LiteFold/DisProt huggingface dataset:
Protein: DP03577 (UniProt P15659)
Region: residues 197	to 257
Annotation: protein import into nucleus (Biological process)
Evidence: fluorescence microscopy evidence used in manual assertion
Supporting statements:
PA ts (and lethal) mutations block the recruitment and the transport of PB1 toward the nucleus at nonpermissive temperature.
In order to determine whether the ts mutations may interfere with the nuclear import of PA or the formation of the PA-PB1 complex in the cytoplasm and its transport to the nucleus, we generated a series of plasmid constructs to express or coexpress the PA and PB1 subunits. Fluorescently labeled PB1 and PA (wild-type and mutant) subunits were first expressed separately to study their intracellular localization (data not shown). Both types of subunits showed an accumulation in the cytoplasm and a faint localization in the nucleus, in accordance with previous data (5, 6, 7). 
Next, we analyzed the localization of the PB1 subunit when coexpressed with PA (Fig. 7; Table 2). Our experiments confirmed that when the wild-type PA and PB1 were expressed together, PB1 and PA localized into the nucleus, in contrast to what was observed when PB1 or PA was expressed alone. The temperature used during protein expression (33°C, 37°C, or 39.5°C) did not modulate the PB1 targeting to the nucleus: about 80% of the PB1-expressing cells were labeled in the nucleus at any temperature (Fig. 7B).
Protein: DP03578 (UniProt F8UU09)
Region: residues 1	to 82
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Missing residues reported at PDB entries 4B7N, 4B7J and 4B7M
Cross-references: PDB:4B7N
PDB:4B7J
PDB:4B7M
Protein: DP03579 (UniProt Q9JYY3)
Region: residues 1	to 62
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Even though the full-length constructs of ClpX included the zinc binding domains (residues 1–62), no density was found for these domains in either conformation, likely due to their flexibility.
Cross-references: PDB:6VFX
PDB:6VFS
EMDB:EMD-21187
Protein: DP03579 (UniProt Q9JYY3)
Region: residues 1	to 62
Annotation: flexible N-terminal tail (Disorder function)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Even though the full-length constructs of ClpX included the zinc binding domains (residues 1–62), no density was found for these domains in either conformation, likely due to their flexibility.
Cross-references: PDB:6VFX
PDB:6VFS
EMDB:EMD-21187
Protein: DP03579 (UniProt Q9JYY3)
Region: residues 265	to 280
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
The lack of density for the IGF loop belonging to protomer X6 in Conformation A (Figure 2—figure supplement 1) is likely due to conformational flexibility and sub-stoichiometric binding of this IGF loop into the ClpP-binding pocket.
All six IGF loops in ClpX adopt different configurations in Conformations A and B (Figure 2—figure supplement 1).
The ClpX residues immediately following where the IGF loops contact ClpP (residues 275–280) show weak or no density, likely indicating flexibility. This property allows the IGF loops to accommodate movement of the ClpX protomers relative to ClpP (Figure 2D–F), analogous to a set of springs.
Cross-references: PDB:6VFX
PDB:6VFS
EMDB:EMD-21187
Protein: DP03579 (UniProt Q9JYY3)
Region: residues 265	to 280
Annotation: flexible linker (Disorder function)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
The lack of density for the IGF loop belonging to protomer X6 in Conformation A (Figure 2—figure supplement 1) is likely due to conformational flexibility and sub-stoichiometric binding of this IGF loop into the ClpP-binding pocket.
All six IGF loops in ClpX adopt different configurations in Conformations A and B (Figure 2—figure supplement 1).
The ClpX residues immediately following where the IGF loops contact ClpP (residues 275–280) show weak or no density, likely indicating flexibility. This property allows the IGF loops to accommodate movement of the ClpX protomers relative to ClpP (Figure 2D–F), analogous to a set of springs.
Cross-references: PDB:6VFX
PDB:6VFS
EMDB:EMD-21187
Protein: DP03580 (UniProt Q9JZ38)
Region: residues 11	to 21
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Electron density for N-terminal residues that form the axial loops of EcClpP is unclear in all but one subunit (Chain B). In previously published structures, these axial loops are highly flexible and are usually disordered in the crystal in the absence of activators or through preclusion by crystal packing23.
The structure of apo-NmClpP contains a tetradecamer in the asymmetric unit and shows no clear density for any of the 14 N-terminal axial loops.
Cross-references: PDB:6NAQ
Protein: DP03580 (UniProt Q9JZ38)
Region: residues 1	to 22
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No electron density was observed for residues 1–22 of all 28 subunits due to crystal packing (Fig. 1c, Supplementary Fig. 1d).
The structure of apo-NmClpP contains a tetradecamer in the asymmetric unit and shows no clear density for any of the 14 N-terminal axial loops.
Cross-references: PDB:6NAH
Protein: DP03580 (UniProt Q9JZ38)
Region: residues 6	to 22
Annotation: order (Structural state)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
These β-hairpins closely resemble the conformation seen in the ADEP-bound structures of NmClpP (Goodreid et al., 2016) and are notably different from the disordered conformations observed in NmClpP when it is not bound to either ClpX or ADEP (Figure 2—figure supplement 2B; Mabanglo et al., 2019). By forming ordered gates, ClpX binding creates a wide entrance pore with a diameter of ~23 Å for substrates to pass through into the ClpP degradation chamber (Figure 2G, left; Figure 2—figure supplement 2). While it has long been suspected that the activating mechanism of ADEPs involves a disorder-to-order transition of these gates (Li et al., 2010), this observation provides direct evidence that ClpX binding has the same effect.
Cross-references: EMDB:EMD-21187
PDB:6NAQ
PDB:6NAH
EMDB:EMD-21194
Protein: DP03580 (UniProt Q9JZ38)
Region: residues 6	to 22
Annotation: protein binding (Molecular function)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
These β-hairpins closely resemble the conformation seen in the ADEP-bound structures of NmClpP (Goodreid et al., 2016) and are notably different from the disordered conformations observed in NmClpP when it is not bound to either ClpX or ADEP (Figure 2—figure supplement 2B; Mabanglo et al., 2019). By forming ordered gates, ClpX binding creates a wide entrance pore with a diameter of ~23 Å for substrates to pass through into the ClpP degradation chamber (Figure 2G, left; Figure 2—figure supplement 2). While it has long been suspected that the activating mechanism of ADEPs involves a disorder-to-order transition of these gates (Li et al., 2010), this observation provides direct evidence that ClpX binding has the same effect.
Cross-references: EMDB:EMD-21187
PDB:6NAQ
PDB:6NAH
EMDB:EMD-21194
Protein: DP03580 (UniProt Q9JZ38)
Region: residues 6	to 22
Annotation: disorder to order (Structural transition)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
These β-hairpins closely resemble the conformation seen in the ADEP-bound structures of NmClpP (Goodreid et al., 2016) and are notably different from the disordered conformations observed in NmClpP when it is not bound to either ClpX or ADEP (Figure 2—figure supplement 2B; Mabanglo et al., 2019). By forming ordered gates, ClpX binding creates a wide entrance pore with a diameter of ~23 Å for substrates to pass through into the ClpP degradation chamber (Figure 2G, left; Figure 2—figure supplement 2). While it has long been suspected that the activating mechanism of ADEPs involves a disorder-to-order transition of these gates (Li et al., 2010), this observation provides direct evidence that ClpX binding has the same effect.
Protein: DP03581 (UniProt P55127)
Region: residues 415	to 591
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H−15N1H−15N HSQC spectrum of SPM exhibited a low dispersion of chemical shifts typical for disordered proteins (not shown).
The chemical shifts assigned in this study represent the major source of structural information for intrinsically disordered SPM.
Cross-references: BMRB:26530
Protein: DP03581 (UniProt P55127)
Region: residues 430	to 450
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Conventional triple resonance and nuclear Overhauser effect spectroscopy (NOESY) NMR spectra provided structural information for the whole protein, except of a region of 21 residues between T430 and G450. These residues were affected by conformational or chemical exchange and likely formed a loop lacking a unique structure.
Cross-references: PDB:6SJW
PDB:6SJX
BMRB:34424
Protein: DP03581 (UniProt P55127)
Region: residues 413	to 417
Annotation: limited proteolysis display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
To unravel the mechanistic details of the D414-P415 cleavage, we prepared a cleavage-incompetent mutant of SPM, where the proline residue (P415) of the D414-P415 cleavage site was replaced by an alanine residue (P415A). Unlike Ca-SPM, which represents a stabilized low-energy conformation of SPM after the cleavage and in which the N-terminal sequence begins with the P415 residue (415PLALD419), the SPM-P415A construct possesses the GSDALALD419 sequence at its N terminus.
Protein: DP03581 (UniProt P55127)
Region: residues 419	to 424
Annotation: metal ion binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Moreover, the SPM sequence contains a stretch of conserved residues (D419, D421, D423, and G424) that strongly resemble the conserved residues (positions 1, 3, 5, and 6) of an incomplete EF-hand-like motif. These residues form a stable loop in the Ca-SPM structure. Along with the adjacent D456 residue, these can provide two oxygens for calcium coordination and are likely to constitute the fourth Ca2+-binding site in Ca-SPM.
Cross-references: PDB:6SJW
PDB:6SJX
BMRB:34424
Protein: DP03581 (UniProt P55127)
Region: residues 462	to 532
Annotation: metal ion binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Three of the four Ca2+-binding sites are made up of sequential motifs (D462 to E474, D499 to D511, and D521 to E532) that closely resemble that of EF hands, while the fourth Ca2+-binding site consists of a structural motif, where the position 12 of an incomplete EF-hand-like motif (D419 to G424) is structurally supplemented by D456.
Cross-references: PDB:6SJW
PDB:6SJX
BMRB:34424
Protein: DP03581 (UniProt P55127)
Region: residues 415	to 591
Annotation: disorder to order (Structural transition)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
As shown in Fig. 1B, the 1H-15N heteronuclear single-quantum coherence (HSQC) spectrum of Ca-SPM exhibited the broad dispersion of backbone amide cross-peaks typical for structured proteins.
Cross-references: BMRB:34424
Protein: DP03582 (UniProt Q9JWM8)
Region: residues 365	to 389
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Indeed, for all of these structures, no electron density is observed for about the last 25 residues either in the 3Fo − 2Fc or in the Fo − Fc sigma-A weighted electron density maps, indicating an extremely high mobility of the last C-terminal residues in the crystal.
Cross-references: PDB:3BQF
PDB:3BQG
PDB:3BQE
PDB:3BQH
Protein: DP03583 (UniProt A1KVD0)
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:
The residual glycine residue from the TEV protease cleavage site and residues 1-12 of the protein are disordered in both monomers.
Cross-references: PDB:2F46
Protein: DP03584 (UniProt M4GGR4)
Region: residues 1	to 14
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal is missing from the pdb structure but was not mentioned in the paper.
Cross-references: PDB:7DE8
Protein: DP03585 (UniProt P0A0V3)
Region: residues 230	to 242
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The last 13 residues are not visible in the electron density map and are probably disordered.
Cross-references: PDB:1R1M
Protein: DP03585 (UniProt P0A0V3)
Region: residues 230	to 242
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 last 13 residues are not visible in the electron density map and are probably disordered.
Cross-references: PDB:1R1M
Protein: DP03586 (UniProt Q6VRY4)
Region: residues 2	to 17
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
D, overlay of the structured residues for both domains excluding the interdomain linker; r.m.s. deviation 0.96 Å. b-d, the unfolded N-terminal chain (residues 1-16) has been excluded for purposes of clarity. E, electrostatic surface representation for the entire LP2086-B01.
Cross-references: PDB:2KDY
Protein: DP03586 (UniProt Q6VRY4)
Region: residues 2	to 17
Annotation: flexible N-terminal tail (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
D, overlay of the structured residues for both domains excluding the interdomain linker; r.m.s. deviation 0.96 Å. b-d, the unfolded N-terminal chain (residues 1-16) has been excluded for purposes of clarity. E, electrostatic surface representation for the entire LP2086-B01.
Cross-references: PDB:2KDY
Protein: DP03586 (UniProt Q6VRY4)
Region: residues 141	to 155
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
A long flexible chain connects the folded part of the protein to the lipid anchor and acts as spacer, making both domains accessible to the host immune system.
The two domains are connected by a 15-residue linker (residues 140-154), which contains a short helical turn (α2) and crosses one end of the β-barrel, forming hydrophobic contacts through Phe147.
Cross-references: PDB:2KDY
Protein: DP03586 (UniProt Q6VRY4)
Region: residues 141	to 155
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
A long flexible chain connects the folded part of the protein to the lipid anchor and acts as spacer, making both domains accessible to the host immune system.
The two domains are connected by a 15-residue linker (residues 140-154), which contains a short helical turn (α2) and crosses one end of the β-barrel, forming hydrophobic contacts through Phe147.
Cross-references: PDB:2KDY
Protein: DP03586 (UniProt Q6VRY4)
Region: residues 3	to 33
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
As expected, at the higher pH, residues 3–13, 15, 17, 19–22, 25–26, 28, 31–33, 36, 48–49, 60, 73, 207, 235, 245, 249, mostly belonging to unstructured regions, were not observable due to the increased rate of solvent exchange (88% backbone assignment).
Cross-references: BMRB:16108
Protein: DP03587 (UniProt Q9JZG1)
Region: residues 298	to 310
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In NmeE365Term (PDB entry 3RMJ), each monomer comprised residues 1−364 of the full-length protein, with residues 4−296 and 311−324 being modeled for chain A and residues 4−297 and 311−324 for chain B; no interpretable electron density could be found for the remaining residues, which were presumed to be disordered.
Cross-references: PDB:3RMJ
Protein: DP03587 (UniProt Q9JZG1)
Region: residues 325	to 364
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In NmeE365Term (PDB entry 3RMJ), each monomer comprised residues 1−364 of the full-length protein, with residues 4−296 and 311−324 being modeled for chain A and residues 4−297 and 311−324 for chain B; no interpretable electron density could be found for the remaining residues, which were presumed to be disordered.
Cross-references: PDB:3RMJ
Protein: DP03588 (UniProt Q96C86)
Region: residues 1	to 37
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the structure of apo-DcpS, residues 1–39, 71–76, 286–293 and 337 for protomer A, and residues 1–39, 70–77, 286–292 and 337 for protomer B were not modeled, as these regions are not visible in the electron density map and are assumed to be disordered. In the structure of m7GDP-DcpS, residues 1–39, 69–77, 111, and 337 for chain A, residues 1–39, 70–78, and 337 for chain B, residues 1–38, 68–76, and 337 for chain C, and residues 1–37, 71–74, 99–101, and 110 for chain D are assumed to be disordered, as interpretable electron densities are not observed for these regions.
Region 1-37 is disordered in all structures.
Cross-references: PDB:1XMM
PDB:1XML
Protein: DP03589 (UniProt P47897)
Region: residues 183	to 216
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
One boomerang wing is composed of an appended NTD (residues 1–182) that is linked to the second wing by a long and flexible hinge domain. An 8-helical bundle (N1) and a 3-helical tail (N2) form a bi-lobed structure of NTD that protrudes from the enzyme body. An 82-residue long hinge connects the N2 subdomain to the catalytic domain (CATD; residues 264–335 and 438–564). While the first part of the hinge, covering residues 183–216, is disordered, the second part adopts a predominantly - helical structure that intimately interacts with CATD (Figure 1A).
Next, we compared structures of other domains in hGlnRS. Because of the partial disorder in our crystal form, we excluded the hinge domain from our analysis.
Cross-references: PDB:4YE6
PDB:4YE9
PDB:4YE8
Protein: DP03589 (UniProt P47897)
Region: residues 183	to 216
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
One boomerang wing is composed of an appended NTD (residues 1–182) that is linked to the second wing by a long and flexible hinge domain. An 8-helical bundle (N1) and a 3-helical tail (N2) form a bi-lobed structure of NTD that protrudes from the enzyme body. An 82-residue long hinge connects the N2 subdomain to the catalytic domain (CATD; residues 264–335 and 438–564). While the first part of the hinge, covering residues 183–216, is disordered, the second part adopts a predominantly - helical structure that intimately interacts with CATD (Figure 1A).
Protein: DP03590 (UniProt B2RLE7)
Region: residues 23	to 54
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
In agreement with in silico analyses, we also found that the N- and C-terminal regions of PorN are intrinsically disordered.
PorN presents N- and C-terminal intrinsically disordered regions
Edman sequencing of PorNP-G revealed that the protease resistant folded domain starts at residue 55, and the molecular mass (24,949Da) obtained by mass spectrometry suggested that it ends at residue 265.
Protein: DP03590 (UniProt B2RLE7)
Region: residues 266	to 359
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
In agreement with in silico analyses, we also found that the N- and C-terminal regions of PorN are intrinsically disordered.
PorN presents N- and C-terminal intrinsically disordered regions
Edman sequencing of PorNP-G revealed that the protease resistant folded domain starts at residue 55, and the molecular mass (24,949Da) obtained by mass spectrometry suggested that it ends at residue 265.
Protein: DP03590 (UniProt B2RLE7)
Region: residues 23	to 54
Annotation: protein binding (Molecular function)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
Our functional studies showed that the N-terminal disordered region is involved in PorN dimerization while the C-terminal disordered region is involved in the interaction with PorK.
Our results show that PorNP and PorNΔC oligomerize but not PorNΔN nor PorNΔNΔC (Fig. 3A), suggesting that the N-terminal region is required for PorN oligomerization. This result was confirmed in vitro. The different PorN constructs, fused to an N-terminal His6 tag, were purified by metal affinity chromatography and gel filtration, and subjected to SEC-MALS experiments. Figure 2 shows that PorNP and PorNΔC are dimeric in solution, whereas, similarly to PorNΔNΔC, PorNΔN is monomeric (Fig. 2). Taken together, the in vivo and in vitro assays demonstrate that PorN dimer formation is mediated by the N-terminal intrinsically disordered region.
Protein: DP03590 (UniProt B2RLE7)
Region: residues 266	to 358
Annotation: protein binding (Molecular function)
Evidence: bacterial 2-hybrid assay evidence used in manual assertion
Supporting statements:
Our functional studies showed that the N-terminal disordered region is involved in PorN dimerization while the C-terminal disordered region is involved in the interaction with PorK.
In addition, all PorN constructs interact with the CTDs of T9SS substrates (Fig. 3C). These results demonstrate that the PorN C-terminal disordered region is required for the interaction with PorK, whereas the PorN central core is sufficient to mediate contacts with PorM and the CTDs.