LiteFold/DisProt huggingface dataset:
Protein: DP00195 (UniProt P02313)
Region: residues 1	to 90
Annotation: disorder (Structural state)
Evidence: Fourier-transform infrared spectroscopy evidence used in manual assertion
Supporting statements:
The 6-pm region of the infrared spectrum of protein HMG 17 was obtained in solution at pH 6.8,1 M NaCl to check for the formation of p-structure. The amide 1 band was centred at  1644cm-1 and showed no evi- dence of any low-frequency components between 1630 and 1610 cm-1  that would indicate the formation of 8-structure [16,17].
Protein: DP00195 (UniProt P02313)
Region: residues 1	to 90
Annotation: disorder (Structural state)
Evidence: small-angle neutron scattering evidence used in manual assertion
Supporting statements:
The high R, value must  therefore be the result of a  disordered structure.
Protein: DP00195 (UniProt P02313)
Region: residues 1	to 90
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The circular dichroism spectrum of protein HMG 17 in a  high-ionic-strength  buffer at pH 7.9  is shown in Fig. 1 ; the low ellipticity at 222 nm  indicates that under these conditions the protein has little or no helicity. Changing the pH and ionic strength does not alter  the ellipticity at 222 nm substantially  (Table 1) nor the overall shape of the curve.
Protein: DP00195 (UniProt P02313)
Region: residues 16	to 41
Annotation: nucleic acid binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
This was done as described in Materials and Methods, using the same ratio of DNA/ protein as in the NMR experiments,  with NACl added to 0.35,O. 1 and 0 M. No free protein was found in the NaC1-free and 0.1 M NaCl  solutions,  but 75 2, of the  input  protein was  recovered from the 0.35 M NaCl  solution.
 It is  striking that when the protein is bound at low ionic strength, certain resonan- ces are only  slightly affected whilst others are consid- erable reduced in apparent area by line broadening. Thus the arginine,  proline, serine, and to a  certain extent,  valine,  plus leucine  residues are bound. This indicates that the region  between about residues  15 and 40 is the primary binding site.
Since authors do not consider the first Met residue, the binding region boundaries are 16-41.
Protein: DP00195 (UniProt P02313)
Region: residues 1	to 90
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Both spectra look like that of a  random coil protein with  residues of the same type giving a single sharp peak not showing any spread of chemical shift values. Furthermore, no meth- yl resonances are observed   between 0 and 1 ppm as is normally found with globular  proteins.
Protein: DP00196 (UniProt P20810)
Region: residues 137	to 277
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
In accordance with this expectation, proteolysis of CSD1 and MAP2c under such conditions results in a picture typical of limited proteolysis, featuring the formation of only a few, relatively stable, fragments.
Protein: DP00196 (UniProt P20810)
Region: residues 137	to 277
Annotation: pre-molten globule (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
For CSD1, the CD spectrum of the full-length protein has a minimum at 201 nm, characteristic of a protein in a largely disordered conformation (Figure 5A). The spectra of the two halves of the protein, however, are different, with the minimum of the C-terminal half shifted to about 205 nm.
Protein: DP00196 (UniProt P20810)
Region: residues 137	to 277
Annotation: pre-molten globule (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Because the mean hydrophobicity of MAP2c and CSD1 is practically the same (-0.780 for CSD1 and -0.781 for MAP2c, cf. other methods), the difference in their hydration indicates a substantial difference in the extent of their intramolecular interactions: judged simply by the amount of water that they bind, CSD1 appears more ordered than MAP2c.
In other words, its two halves interact in the intact molecule and partially replace each other’s bound water.
Protein: DP00196 (UniProt P20810)
Region: residues 137	to 277
Annotation: limited proteolysis display site (Disorder function)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
In accordance with this expectation, proteolysis of CSD1 and MAP2c under such conditions results in a picture typical of limited proteolysis, featuring the formation of only a few, relatively stable, fragments.
Protein: DP00196 (UniProt P20810)
Region: residues 137	to 277
Annotation: pre-molten globule (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The flexible nature of the backbone leads to narrower, lines resulting in an adequate signal-to-noise ratio.
As the typical helical 3JHNCR value is 4 Hz, the observed values correspond to the mainly random character of hCSD1 (data not shown).
Protein: DP00197 (UniProt P0A707)
Region: residues 78	to 89
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Taken altogether, these results strongly suggest that, in solution, the inter-domain linker is disordered rather than α-helical. Indeed, most of the chemical shifts of the amide groups of these residues are clustered in the “random coil” region.
Protein: DP00197 (UniProt P0A707)
Region: residues 78	to 89
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Taken altogether, these results strongly suggest that, in solution, the inter-domain linker is disordered rather than α-helical. Indeed, most of the chemical shifts of the amide groups of these residues are clustered in the “random coil” region.
Protein: DP00200 (UniProt P20963)
Region: residues 49	to 164
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
As shown in Figure 4B, the spectrum presents features resembling that of an unfolded state, particularly with the backbone amide 1H chemical shifts spanning only 7.6−8.6 ppm (1.0 ppm). This low dispersion of the backbone amide 1H chemical shifts is typical for unfolded or intrinsically disordered proteins (54, 55, 57)   .
Protein: DP00200 (UniProt P20963)
Region: residues 49	to 164
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
ζcyt Is an Unstructured, Random-Coil Protein, and Its Oligomerization Does Not Result in Formation of Detectable Secondary or Tertiary Structure. (1) CD Spectroscopy. The far-ultraviolet CD spectra of ζcyt show the characteristics of an unfolded protein (Figure 4A), consistent with earlier published results ( 40, 49).
Protein: DP00200 (UniProt P20963)
Region: residues 49	to 164
Annotation: protein complex oligomerization (Biological process)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
The ζcyt Is Predominantly Dimeric, and the Oligomerization Is Reversible and Dependent on Concentration and Temperature. The apparent molecular mass of ζcyt was determined using gel filtration, sedimentation equilibrium, and light scattering (Table 1). As compared to the molecular mass predicted from the sequence and confirmed by mass spectroscopy (13157 Da), the native apparent molecular mass indicated the formation of oligomeric forms, with the predominant species a dimer in rapid equilibrium with monomer and larger oligomers.
The apparent native molecular mass of ζcyt−ζcyt (0.3 mg/mL) as determined by gel filtration was ∼27 kDa (data not shown), as expected for the covalent dimer and consistent with the molecular mass observed by ES-MS and predicted by the protein sequence (27118 Da).
The analysis estimated the apparent monomer−dimer and the dimer−tetramer equilibrium dissociation constants, Kd(monomer-dimer) and Kd(dimer-tetramer), as 9.2 ± 1.6 μM and 0.9 ± 0.2 mM (mean ± a standard deviation), respectively.
Protein: DP00200 (UniProt P20963)
Region: residues 49	to 164
Annotation: protein complex oligomerization (Biological process)
Evidence: cross-linking evidence used in manual assertion
Supporting statements:
The ζcyt Is Predominantly Dimeric, and the Oligomerization Is Reversible and Dependent on Concentration and Temperature. The apparent molecular mass of ζcyt was determined using gel filtration, sedimentation equilibrium, and light scattering (Table 1). As compared to the molecular mass predicted from the sequence and confirmed by mass spectroscopy (13157 Da), the native apparent molecular mass indicated the formation of oligomeric forms, with the predominant species a dimer in rapid equilibrium with monomer and larger oligomers.
Neither glutaraldehyde nor dimethyl suberimidate cross-linking resulted in detectable amounts of ζcyt oligomers, as analyzed by SDS−PAGE, but bis(sulfosuccinimidyl) suberate (BS3) cross-linking (Figure 1C, inset) resulted in monomeric (∼13 kDa), dimeric (∼26 kDa), trimeric (∼39 kDa), and tetrameric (∼52 kDa) species.
Protein: DP00200 (UniProt P20963)
Region: residues 49	to 164
Annotation: protein complex oligomerization (Biological process)
Evidence: analytical ultracentrifugation evidence used in manual assertion
Supporting statements:
The ζcyt Is Predominantly Dimeric, and the Oligomerization Is Reversible and Dependent on Concentration and Temperature. The apparent molecular mass of ζcyt was determined using gel filtration, sedimentation equilibrium, and light scattering (Table 1). As compared to the molecular mass predicted from the sequence and confirmed by mass spectroscopy (13157 Da), the native apparent molecular mass indicated the formation of oligomeric forms, with the predominant species a dimer in rapid equilibrium with monomer and larger oligomers.
The best fit, as judged by (1) estimated monomeric molecular mass closest to that predicted from the amino acid sequence and confirmed by ES-MS, (2) the lowest goodness-of-fit value, and (3) random distribution of residuals, was obtained with a model for reversible monomer−dimer−tetramer equilibrium (Figure 2, solid line).
Protein: DP00201 (UniProt P02721)
Region: residues 55	to 66
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
However, it is clear both from the superpositions and from the identities of the particularly sharp signals in the spectra that most of the residues not involved in the helices are substantially disordered. In addition to the N and C termini, these regions also include the loop connecting the two helices (residues 23–33).
Cross-references: PDB:1VZS
Protein: DP00201 (UniProt P02721)
Region: residues 84	to 108
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
However, it is clear both from the superpositions and from the identities of the particularly sharp signals in the spectra that most of the residues not involved in the helices are substantially disordered.
Cross-references: PDB:1VZS
Protein: DP00202 (UniProt P0A8H9)
Region: residues 40	to 65
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The first 3 and last 25 residues are unstructured and shown in a random configuration.
Protein sequence is 100% identical to the one from K12 strain, used in this publication.
Cross-references: PDB:1LV3
DisProt:DP01714r002
Protein: DP00207 (UniProt P21513)
Region: residues 498	to 1061
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectra display the characteristics of a partly unstructured protein: a large negative peak at 200 nm and a value close to zero at 220 nm. A temperature-melt experiment indicated a loss of CD spectral signal at 200 nm, suggesting that some secondary structural elements are present.
Protein: DP00207 (UniProt P21513)
Region: residues 628	to 843
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
. In this regard we also note that the complex elutes aberrantly in size-exclusion chromatography (>500 kDa) and is well in excess of its predicted mass of 74 kDa, which further suggests that it has a largely unstructured portion.
Protein: DP00207 (UniProt P21513)
Region: residues 498	to 1061
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
The predicted weight of the CTD is 67.7 kDa, but the purified protein runs closer to 90 kDa by SDS-PAGE.
Protein: DP00207 (UniProt P21513)
Region: residues 603	to 850
Annotation: disorder (Structural state)
Evidence: electrospray ionization fourier transform ion cyclotron resonance mass spectrometry evidence used in manual assertion
Supporting statements:
The native ESI mass spectrometry analysis also reveals that RNase E 603–850 has a broad charge distribution in the spectra, which indicates that it has conformational disordered character.
Protein: DP00207 (UniProt P21513)
Region: residues 603	to 850
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
To further investigate the overall structural conformation and degree of flexibility of the subassemblies in solution, SAXS was employed (Figure 3). The Guinier derived radius of gyration (Rg) values for RNase E 603–850, the binary complex and the ternary complex are ∼53, ∼54 and ∼64 Å, respectively (Supplementary Table S1). Comparing these values with expectations for globular proteins of the corresponding Mw suggests that all three particles have non-globular shapes.
The comparatively featureless scattering intensity curve and the smooth and extended P(r) distribution function of RNase E 603–850 indicate that the protein is highly flexible in solution (Figure 3A and B, respectively). Moreover, the dimensionless Kratky profile (dKratky) (54) of this RNase E segment is characteristic of an intrinsically disordered protein (IDP), with the intensity increasing gradually and the absence of a peak at lower angles (Figure 3C).
The calculated distribution of Rg values from the ensemble samples a similar space to that of the random pool, suggesting that the isolated RNase E 603–850, in the absence of its helicase and enolase partners, is indeed highly flexible (Rflex values of the ensemble and random pool are very close at 89.4% and 87.3%, respectively). Interestingly, the average Rg value of the ensemble distribution is slightly higher than that of the random pool. Furthermore, the experimental Rg of RNase E 603–850 is greater than the value of ∼46 Å predicted for a typical IDP of the same length (45,55), indicating that the construct is not only highly flexible but also favors extended conformations in solution.
Protein: DP00207 (UniProt P21513)
Region: residues 816	to 850
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
We have structurally characterized a subassembly of the degradosome-comprising a 248-residue segment of the natively unstructured part of RNase E, the DEAD-box helicase RhlB and the glycolytic enzyme enolase, and provide evidence that it serves as a flexible recognition centre that can co-recruit small regulatory RNA and the RNA chaperone Hfq
In this model, the binding of RhlB and enolase facilitates their partner RNase E 603–850 to transition from a highly dynamic state to a molten globule with transient secondary structure elements
Cross-references: PDB:5OHG
Protein: DP00207 (UniProt P21513)
Region: residues 816	to 850
Annotation: disorder to molten globule (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
We have structurally characterized a subassembly of the degradosome-comprising a 248-residue segment of the natively unstructured part of RNase E, the DEAD-box helicase RhlB and the glycolytic enzyme enolase, and provide evidence that it serves as a flexible recognition centre that can co-recruit small regulatory RNA and the RNA chaperone Hfq
In this model, the binding of RhlB and enolase facilitates their partner RNase E 603–850 to transition from a highly dynamic state to a molten globule with transient secondary structure elements
Cross-references: PDB:5OHG
Protein: DP00207 (UniProt P21513)
Region: residues 816	to 850
Annotation: molecular adaptor activity (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The RNA degradosome is a multi-enzyme assembly that plays a central role in the RNA metabolism of Escherichia coli and numerous other bacterial species including pathogens. At the core of the assembly is the endoribonuclease RNase E, one of the largest E. coli proteins and also one that bears the greatest region predicted to be natively unstructured. This extensive unstructured region, situated in the C-terminal half of RNase E, is punctuated with conserved short linear motifs that recruit partner proteins, direct RNA interactions, and enable association with the cytoplasmic membrane.
We have structurally characterized a subassembly of the degradosome–comprising a 248-residue segment of the natively unstructured part of RNase E, the DEAD-box helicase RhlB and the glycolytic enzyme enolase, and provide evidence that it serves as a flexible recognition centre that can co-recruit small regulatory RNA and the RNA chaperone Hfq.
Our results support a model in which the degradosome captures substrates and regulatory RNAs through the recognition centre, facilitates pairing to cognate transcripts and presents the target to the ribonuclease active sites of the greater assembly for cooperative degradation or processing.
Cross-references: PDB:5OHG
Protein: DP00207 (UniProt P21513)
Region: residues 498	to 1061
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The scattering profile for the CTD has the characteristics of less well-folded proteins, such as the asymptotic behaviour of the Kratky plot (Figure 2A, green profile in the inset) that is characteristic of random chains.
Protein: DP00207 (UniProt P21513)
Region: residues 498	to 1061
Annotation: protein binding (Molecular function)
Evidence: cross-linking evidence used in manual assertion
Supporting statements:
Protein–protein interactions were tested using the chemical cross-linking agent dimethyl suberimidate (DMS) (Figure 3A). Using denaturing gels, a cross-linked complex was observed with helicase (Figure 3A, lane 4).
The circled band was shown to contain both helicase RhlB and CTD using in-gel protease digestion and MALDI-mass spectrometry analysis.
Protein: DP00207 (UniProt P21513)
Region: residues 498	to 1061
Annotation: protein complex oligomerization (Biological process)
Evidence: cross-linking evidence used in manual assertion
Supporting statements:
The CTD was also observed to self-associate (Figure 3A, lane 2).
The circled band corresponds to a homodimer of the CTD. 
We have found that the CTD can be cross-linked to itself, which is consistent with the findings reported by Vanzo et al.,19 that RNase E can self-interact.
Protein: DP00207 (UniProt P21513)
Region: residues 628	to 843
Annotation: 7S RNA binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
The refolded CTD was also tested for RNA binding by an electrophoretic mobility-shift assay. It was observed to bind to 7 S rRNA with high affinity forming two well-defined complexes (Figure 3B).
The ability of R-domain to bind to structured RNA was tested by electrophoretic mobility-shift assays. Like the CTD, shown in Figure 3B, the R-domain was also observed to form two complexes with 7 S rRNA (Figure 5C).
The affinity of the R-domain for the 7 S rRNA is comparable to that of the CTD (Figure 3B). Therefore, it is likely that the coiled-coil region identified here is involved in binding to structured RNAs.
Protein: DP00207 (UniProt P21513)
Region: residues 628	to 843
Annotation: protein binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
Purified helicase RhlB binds avidly to this domain, and the R-domain–helicase complex can be isolated by size-exclusion chromatography as an earlier-eluting species in an approximate 1 : 1 stoichiometric complex (Figure 5A, Lane 1). 
Lane 1 corresponds to the first peak, identified as a complex of R-domain and helicase RhlB.
Protein: DP00207 (UniProt P21513)
Region: residues 628	to 843
Annotation: positive regulation of ATP-dependent activity (Biological process)
Evidence: enzymatic activity assay evidence used in manual assertion
Supporting statements:
In comparison with the ATPase activity of the isolated helicase, the purified helicase RhlB–R-domain complex is 25-fold more active. This suggests that the protein–protein interaction is stimulatory, in agreement with the findings reported by Vanzo et al.
Protein: DP00207 (UniProt P21513)
Region: residues 628	to 843
Annotation: protein binding (Molecular function)
Evidence: mass spectrometry evidence used in manual assertion
Supporting statements:
Series B corresponds to the R-domain with a measured mass of 29,044(±41) Da (theoretical mass of 28,822 Da) and the charge state series C with a mass of 76,763(±13) Da corresponds to one R-domain bound to one helicase RhlB (theoretical mass 75,817 Da) (Figure 6A).
Tandem mass spectrometry (MS/MS) of the complex ion (C+19) confirmed the composition of the species to be that of R-domain and helicase RhlB (Figure 6B).
Protein: DP00207 (UniProt P21513)
Region: residues 628	to 843
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Circular dichroism indicates that the R-domain is predominantly unstructured and that the R-domain–helicase RhlB complex has the same secondary structural composition as the helicase RhlB alone. Thus, it seems that the R-domain does not undergo appreciable folding on interaction with the helicase, despite the apparent avidity of the complex.
Protein: DP00207 (UniProt P21513)
Region: residues 580	to 1038
Annotation: disorder (Structural state)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
Based on its elution volume from the S200 column, the apparent molecular mass of the complex was 103 kDa, which is nearly three times the expected size for an enolase dimer with two CTD proteins bound. The apparently large mass of the complex is most likely due to the anomalous volume of the predominantly unstructured CTD.
Protein: DP00207 (UniProt P21513)
Region: residues 816	to 1038
Annotation: protein binding (Molecular function)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
The native-CTD–enolase complex is very sensitive to partial proteolysis by protease K. It is less sensitive to partial digestion by chymotrypsin (Figure 7B), and this enabled identification of the minimal binding fragment of native-CTD to enolase by native PAGE and N-terminal sequencing analysis. The fragment bound to enolase was found to start at residue 816 of RNase E (Figure 7C), and from its molecular mass was presumed to extend roughly to residue 1038.