LiteFold/DisProt huggingface dataset:
Protein: DP00588 (UniProt P27958)
Region: residues 2212	to 2307
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Our  NMR  data demonstrated that the 1D 1H spectrum of NS5A-D2 lacks  NMR  signals  in  the  region  of  the  methyl  protons  and the 2D 1H -15N HSQC spectrum show a narrow dispersion  in  the  backbone  amide  proton  resonance  signals  which  only  covers  the  range  of  6.7−8.5  ppm.  Taken  together, our data suggest that the NS5A-D2 is natively dis-ordered or dynamic and is not well structured.
Protein: DP00588 (UniProt P27958)
Region: residues 2212	to 2307
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The NMR result showed that some perturbations  in  the  chemical  shifts  were  detected  in  the  15N-HSQC  spectrum  of  15N  labeled  NS5A-D2  protein  upon  the addition of NS5B MK-17 peptide (Figs. 7A and 7B), indicating  that  the  purified  NS5A-D2  shows  binding  to  the peptide. 
NS5A-D2 comprises the region 2212-2307 of the Hepatitis C virus genotype 1a (isolate H) genome polyprotein. The MK-17 peptide consist on the 139−155 residues of NS5B, which corresponds to 2559-2575 region of the Hepatitis C virus genotype 1a (isolate H) genome polyprotein.
Protein: DP00588 (UniProt P27958)
Region: residues 2242	to 2307
Annotation: protein binding (Molecular function)
Evidence: glutathione S-transferase pull-down assay evidence used in manual assertion
Supporting statements:
Both  NS5AΔN  and  NS5A-D2  were pulled down with GST-NS5Bt (Fig. 3C, lane 2 and lane  5)  but  not  with  GST  (Fig.  3C,  lane  3  and  lane  6),  indicating  the  specific  interaction  of  NS5A-D2  with  NS5B in  vitro.
NS5A-D2 comprises the region 2212-2307 and the NS5Bt peptide consist on the 2421-2990 region of the Hepatitis C virus genotype 1a (isolate H) genome polyprotein.
Protein: DP00591 (UniProt J7QLC0)
Region: residues 1006	to 1706
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The far-UV CD spectrum of the apo-state of RD (apo-RD, in the absence of calcium) was typical of a predominantly unfolded protein, as shown by the strong negative π0-π* band around 200 nm (Fig. 1). 
Here, we have characterized the structural and hydrodynamic properties of the RTX Repeat Domain (RD) of the CyaA toxin from Bordetella pertussis. This 701-amino acid long domain contains about 40 RTX motifs. We showed that, in the absence of calcium, RD was natively disordered, weakly stable, and highly hydrated.
In summary, CD and NMR data indicate that the apo-form of RD was largely unfolded with a weak secondary and tertiary structure content, while calcium binding triggered the folding of the protein into a compact and β-rich (>30-35%) conformation.
Protein: DP00591 (UniProt J7QLC0)
Region: residues 1006	to 1706
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Upon addition of 2 mm calcium to apo-RD, secondary structures were formed, as revealed by the concomitant intensity decrease of the π0-π* band and the increase of the n′-π* band in the holo-RD spectrum, as previously reported (10, 26).
In summary, CD and NMR data indicate that the apo-form of RD was largely unfolded with a weak secondary and tertiary structure content, while calcium binding triggered the folding of the protein into a compact and β-rich (>30-35%) conformation.
Protein: DP00591 (UniProt J7QLC0)
Region: residues 1006	to 1706
Annotation: disorder (Structural state)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Thermal-induced unfolding of RD was followed by intrinsic fluorescence of tryptophan at various calcium concentrations. The ratio of fluorescence intensities at 360 and 320 nm (rFI360/320) was used to follow the unfolding of RD (Fig. 4A). The van't Hoff free enthalpy (ΔHvH) and temperature of half-melting (Tm) were then determined. As shown in Fig. 4B, both Tm and ΔHvH increased with calcium concentrations to reach a plateau above 1.5-2 mm. We obtained similar results from thermal-induced denaturation of RD followed by far- and near-UV CD (data not shown). All together these data indicated that apo-RD was unstable, as expected for a disordered state, while holo-RD was strongly stabilized by calcium binding. 
Here, we have characterized the structural and hydrodynamic properties of the RTX Repeat Domain (RD) of the CyaA toxin from Bordetella pertussis. This 701-amino acid long domain contains about 40 RTX motifs. We showed that, in the absence of calcium, RD was natively disordered, weakly stable, and highly hydrated.
Protein: DP00591 (UniProt J7QLC0)
Region: residues 1006	to 1706
Annotation: disorder to order (Structural transition)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Thermal-induced unfolding of RD was followed by intrinsic fluorescence of tryptophan at various calcium concentrations. The ratio of fluorescence intensities at 360 and 320 nm (rFI360/320) was used to follow the unfolding of RD (Fig. 4A). The van't Hoff free enthalpy (ΔHvH) and temperature of half-melting (Tm) were then determined. As shown in Fig. 4B, both Tm and ΔHvH increased with calcium concentrations to reach a plateau above 1.5-2 mm. We obtained similar results from thermal-induced denaturation of RD followed by far- and near-UV CD (data not shown). All together these data indicated that apo-RD was unstable, as expected for a disordered state, while holo-RD was strongly stabilized by calcium binding.
Protein: DP00591 (UniProt J7QLC0)
Region: residues 1006	to 1706
Annotation: disorder (Structural state)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
The one-dimensional spectrum of apo-RD in the presence of the denaturant GdnHCl (5.3 m) showed no evident secondary chemical shifts, with all peaks appearing at the expected frequencies for an unfolded protein, the so-called “random-coil” chemical shifts (Fig. 2A). The low chemical-shift dispersion was consistent with a protein with no stable secondary and tertiary structures.
Here, we have characterized the structural and hydrodynamic properties of the RTX Repeat Domain (RD) of the CyaA toxin from Bordetella pertussis. This 701-amino acid long domain contains about 40 RTX motifs. We showed that, in the absence of calcium, RD was natively disordered, weakly stable, and highly hydrated.
The one-dimensional spectrum of apo-RD in the presence of the denaturant GdnHCl (5.3 m) showed no evident secondary chemical shifts, with all peaks appearing at the expected frequencies for an unfolded protein, the so-called “random-coil” chemical shifts (Fig. 2A). The low chemical-shift dispersion was consistent with a protein with no stable secondary and tertiary structures. The spectrum of the apo-form under native conditions also showed very poor chemical shift dispersion, and resembled that of the protein denatured in GdnHCl, but with somewhat narrower lines. Noticeably, the bands of the apo-RD spectrum were strikingly narrow for a 701-residue long protein, suggesting that apo-RD had a highly dynamic structure in which most of its side-chains could freely reorient in solution. These observations suggested that apo-RD was mainly natively disordered." as they test both apo-RD alone and with denaturant (see fig.2a) and "As shown in Fig. 2C, The nOe build-up curves obtained for apo-RD in 5.3 m GdnHCl showed practically no transfer of saturation, as expected for the disordered conformations adopted by the protein in these conditions. Apo-RD in the absence of denaturant showed also very limited nOes, albeit significantly higher than that of RD in GdnHCl.
In summary, CD and NMR data indicate that the apo-form of RD was largely unfolded with a weak secondary and tertiary structure content, while calcium binding triggered the folding of the protein into a compact and β-rich (>30-35%) conformation.
Protein: DP00591 (UniProt J7QLC0)
Region: residues 1006	to 1706
Annotation: disorder to order (Structural transition)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
As both states were monomeric (see below), the short T2 value (characteristic of slow dynamic processes) of holo-RD mainly reflected the compactness of the folded protein, while the T2 value of apo-RD most likely resulted from the fast internal motions within the unstructured conformations of the Ca2+-free polypeptide. The high β-sheet content of holo-RD, as evidenced by the envelope of upfield-shifted Hα signals, also strongly suggested that the observed line-broadening resulted from a calcium-induced folding-compaction process.
The NMR spectrum of calcium-bound RD was drastically different. First, it exhibited an increase of the envelope of upfield-shifted Hα protons, providing direct evidence that holo-RD was more structured, with a β-sheet content (calculated as above) of at least 30-35%. Second, the signals became very broad as expected for a compact protein of 72.6 kDa. The line broadening of the 1H spectrum reflected a major change in the dynamic behavior of the protein upon calcium binding." and "The high β-sheet content of holo-RD, as evidenced by the envelope of upfield-shifted Hα signals, also strongly suggested that the observed line-broadening resulted from a calcium-induced folding-compaction process." and "In contrast, holo-RD showed a very efficient transfer of saturation: the apparent cross-relaxation rate of the holo-form (σ = 3.1 ± 0.1 s-1) was respectively, 14- and 100-fold higher than that of apo-RD or that of apo-RD in the presence of GdnHCl. Therefore, the holo state was much more compact than the apo-form.
In summary, CD and NMR data indicate that the apo-form of RD was largely unfolded with a weak secondary and tertiary structure content, while calcium binding triggered the folding of the protein into a compact and β-rich (>30-35%) conformation.
Protein: DP00591 (UniProt J7QLC0)
Region: residues 1006	to 1706
Annotation: disorder (Structural state)
Evidence: analytical ultracentrifugation evidence used in manual assertion
Supporting statements:
Equilibrium AUC experiments confirmed that apo-RD and holo-RD had both a same molecular mass of 73 kDa (Table 1), while velocity AUC indicated that the two states displayed different sedimentation coefficients (values of 2.5 S and 4.5 S for the apo and holo states, respectively) resulting from distinct hydrodynamic properties.
Here, we have characterized the structural and hydrodynamic properties of the RTX Repeat Domain (RD) of the CyaA toxin from Bordetella pertussis. This 701-amino acid long domain contains about 40 RTX motifs. We showed that, in the absence of calcium, RD was natively disordered, weakly stable, and highly hydrated.
Protein: DP00591 (UniProt J7QLC0)
Region: residues 1006	to 1706
Annotation: disorder to order (Structural transition)
Evidence: analytical ultracentrifugation evidence used in manual assertion
Supporting statements:
Equilibrium AUC experiments confirmed that apo-RD and holo-RD had both a same molecular mass of 73 kDa (Table 1), while velocity AUC indicated that the two states displayed different sedimentation coefficients (values of 2.5 S and 4.5 S for the apo and holo states, respectively) resulting from distinct hydrodynamic properties.
Protein: DP00591 (UniProt J7QLC0)
Region: residues 1006	to 1706
Annotation: disorder (Structural state)
Evidence: dynamic light scattering assay evidence used in manual assertion
Supporting statements:
As shown in Fig. 5A, holo-RD eluted at a retention volume (RV) of 13.8 ml. This RV value was close to that expected for a globular protein of 73 kDa (RV ∼15 ml). In marked contrast, apo-RD eluted at a retention volume of 10.4 ml, a value corresponding to a globular protein of ∼600 kDa. In both cases, the molecular mass determined on-line by static light scattering corresponded to that of the monomeric RD protein (Fig. 5B and Table 1). Hence, the low retention volume of apo-RD was not due to oligomerization.
Here, we have characterized the structural and hydrodynamic properties of the RTX Repeat Domain (RD) of the CyaA toxin from Bordetella pertussis. This 701-amino acid long domain contains about 40 RTX motifs. We showed that, in the absence of calcium, RD was natively disordered, weakly stable, and highly hydrated.
Protein: DP00591 (UniProt J7QLC0)
Region: residues 1006	to 1706
Annotation: disorder to order (Structural transition)
Evidence: dynamic light scattering assay evidence used in manual assertion
Supporting statements:
As shown in Fig. 5A, holo-RD eluted at a retention volume (RV) of 13.8 ml. This RV value was close to that expected for a globular protein of 73 kDa (RV ∼15 ml). In marked contrast, apo-RD eluted at a retention volume of 10.4 ml, a value corresponding to a globular protein of ∼600 kDa. In both cases, the molecular mass determined on-line by static light scattering corresponded to that of the monomeric RD protein (Fig. 5B and Table 1). Hence, the low retention volume of apo-RD was not due to oligomerization.
Protein: DP00591 (UniProt J7QLC0)
Region: residues 1006	to 1706
Annotation: calcium ion binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Upon addition of 2 mM calcium to apo-RD, secondary structures were formed, as revealed by the concomitant intensity decrease of the0-* band and the increase of the n-* band in the holo-RD spectrum, as previously reported (10, 26). The structures of holo-RD were readily denatured upon addition of 5MGdnHCl,leading to a spectrum similar to that of the apo-state.
Protein: DP00591 (UniProt J7QLC0)
Region: residues 1006	to 1706
Annotation: calcium ion binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The NMR spectrum of calcium-bound RD was drastically different. First, it exhibited an increase of the envelope of upfield-shifted Ha protons, providing direct evidence that holo-RD was more structured, with a-sheet content (calculated as above) of at least 30–35%. Second, the signals became very broad as expected for a compact protein of 72.6 kDa. The line broadening of the 1H spectrum reflected a major change in the dynamic behavior of the protein upon calcium binding.
Protein: DP00591 (UniProt J7QLC0)
Region: residues 1006	to 1706
Annotation: calcium ion binding (Molecular function)
Evidence: dynamic light scattering assay evidence used in manual assertion
Supporting statements:
As shown in Fig. 5A, holo-RD eluted at a retention volume (RV) of 13.8 ml. This RV value was close to that expected for a globular proteinof 73 kDa (RV ~15 ml).
 Equilibrium AUC experiments confirmed that apo-RD and holo-RD had both a same molecular mass of 73 kDa (Table 1), while velocity AUC indicated that the two states displayed different sedimentation coefficients (values of 2.5 S and 4.5 S for the apo and holo states, respectively) resulting from distinct hydrodynamic properties. In agreement with these data, quasi-elastic light scattering (QELS) analysis showed that upon calcium binding, RD was strongly compacted with its hydrodynamic radius (RH) decreasing from about 7 nm to about 3 nm (Table 1).
Protein: DP00591 (UniProt J7QLC0)
Region: residues 1006	to 1706
Annotation: calcium ion binding (Molecular function)
Evidence: analytical ultracentrifugation evidence used in manual assertion
Supporting statements:
 Equilibrium AUC experiments confirmed that apo-RD and holo-RD had both a same molecular mass of 73 kDa (Table 1), while velocity AUC indicated that the two states displayed different sedimentation coefficients (values of 2.5 S and 4.5 S for the apo and holo states, respectively) resulting from distinct hydrodynamic properties. In agreement with these data, quasi-elastic light scattering (QELS) analysis showed that upon calcium binding, RD was strongly compacted with its hydrodynamic radius (RH) decreasing from about 7 nm to about 3 nm (Table 1).
Protein: DP00591 (UniProt J7QLC0)
Region: residues 1006	to 1706
Annotation: calcium ion binding (Molecular function)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Thermal-induced unfolding of RD was followed by intrinsic fluorescence of tryptophan at various calcium concentrations. The ratio of fluorescence intensities at 360 and 320 nm (rFI360/320) was used tofollow the unfolding of RD (Fig. 4A). The van’t Hoff free enthalpy (deltaHvH) and temperature of half-melting (Tm) were then determined. As shown in Fig. 4B, both Tm and deltaHvH increased with calcium concentrations to reach a plateau above 1.5–2 mM. We obtained similar results from thermal-induced denaturation of RD followed by far- and near-UV CD (data not shown). All together these data indicated that apo-RD was unstable, as expected for a disordered state, while holo-RD was strongly stabilized by calcium binding.
Protein: DP00591 (UniProt J7QLC0)
Region: residues 1009	to 1681
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
 A prominent negative peak at 217 nm, corresponding to formation of the β-roll structures (Chenal et al., 2010), was indeed observed for the complete purified CyaA-RTX domain (residues 1,009 to 1,681 of CyaA), which underwent a characteristic Ca2+-induced transition from the intrinsically disordered to the folded state already at 2 mM Ca2+.
Protein: DP00591 (UniProt J7QLC0)
Region: residues 1009	to 1681
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
A prominent negative peak at 217 nm, corresponding to formation of the β-roll structures (Chenal et al., 2010), was indeed observed for the complete purified CyaA-RTX domain (residues 1,009 to 1,681 of CyaA), which underwent a characteristic Ca2+-induced transition from the intrinsically disordered to the folded state already at 2 mM Ca2+.
Protein: DP00591 (UniProt J7QLC0)
Region: residues 1529	to 1681
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
To decipher the folding pathway in a residue-specific manner, Ca2+-induced conformational changes of 15N-labeled CyaA1529-1681 were followed by NMR spectroscopy. In the absence of Ca2+, the 1H-15N HSQC spectrum of the CyaA1529-1681 yielded a characteristic narrow dispersion of amide resonances of a disordered protein that lacks regular conformation (Figure 2B).
Analysis of chemical shifts revealed that in the absence of Ca2+, the secondary structure formation propensities of individual residues were very low, revealing absence of regular structural elements in the apo form.
Protein: DP00591 (UniProt J7QLC0)
Region: residues 1529	to 1681
Annotation: disorder to order (Structural transition)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
Upon exposure to Ca2+, these HSQC crosspeaks were replaced by distinct and well-dispersed resonances characteristic of folded proteins.
In contrast, the secondary structure propensities in the Ca2+-loaded CyaA1529-1681 revealed a series of short β strands and a C-terminal α helix (Figure S3; cf. X-ray structure in Figure 1D).
Protein: DP00591 (UniProt J7QLC0)
Region: residues 1632	to 1706
Annotation: toxin activity (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
The truncated RTX domains were then assessed for the capacity to fold in the presence of Ca2+ ions into a functional structure that would mediate CyaA binding to the CR3 and enable AC toxin penetration into macrophages (El-Azami-El-Idrissi et al., 2003). At physiological Ca2+ concentration (2 mM), these toxin activities were progressively lost with removal of the last 27, 40, 53, or 75 residues of CyaA (Figure 1B).
Protein: DP00591 (UniProt J7QLC0)
Region: residues 1632	to 1706
Annotation: host cell surface binding (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
The truncated RTX domains were then assessed for the capacity to fold in the presence of Ca2+ ions into a functional structure that would mediate CyaA binding to the CR3 and enable AC toxin penetration into macrophages (El-Azami-El-Idrissi et al., 2003). At physiological Ca2+ concentration (2 mM), these toxin activities were progressively lost with removal of the last 27, 40, 53, or 75 residues of CyaA (Figure 1B).
However, the cell-binding activities of CyaAΔC40 and CyaAΔC53, devoid of 40 or 53 C-terminal residues, were almost intact at 10 mM Ca2+
CyaA binding was assessed on J774A.1 cells exposed to 6 nM CyaA for 30 min at 4°C.
Protein: DP00605 (UniProt Q24246)
Region: residues 1	to 289
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
CD, fluorescence, and sedimentation velocity demonstrate
that IC1-289 is disordered at physiological temperature and
pH, but upon addition of LC8, it gains CD-detected secondary
structure and becomes more resistant to proteolysis (27,
37).
Protein: DP00605 (UniProt Q24246)
Region: residues 1	to 30
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
CD spectra of IC1-143 are consistent with residues
1-30 being helical, while CD spectra of IC114-260 show no
evidence of a folded structure (Figure 5), indicating that
residues 209-250 are unable to form a helix or a coiled-coil
on their own.
This suggests
that, while free IC1-289 is unfolded in its native state, it has
a short segment with a propensity for helix formation, which
is triggered with addition of either LC8 or TMAO.
Protein: DP00605 (UniProt Q24246)
Region: residues 114	to 260
Annotation: protein binding (Molecular function)
Evidence: gel electrophoresis evidence used in manual assertion
Supporting statements:
To determine the stoichiometry of binding, a constant
concentration of IC114-260 was incubated with increasing
concentrations of LC8 and the formation of the complex was
visualized using native gel electrophoresis.
Protein: DP00606 (UniProt P42759)
Region: residues 1	to 260
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H-NMR spectra of ERD10 and ERD14 (Fig. 3A; only ERD10 is shown) also suggest their disordered nature, because the chemical shift dispersion is narrower than is typical for globular proteins. For globular proteins, 1H chemical shifts usually spread out in the region 9.5 to 6.0 ppm, whereas for IDPs, they are usually confined in the region 8.0 to 8.5 ppm (Dyson and Wright, 2004).
Protein: DP00606 (UniProt P42759)
Region: residues 1	to 260
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
In SDS-PAGE, they show a characteristic low mobility: the real molecular mass of ERD10 is 29 kD but it runs at 45 kD, whereas the real molecular mass of ERD14 is 20 kD but it runs at 37 kD (Fig. 2A). This high apparent molecular mass caused by a highly hydrophilic character is often diagnostic of IDPs (Tompa, 2002). In addition, both proteins are heat stable (Fig. 2B) and are very sensitive to proteases (Fig. 2A).