LiteFold/DisProt huggingface dataset:
Protein: DP03421 (UniProt P12464)
Region: residues 84	to 173
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
Here, we investigate the conformational behavior of the δ subunit of RNA polymerase from Bacillus subtilis whose unfolded domain is highly charged, with 7 positively charged amino acids followed by 51 acidic amino acids. Using a specifically designed analytical strategy, we identify transient contacts between the two regions using a combination of NMR paramagnetic relaxation enhancements, residual dipolar couplings (RDCs), chemical shifts, and small-angle scattering.
The unstructured C-terminal domain is 90 aa long and highly charged. The charge distribution of this domain is distinct, with a conserved stretch of 9 residues (96–104) containing 7 positive charges followed by the rest of the domain with 51 acidic residues (K-D/E motif).
Here, the ASTEROIDS approach(11−13) is used to describe the conformational behavior of the CTD of δ subunit in solution using a combination of NMR chemical shifts (CSs), paramagnetic relaxation enhancements (PREs), and residual dipolar couplings (RDCs) as well as small-angle scattering (SAXS).
The Kratky plot depicted in Figure 1 as well as the normalized distribution of radius of gyrations of the selected ensembles compared to the statistical coil is typical for IDRs.
Cross-references: SASBDB:SASDF58
Protein: DP03421 (UniProt P12464)
Region: residues 96	to 104
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The most visible feature of the distance map are contacts observed between the lysine-rich stretch (K-tract, K96–K104) and the acidic region (F115–E170).
Cross-references: BMRB:27963
Protein: DP03421 (UniProt P12464)
Region: residues 115	to 170
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The most visible feature of the distance map are contacts observed between the lysine-rich stretch (K-tract, K96–K104) and the acidic region (F115–E170).
Cross-references: BMRB:27963
Protein: DP03421 (UniProt P12464)
Region: residues 93	to 173
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1HN chemical shift dispersion of the disordered C-terminal domain of the δ subunit is lower than that of the retroviral protease: 0.5 ppm versus 0.7 ppm. The 15N chemical shifts of the unstructured regions cover 6.4 and 11.1 ppm for the δ subunit and retroviral protease, respectively, with the most crowded regions spanning 3.4 ppm and 4.8 ppm, respectively.
The HSQC spectrum is typically that of a highly disordered protein. The authors provide the boundaries of the disordered C-terminus in Figure 1.
Cross-references: BMRB:16912
Protein: DP03421 (UniProt P12464)
Region: residues 96	to 104
Annotation: molecular function regulator (Molecular function)
Evidence: mutant phenotype evidence used in manual assertion
Supporting statements:
Experiments addressing the effect of the charge perturbation in δKE on the affinity of RNAP to DNA (Pilv promoter on a supercoiled plasmid) showed that δKE decreased the affinity of RNAP to DNA in comparison with RNAP with δ (Figure 5a). Experiments testing the effect of δ/δKE on the [iNTP] requirement (Pilv promoter on supercoiled plasmid) revealed that δ increased the requirement of RNAP for [GTP] in comparison to RNAP lacking δ, and this effect was more pronounced with δKE (Figure 5b).
Protein: DP03422 (UniProt A0A142G2L5)
Region: residues 21	to 181
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
BilRI is an intrinsically disordered protein (IDP), as demonstrated by its 1H, 15N HSQC spectrum, which displays very limited signal dispersion (Ahlstrand et al. 2017). In the HN dimension their dispersion is only 0.63 ppm.
Peaks in the BilRI 2D 1H, 15N-HSQC spectrum display overwhelming overlap (Fig. 2a) and a very narrow distribution in the HN dimension.
Cross-references: BMRB:27824
Protein: DP03422 (UniProt A0A142G2L5)
Region: residues 21	to 181
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The proton (1H) spectrum of BilRI measured at 600 MHz exhibits features typical of a disordered protein, including a collapsed chemical shift dispersion in the amide proton region (8.2 ± 0.3 1H ppm) and the lack of shielded methyl protons, i.e., clustering of methyl protons to so-called random coil shift, 0.7 ppm (Fig. 1A).
To slow down the chemical exchange of labile amide protons with solvent protons, we measured the 15N HSQC spectrum of BilRI under mildly acidic conditions (pH 5). This spectrum more clearly highlights the same features already visible in the corresponding 1H spectrum, i.e., poor dispersion of amide proton chemical shifts, indicating that BilRI remains disordered in solution and under slightly acidic conditions.
The results of the nuclear magnetic resonance (NMR) studies, which indicated the absence of a specific fold, were supported by the amino acid analysis showing high numbers of charged and polar residues and a low number of hydrophobic bulky amino acids, a composition that is typical for IDPs.
Protein: DP03422 (UniProt A0A142G2L5)
Region: residues 21	to 181
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We further characterized its structural features by analyzing the recently assigned chemical shifts of BilRI [37] and its {1H}-15N heteronuclear nuclear Overhauser effect (NOE), T1 and 1H, 15N nuclear Overhauser effect spectroscopy-heteronuclear single quantum coherence spectroscopy (NOESY-HSQC) spectra.
Chemical shift assignment for BilRI was extremely complicated due to the presence of repeating segments in the amino acid sequence leading to considerable overlap of NMR peaks [37]. This overlap also hampered the analyses of 15N relaxation and NOESY spectra because of the crowded 1H, 15N HSQC spectrum.
The deviations of the experimental BilRI chemical shifts from their random coil values were small (−0.13< SSP <0.23) throughout the sequence and were biased toward helical propensity (positive SSP scores). The score pattern was similar within the three repeating segments of the sequence (51–80, 91–120, and 131–160), suggesting that the minute residual structural propensity is not random: the N-terminal residues of these repeats show a helical tendency.
Overall, the BilRI backbone appears to be very flexible, as expected, and there is no evidence of specific long-range contacts in BilRI. The repeat regions, especially their N-terminal 2/3, appear to be slightly more rigid than the rest of the protein.
Protein: DP03422 (UniProt A0A142G2L5)
Region: residues 21	to 181
Annotation: protein binding (Molecular function)
Evidence: enzyme-linked immunoabsorbent assay evidence used in manual assertion
Supporting statements:
A microplate assay showed that recombinant BilRI bound to various cytokines, of which the binding to IL-8 was high compared with the binding of BilRI to the negative control protein bovine serum albumin (BSA; p = 0.008; paired-samples T-test; Fig. 2A).
Figure2. A) Recombinant BilRI containing an 8-histidine-long C-terminal tag bound to various recombinant human cytokines in a microplate assay. BSA served as a negative control and was used as a blocking agent in the assays. The bound BilRI was detected with HRP-labeled HisProbe™. The BilRI binding to IL-8 was high compared to the binding to the control protein BSA (**:p = 0.008, paired-samples T-test).
Protein: DP03423 (UniProt F1NGB1)
Region: residues 190	to 455
Annotation: disorder (Structural state)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
Surprisingly, the hydrogen-deuterium exchange mass spectrometry results revealed
that Nucb2 is divided into two parts: an N-terminal half with a stable mosaic-like structure and a disordered C-terminal half.
The HDX pattern of this part of the proteins resembles a mosaic-like character, which contains regions with fast and slow HDX interlacing with each other. 
On the other hand, the carboxyl-terminal halves of both the Nucb2s (corresponding to nesfatin-3) were observed to exhibit a more uniform and fast exchange rate, even within the first 10 s, which indicates a very high level of solvent exposure and flexibility.
The authors do not mention exact residue boundaries, but the region corresponding to nesfatin-3 was shown for their construct in Figure 1 as starting from residue 166. There is a 24 residues long signal peptide in the UniProt sequence that was not present in the studied construct, so residue 166 corresponds to UniProt residue 190.
Protein: DP03423 (UniProt F1NGB1)
Region: residues 265	to 284
Annotation: calcium ion binding (Molecular function)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
The presence of Ca2+ induces the structural changes within the C-terminal half, leading to the formation of the mosaic-like structure in these parts of Nucb2s. Additionally, in the presence of Ca2+, both proteins undergo significant disorder-to-order transition, which is a feature characteristic for Ca2+ sensors (i.e. calmodulin).
Upon Ca2+ binding, both the Nucb2s showed significant changes in deuterium incorporation, but only at their carboxyl-terminal half (Fig. 7C and D). The effects of Ca2+ binding were mainly detected for peptides 241–260 and 285–310 (ggNucb2), as well as for peptides 241–258 and 285–310 (hsNucb2).
There is a 24 residues long signal peptide in the UniProt sequence that was not present in the studied construct, so residue 241 corresponds to UniProt residue 265.
Protein: DP03423 (UniProt F1NGB1)
Region: residues 309	to 334
Annotation: calcium ion binding (Molecular function)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
The presence of Ca2+ induces the structural changes within the C-terminal half, leading to the formation of the mosaic-like structure in these parts of Nucb2s. Additionally, in the presence of Ca2+, both proteins undergo significant disorder-to-order transition, which is a feature characteristic for Ca2+ sensors (i.e. calmodulin).
Upon Ca2+ binding, both the Nucb2s showed significant changes in deuterium incorporation, but only at their carboxyl-terminal half (Fig. 7C and D). The effects of Ca2+ binding were mainly detected for peptides 241–260 and 285–310 (ggNucb2), as well as for peptides 241–258 and 285–310 (hsNucb2).
There is a 24 residues long signal peptide in the UniProt sequence that was not present in the studied construct, so residue 241 corresponds to UniProt residue 265.
Protein: DP03423 (UniProt F1NGB1)
Region: residues 309	to 334
Annotation: disorder to order (Structural transition)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
The presence of Ca2+ induces the structural changes within the C-terminal half, leading to the formation of the mosaic-like structure in these parts of Nucb2s. Additionally, in the presence of Ca2+, both proteins undergo significant disorder-to-order transition, which is a feature characteristic for Ca2+ sensors (i.e. calmodulin).
Upon Ca2+ binding, both the Nucb2s showed significant changes in deuterium incorporation, but only at their carboxyl-terminal half (Fig. 7C and D). The effects of Ca2+ binding were mainly detected for peptides 241–260 and 285–310 (ggNucb2), as well as for peptides 241–258 and 285–310 (hsNucb2).
There is a 24 residues long signal peptide in the UniProt sequence that was not present in the studied construct, so residue 241 corresponds to UniProt residue 265.
Protein: DP03423 (UniProt F1NGB1)
Region: residues 265	to 284
Annotation: disorder to order (Structural transition)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
The presence of Ca2+ induces the structural changes within the C-terminal half, leading to the formation of the mosaic-like structure in these parts of Nucb2s. Additionally, in the presence of Ca2+, both proteins undergo significant disorder-to-order transition, which is a feature characteristic for Ca2+ sensors (i.e. calmodulin).
Upon Ca2+ binding, both the Nucb2s showed significant changes in deuterium incorporation, but only at their carboxyl-terminal half (Fig. 7C and D). The effects of Ca2+ binding were mainly detected for peptides 241–260 and 285–310 (ggNucb2), as well as for peptides 241–258 and 285–310 (hsNucb2).
There is a 24 residues long signal peptide in the UniProt sequence that was not present in the studied construct, so residue 241 corresponds to UniProt residue 265.
Protein: DP03424 (UniProt P80303)
Region: residues 190	to 420
Annotation: disorder (Structural state)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
Surprisingly, the hydrogen-deuterium exchange mass spectrometry results revealed that Nucb2 is divided into two parts: an N-terminal half with a stable mosaic-like structure and a disordered C-terminal half.
The HDX pattern of this part of the proteins resembles a mosaic-like character, which contains regions with fast and slow HDX interlacing with each other.
On the other hand, the carboxyl-terminal halves of both the Nucb2s (corresponding to nesfatin-3) were observed to exhibit a more uniform and fast exchange rate, even within the first 10 s, which indicates a very high level of solvent exposure and flexibility.
The authors do not mention exact residue boundaries, but the region corresponding to nesfatin-3 was shown for their construct in Figure 1 as starting from residue 166. There is a 24 residues long signal peptide in the UniProt sequence that was not present in the studied construct, so residue 166 corresponds to UniProt residue 190."
Protein: DP03424 (UniProt P80303)
Region: residues 265	to 282
Annotation: disorder to order (Structural transition)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
The presence of Ca2+ induces the structural changes within the C-terminal half, leading to the formation of the mosaic-like structure in these parts of Nucb2s. Additionally, in the presence of Ca2+, both proteins undergo significant disorder-to-order transition, which is a feature characteristic for Ca2+ sensors (i.e. calmodulin).
Upon Ca2+ binding, both the Nucb2s showed significant changes in deuterium incorporation, but only at their carboxyl-terminal half (Fig. 7C and D). The effects of Ca2+ binding were mainly detected for peptides 241–260 and 285–310 (ggNucb2), as well as for peptides 241–258 and 285–310 (hsNucb2).
There is a 24 residues long signal peptide in the UniProt sequence that was not present in the studied construct, so residue 241 corresponds to UniProt residue 265.
Protein: DP03424 (UniProt P80303)
Region: residues 309	to 334
Annotation: disorder to order (Structural transition)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
The presence of Ca2+ induces the structural changes within the C-terminal half, leading to the formation of the mosaic-like structure in these parts of Nucb2s. Additionally, in the presence of Ca2+, both proteins undergo significant disorder-to-order transition, which is a feature characteristic for Ca2+ sensors (i.e. calmodulin).
Upon Ca2+ binding, both the Nucb2s showed significant changes in deuterium incorporation, but only at their carboxyl-terminal half (Fig. 7C and D). The effects of Ca2+ binding were mainly detected for peptides 241–260 and 285–310 (ggNucb2), as well as for peptides 241–258 and 285–310 (hsNucb2).
There is a 24 residues long signal peptide in the UniProt sequence that was not present in the studied construct, so residue 241 corresponds to UniProt residue 265.
Protein: DP03424 (UniProt P80303)
Region: residues 265	to 282
Annotation: calcium ion binding (Molecular function)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
The presence of Ca2+ induces the structural changes within the C-terminal half, leading to the formation of the mosaic-like structure in these parts of Nucb2s. Additionally, in the presence of Ca2+, both proteins undergo significant disorder-to-order transition, which is a feature characteristic for Ca2+ sensors (i.e. calmodulin).
Upon Ca2+ binding, both the Nucb2s showed significant changes in deuterium incorporation, but only at their carboxyl-terminal half (Fig. 7C and D). The effects of Ca2+ binding were mainly detected for peptides 241–260 and 285–310 (ggNucb2), as well as for peptides 241–258 and 285–310 (hsNucb2).
There is a 24 residues long signal peptide in the UniProt sequence that was not present in the studied construct, so residue 241 corresponds to UniProt residue 265.
Protein: DP03424 (UniProt P80303)
Region: residues 309	to 334
Annotation: calcium ion binding (Molecular function)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
The presence of Ca2+ induces the structural changes within the C-terminal half, leading to the formation of the mosaic-like structure in these parts of Nucb2s. Additionally, in the presence of Ca2+, both proteins undergo significant disorder-to-order transition, which is a feature characteristic for Ca2+ sensors (i.e. calmodulin).
Upon Ca2+ binding, both the Nucb2s showed significant changes in deuterium incorporation, but only at their carboxyl-terminal half (Fig. 7C and D). The effects of Ca2+ binding were mainly detected for peptides 241–260 and 285–310 (ggNucb2), as well as for peptides 241–258 and 285–310 (hsNucb2).
There is a 24 residues long signal peptide in the UniProt sequence that was not present in the studied construct, so residue 241 corresponds to UniProt residue 265.
Protein: DP03425 (UniProt Q7G7J6)
Region: residues 28	to 112
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Furthermore, the results of SAXS, ITC, and gel filtration experiments indicate that when free in solution, SLR1(M28-A112) is a natively unfolded protein. The NMR experiments expand this observation to show that the unfolded mutant also contains a small amount of marginally stable secondary structure. 
The 1H-15N HSQC NMR spectrum of free SLR1(M28-A112) is very similar to that expected for a disordered protein (Fig. 5a)
Protein: DP03425 (UniProt Q7G7J6)
Region: residues 28	to 112
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
Furthermore, the results of SAXS, ITC, and gel filtration experiments indicate that when free in solution, SLR1(M28-A112) is a natively unfolded protein.
The molecular weight of SLR1(M28-A112) is estimated to be 12.9 kDa, which is approximately 1.5-fold larger than the theoretical value (8.9 kDa). Information about molecular shape can be obtained using the entire scattering profile in a Kratky plot. The presence of a peak in a Kratky plot indicates that a protein has a globular shape, while a plateau between 0.1 and 0.3 Å−1 indicates that an unfolded protein exists14. The plots of Fig. S3B clearly indicate that OsGID1/GA3 is globular and that SLR1(M28-A112) is unfolded. The larger than expected Rg value for SLR1(M28-A112), given its MW, is obviously a consequence of an unfolded structure.
Protein: DP03425 (UniProt Q7G7J6)
Region: residues 28	to 112
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Furthermore, the results of SAXS, ITC, and gel filtration experiments indicate that when free in solution, SLR1(M28-A112) is a natively unfolded protein.
As reported previously, all of the truncated SLR1 mutants elute as proteins of much larger size than would be predicted on the basis of their estimated molecular weights (MWs).
Protein: DP03425 (UniProt Q7G7J6)
Region: residues 28	to 112
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
We have identified the shortest SLR1 sequence (M28-A112) that binds the rice GID/GA complex tightly. 
The ITC results also show that SLR1(M28-A112) is the shortest sequence that can bind OsGID1/GA3 with high affinity.
Protein: DP03425 (UniProt Q7G7J6)
Region: residues 28	to 112
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H-15N HSQC NMR spectrum of free SLR1(M28-A112) is very similar to that expected for a disordered protein (Fig. 5a). Conversely, the cross peaks of the 1H-15N HSQC NMR spectrum of SLR1(M28-A112) acquired when unlabelled OsGID1/GA3 is present are well dispersed (Fig. 5b).
Examination of the values of the SLR1 13Cα chemical shifts of GID1/GA3/SLR1(M28-A112) shows that the 13Cα resonances of the residues of the sequences E39-A44, R50-G69, D81-A88, and L99-E109 shift ca. 3.0–4.0 ppm downfield compared with those of free SLR1(M28-A112). This shift is consistent the formation of α-helices (Fig. 5c). Therefore, while the structure of free SLR1(M28-A112) is mostly disordered, the protein acquires a defined fold when bound to its physiological target, GID1.
Protein: DP03425 (UniProt Q7G7J6)
Region: residues 28	to 112
Annotation: disorder to order (Structural transition)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
Taken together, the Rg values, calculated molecular weights, and Kratky plots strongly suggest the following: OsGID1/GA3 and SLR1(M28-A112) form a 1:1 complex with a globular shape; as an isolated species, OsGID1/GA3 has a propensity to dimerize; and SLR1(M28-A112) is a natively unfolded protein.
Protein: DP03425 (UniProt Q7G7J6)
Region: residues 28	to 112
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
On the other hand, large positive deviations (ca. 3.0–4.0 ppm) in the 13Cα chemical shifts of the residues of E39-A44, R50-G69, D81-A88, and L99-E109 are observed when SLR1(M28-A112) and OsGID1/GA3 are both present, suggesting that these sequences form α-helices.
Protein: DP03426 (UniProt P25024)
Region: residues 1	to 28
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Overall, 97% of the backbone resonances for residues 20 to 325 were assigned. The missing resonances are from seven Pro (P22, P93, P170, P180, P185, P214, P257) and one Arg (R285). None of the 15N and 13C signals from the mobile N-and C-termini (residues 1-19 and 326-350) could be detected in the spectra, consistent with our observation of these signals in solid-state NMR experiments designed to detect only signals from mobile sites (Supplementary Fig. 6), as well as our previous analysis of local and global motions of CXCR124.
Supplementary Figure 6. One-dimensional refocused INEPT solid-state NMR MAS spectra of CXCR1 in proteoliposomes. Only
signals from mobile sites in the termini are detected.
Cross-references: PDB:2LNL
BMRB:18170