB9Ct and VirB7Nt, respectively, and the millisecond exchange time scale
between unbound and bound VirB9Ct states, favored the use of stopped-flow fluorescence to follow the VirB9Ct−VirB7Nt association kinetics.
These observations suggest that the VirB9Ct interaction with VirB7Nt could be described by a conformational-selection mechanism at 25 °C.
Protein: DP04391 (UniProt A0AAI7ZGD2)
Region: residues 24	to 46
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: DP04391 (UniProt A0AAI7ZGD2)
Region: residues 24	to 46
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: DP04391 (UniProt A0AAI7ZGD2)
Region: residues 27	to 49
Annotation: type IV secretion system complex (Cellular component)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
This analysis showed that only residues 27–41, within the disordered VirB7 N-terminus, undergo significant chemical shift perturbations (Figure 3C and D). This region is adjacent to, but does not overlap, the N-terminal region involved in VirB7XAC2622 oligomerization (residues 42–49).
Chemical shift perturbation data showed that two regions are involved in VirB7XAC2622 self-interactions: a region in the unfolded N-terminus (residues 42–49) and a patch on the surface of the globular domain made up of residues 63–65, 85–93, 111–119 and 131 (Figure 2B and C).
In well-characterized T4SSs, VirB7 is a lipoprotein attached to the periplasmic side of the outer membrane [28]. It has been shown to interact with several T4SS subunits [29], including itself [30] and the VirB9 C-terminal region [31], [32].
Protein: DP04392 (UniProt Q83RJ4)
Region: residues 1	to 24
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