LiteFold/DisProt huggingface dataset:
Protein: DP01850 (UniProt Q9JK66)
Region: residues 378	to 392
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The repressing REP is surrounded by unstructured regions
Cross-references: PDB:4K7D
Protein: DP01850 (UniProt Q9JK66)
Region: residues 76	to 141
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The long linker following the Ubl is not visible in the crystal structure.
Cross-references: undefined:undefined
Protein: DP01850 (UniProt Q9JK66)
Region: residues 378	to 392
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the new structure, residues 382–391 preceding the REP are again disordered
Cross-references: PDB:4ZYN
Protein: DP01851 (UniProt P10686)
Region: residues 770	to 779
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Although the phosphopeptide consists of 18 residues, only the C-terminal eight have clear electron density in the structure and bury ~430 Å2 of solvent-accessible surface of the cSH2 domain upon complex formation. The remainder of the peptide is presumably disordered and not required for complex formation.
Cross-references: PDB:4k45
Protein: DP01852 (UniProt P04480)
Region: residues 1	to 172
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In agreement with what was previously observed with the N-terminal domain of colicin N (42), the far-UV circular dichroism (CD) spectrum of ATh shows no significant amount of ordered secondary structure (Figure 4) and was similar to that of AT1
Protein: DP01852 (UniProt P04480)
Region: residues 21	to 107
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Even though 107 amino acids of the translocation domain of ColA were included in the crystallization, only residues 9–20 could be resolved in the electron density maps (Fig. 3A). No additional peaks of density were observed at any stage of the model building and refinement, therefore the remaining residues of the TA1–107 polypeptide are assumed to be disordered in the solvent channels within the crystal lattice.
Cross-references: PDB:3iax
Protein: DP01852 (UniProt P04480)
Region: residues 1	to 172
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The HSQC spectra of 15N-labeled ATh result in a significant amount of poorly dispersed signals superimposing in the middle of the spectra (Figure 5), confirming this lack of structure, which is in agreement with the CD data.
Protein: DP01852 (UniProt P04480)
Region: residues 1	to 172
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The  HSQC  spectrum  of 15N-labeled  TolAIII3  is significantly altered after addition of unlabeled ATh.
Protein: DP01852 (UniProt P04480)
Region: residues 1	to 172
Annotation: molecular adaptor activity (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Here  we  show  that  in  vitro  the  translocation  domain  of colicin  A  has  a  strongly  perturbing  effect  on  the  tertiary structure of TolAIII, and thus presumably also on the whole Tol-Pal system within the periplasm of E. coli.
Protein: DP01852 (UniProt P04480)
Region: residues 1	to 172
Annotation: protein binding (Molecular function)
Evidence: immunodetection assay evidence used in manual assertion
Supporting statements:
Purified TolAIII2 and TolAIII3 were analyzed by a Western blot and dot blot, which were incubated with 200 nM ATh followed by immunodetection with 1C11 monoclonal antibody (mAb) directed against the colicin domain. Under these conditions, the ATh protein was found to recognize TolAIII2 and TolAIII3.
Protein: DP01852 (UniProt P04480)
Region: residues 1	to 172
Annotation: protein binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
Immunoprecipitation experiments using mAb 1C11, which recognizes an epitope located within the N-terminal sequenceof ATh, were also checked with ATh and TolAIII derivative mixtures.  Coomassie  blue-stained  SDS-PAGE  analyses indicated that TolAIII2 and TolAIII3 co-immunoprecipitate with ATh
Protein: DP01852 (UniProt P04480)
Region: residues 1	to 172
Annotation: protein binding (Molecular function)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
SDS-PAGE shift experiments(30) were performed with the purified ATh and TolAIII3. A TolAIII3-ATh protein complex could be clearly detected having a relative electrophoretic mobility corresponding to a heterodimer, while this complex slightly dissociated into monomeric forms upon migration (Figure 6).
Protein: DP01852 (UniProt P04480)
Region: residues 1	to 172
Annotation: protein binding (Molecular function)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Gel  filtration  experiments  using  ATh,  TolAIII3,  and TolAIII3 with ATh, loaded at the same concentration and in the same buffer used for NMR interaction analyses, further indicated the formation of a heterodimer.
Protein: DP01852 (UniProt P04480)
Region: residues 9	to 20
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Structure of the TA1–107–TolB complex at 2.6 Å resolution showing the colicin binding site of the β-propeller domain.
Cross-references: PDB:3IAX
Protein: DP01852 (UniProt P04480)
Region: residues 1	to 172
Annotation: localization (Biological process)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
Prior to their action, the import of colicins is mediated by their binding to specific receptors of the outer membrane, and their translocation through the cell envelope which requires either the Tol-Pal system (group A colicins) or the TonB system(group B colicins) (15). The three-dimensional structure of several of these toxins shows a similar type of organization(16-19). It comprises three distinct domains:  the N-terminal domain   involved   in   the   translocation   across   the   outer membrane, the central domain or receptor binding domain,and  the  C-terminal  domain  that  is  responsible  for  lethal activity. Membrane fractionation shows that the Tol proteins form a complex with imported colicin A (20) and that, during pore formation, colicin A retains interactions with its receptor and the Tol machinery (21).
Protein: DP01854 (UniProt Q9M605)
Region: residues 83	to 93
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
As an IDP, all of K2 is flexible but the K-segments show a weak tendency for forming an a- helix, whereas the Φ-segment has no clear secondary structure preference and is even more flexible than the K-regions
Protein: DP01854 (UniProt Q9M605)
Region: residues 93	to 113
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
As an IDP, all of K2 is flexible but the K-segments show a weak tendency for forming an a- helix, whereas the Φ-segment has no clear secondary structure preference and is even more flexible than the K-regions
Protein: DP01854 (UniProt Q9M605)
Region: residues 114	to 130
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
As an IDP, all of K2 is flexible but the K-segments show a weak tendency for forming an a- helix, whereas the Φ-segment has no clear secondary structure preference and is even more flexible than the K-regions
Protein: DP01854 (UniProt Q9M605)
Region: residues 83	to 130
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
As an IDP, all of K2 is flexible but the K-segments show a weak tendency for forming an a- helix, whereas the Φ-segment has no clear secondary structure preference and is even more flexible than the K-regions
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 567	to 748
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The structural properties of Nogo‐A(567–748) were first investigated by CD spectroscopy. As shown in Fig. 3A, the CD spectrum of Nogo‐A(567–748) in aqueous buffer had a maximal negative peak at ≈202 nm and had no significant positive signal at 198 nm, indicating that the polypeptide was not fully structured [[23]]. However, the existence of the maximal negative signal at around 202 nm, rather than 198 nm, together with the negative shoulder signal at ≈225 nm, indicated that the polypeptide was also not assuming a ‘random coil’ structure.
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 1155	to 1187
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Similarly, Nogo-33 identical for all three Nogo proteinswas predicated [Fig. 2(a)] and subsequently experimentally shown to be highly disordered as judged from its far-UV CD [Fig. 4(a)] and narrowly-dispersed HSQC spectrum (only 0.5 ppm over 1H and 19 ppm over 15N dimensions) [Fig. 4(b)].
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 1055	to 1094
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
NMR spectroscopy was further utilized to explore the structural properties of Nogo‐40. The very narrow resonance dispersion of amide protons (≈0.7p.p.m) and the lack of side‐chain packing with aromatic ring protons in aqueous buffer (Fig. 5C) demonstrate that Nogo‐40 in aqueous buffer had no stable structure, which is consistent with the CD results above.
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 1155	to 1187
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Similarly, Nogo-33 identical for all three Nogo proteinswas predicated [Fig. 2(a)] and subsequently experimentally shown to be highly disordered as judged from its far-UV CD [Fig. 4(a)] and narrowly-dispersed HSQC spectrum (only 0.5 ppm over 1H and 19 ppm over 15N dimensions) [Fig. 4(b)].
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 1	to 31
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Unfortunately we found that the first 31 residues were amenable to cellular proteolysis which made it very difficult to obtain the entire Nogo-B (1–200). This observation suggests that Nogo-B is highly disordered because disordered proteins have been extensively found to be very sensitive to proteolytic digestion.
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 1	to 200
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
As seen in Fig. 3(a), Nogo-B (1–200) and Nogo-B (32–200) owned very similar far-UV CD spectra with a negative signal at198 nm and without any positive signal at190 nm. This observation clearly indicated that both Nogo-B (1–200) and Nogo-B (32–200) were lacking predominant secondary structures in solution
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 32	to 200
Annotation: disorder (Structural state)
Evidence: near-UV circular dichroism evidence used in manual assertion
Supporting statements:
We then recorded the near-UV CD spectra of Nogo-B (32–200) in the absence and presence of 8M denaturant urea [Fig. 3(b)]. The high similarity between two near-UV spectra suggested that the N-terminus of Nogo-B had no tight tertiary packing even under the native condition.
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 1	to 200
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Completely consistent with CD results, 1H15N NMR HSQC spectra of both Nogo-B (1–200) and Nogo-B (32–200) were very similar, with very narrow spectral dispersions over both dimensions (1 ppm over 1H and 20ppm over 15N dimensions) [Fig. 3(c)]. Moreover, no significant change in the spectral dispersion and peak numberswere observed for 1H15N NMR HSQC spectra of Nogo-B(32–200) in the absence and in presence of 8Murea [Fig.3(d)]. These results provided the strongest evidence that both Nogo-B (1–200) and Nogo-B (32–200) were highly disordered with no tight tertiary packing.
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 32	to 200
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence used in manual assertion
Supporting statements:
Hydrogen exchange experiment offers a very sensitiveprobe to detect tertiary packing property. When the 15N-labeled Nogo-B (32–200) was lyophilized and redissolved in 100% D2O, all HSQC peaks disappeared withinthe experimental dead time (spectrum not shown). This result again indicated that Nogo-B (32–200) was highly flexible in solution and all of its amide protons were openly accessible to the bulk solvent.
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 1	to 200
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
Consequently, we dissected Nogo-A (201–1016) into two sets of overlapped fragments,with each set having four 200 residue fragments as the size of autonomous protein folding domains usually ranges from120 to 200 residues. The two sets of dissected Nogo-A fragments P1-P8 were successfully expressed and purified by HPLC. Very interestingly, the apparent molecular weights of all eight fragments as estimated from SDS-PAGE were 1.5 times larger than those calculated from their sequences. Moreover, the same phenomenon was observed for Nogo-B (1–200) and Nogo-B (32–200). This observation could serve as evidence that these Nogo fragments are intrinsically unstructured because previously this abnormal behavior on SDS-PAGE was proposed as anindicator of intrinsically unstructured proteins.
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 210	to 408
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
Consequently, we dissected Nogo-A (201–1016) into two sets of overlapped fragments,with each set having four 200 residue fragments as the size of autonomous protein folding domains usually ranges from120 to 200 residues. The two sets of dissected Nogo-A fragments P1-P8 were successfully expressed and purified by HPLC. Very interestingly, the apparent molecular weights of all eight fragments as estimated from SDS-PAGE were 1.5 times larger than those calculated from their sequences. Moreover, the same phenomenon was observed for Nogo-B (1–200) and Nogo-B (32–200). This observation could serve as evidence that these Nogo fragments are intrinsically unstructured because previously this abnormal behavior on SDS-PAGE was proposed as anindicator of intrinsically unstructured proteins.
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 409	to 616
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
Consequently, we dissected Nogo-A (201–1016) into two sets of overlapped fragments,with each set having four 200 residue fragments as the size of autonomous protein folding domains usually ranges from120 to 200 residues. The two sets of dissected Nogo-A fragments P1-P8 were successfully expressed and purified by HPLC. Very interestingly, the apparent molecular weights of all eight fragments as estimated from SDS-PAGE were 1.5 times larger than those calculated from their sequences. Moreover, the same phenomenon was observed for Nogo-B (1–200) and Nogo-B (32–200). This observation could serve as evidence that these Nogo fragments are intrinsically unstructured because previously this abnormal behavior on SDS-PAGE was proposed as anindicator of intrinsically unstructured proteins.
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 617	to 824
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
Consequently, we dissected Nogo-A (201–1016) into two sets of overlapped fragments,with each set having four 200 residue fragments as the size of autonomous protein folding domains usually ranges from120 to 200 residues. The two sets of dissected Nogo-A fragments P1-P8 were successfully expressed and purified by HPLC. Very interestingly, the apparent molecular weights of all eight fragments as estimated from SDS-PAGE were 1.5 times larger than those calculated from their sequences. Moreover, the same phenomenon was observed for Nogo-B (1–200) and Nogo-B (32–200). This observation could serve as evidence that these Nogo fragments are intrinsically unstructured because previously this abnormal behavior on SDS-PAGE was proposed as anindicator of intrinsically unstructured proteins.
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 825	to 1016
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
Consequently, we dissected Nogo-A (201–1016) into two sets of overlapped fragments,with each set having four 200 residue fragments as the size of autonomous protein folding domains usually ranges from120 to 200 residues. The two sets of dissected Nogo-A fragments P1-P8 were successfully expressed and purified by HPLC. Very interestingly, the apparent molecular weights of all eight fragments as estimated from SDS-PAGE were 1.5 times larger than those calculated from their sequences. Moreover, the same phenomenon was observed for Nogo-B (1–200) and Nogo-B (32–200). This observation could serve as evidence that these Nogo fragments are intrinsically unstructured because previously this abnormal behavior on SDS-PAGE was proposed as anindicator of intrinsically unstructured proteins.
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 210	to 358
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
Consequently, we dissected Nogo-A (201–1016) into two sets of overlapped fragments,with each set having four 200 residue fragments as the size of autonomous protein folding domains usually ranges from120 to 200 residues. The two sets of dissected Nogo-A fragments P1-P8 were successfully expressed and purified by HPLC. Very interestingly, the apparent molecular weights of all eight fragments as estimated from SDS-PAGE were 1.5 times larger than those calculated from their sequences. Moreover, the same phenomenon was observed for Nogo-B (1–200) and Nogo-B (32–200). This observation could serve as evidence that these Nogo fragments are intrinsically unstructured because previously this abnormal behavior on SDS-PAGE was proposed as anindicator of intrinsically unstructured proteins.
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 359	to 566
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
Consequently, we dissected Nogo-A (201–1016) into two sets of overlapped fragments,with each set having four 200 residue fragments as the size of autonomous protein folding domains usually ranges from120 to 200 residues. The two sets of dissected Nogo-A fragments P1-P8 were successfully expressed and purified by HPLC. Very interestingly, the apparent molecular weights of all eight fragments as estimated from SDS-PAGE were 1.5 times larger than those calculated from their sequences. Moreover, the same phenomenon was observed for Nogo-B (1–200) and Nogo-B (32–200). This observation could serve as evidence that these Nogo fragments are intrinsically unstructured because previously this abnormal behavior on SDS-PAGE was proposed as anindicator of intrinsically unstructured proteins.
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 567	to 774
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
Consequently, we dissected Nogo-A (201–1016) into two sets of overlapped fragments,with each set having four 200 residue fragments as the size of autonomous protein folding domains usually ranges from120 to 200 residues. The two sets of dissected Nogo-A fragments P1-P8 were successfully expressed and purified by HPLC. Very interestingly, the apparent molecular weights of all eight fragments as estimated from SDS-PAGE were 1.5 times larger than those calculated from their sequences. Moreover, the same phenomenon was observed for Nogo-B (1–200) and Nogo-B (32–200). This observation could serve as evidence that these Nogo fragments are intrinsically unstructured because previously this abnormal behavior on SDS-PAGE was proposed as anindicator of intrinsically unstructured proteins.
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 775	to 1016
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
Consequently, we dissected Nogo-A (201–1016) into two sets of overlapped fragments,with each set having four 200 residue fragments as the size of autonomous protein folding domains usually ranges from120 to 200 residues. The two sets of dissected Nogo-A fragments P1-P8 were successfully expressed and purified by HPLC. Very interestingly, the apparent molecular weights of all eight fragments as estimated from SDS-PAGE were 1.5 times larger than those calculated from their sequences. Moreover, the same phenomenon was observed for Nogo-B (1–200) and Nogo-B (32–200). This observation could serve as evidence that these Nogo fragments are intrinsically unstructured because previously this abnormal behavior on SDS-PAGE was proposed as anindicator of intrinsically unstructured proteins.
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 210	to 408
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Figure 5 shows the far-UV CD and HSQC spectra of the first set of four fragments P1-P4 spanning over the Nogo-A residues 201–1016. Similar to those observed for Nogo-B, all four fragments had far-UV CD spectra typical of disordered proteins and their HSQC spectra showed sharp resonance peaks distributed within very narrow spectral dispersions. Therefore the results indicated that this set of fragments owned no populated secondary structures and tight tertiary packing. Moreover, the second group of the fragments P5-P8 dissected in a very different way also gave rise to far-UV CD and HSQC spectra characteristic of disordered proteins (Fig. 6), again indicating that the second group of fragments were also largely disordered.