LiteFold/DisProt huggingface dataset:
Protein: DP04156 (UniProt Q96B97)
Region: residues 163	to 263
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We accomplished the near-complete assignment of the linker region containing CIN85-PRM1 by acquiring three-dimensional 13C-detected experiments on a shorter construct of the CIN85 protein (CIN85163–333; see Figure S6 for the different protein constructs used in this work and the spectral quality in Figure S7).
Within the disordered linker region (residues 163–263), we were successful in assigning 97% the backbone resonances, including the prolines inside CIN85-PRM1.
The linker connects the 2nd and 3rd SH3 domains of SH3KBP1/CIN85. In the studied construct only the linker and the 3rd SH3 domain was included.
Cross-references: BMRB:52081
Protein: DP04156 (UniProt Q96B97)
Region: residues 219	to 232
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We further used NMR titrations to assess the interaction of CIN85-PRM1 with isolated SH3 domains of CIN85, observing chemical shift perturbations (CSP) in the 15N-labeled SH3 domains upon titration with a synthetic 14-residue peptide of the sequence 219FKDKPIKLRPRSIE232 (see Figure S2). All three domains displayed moderate to weak affinity, with SH3C showing 3- and 5-fold lower dissociation constants (KD) than SH3A and SH3B, respectively (KD ∼ 0.2–1.1 mM; see Table 1). This suggested the SH3C domain to be the dominant interaction partner to CIN85-PRM1.
Protein: DP04156 (UniProt Q96B97)
Region: residues 219	to 232
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Additionally, the secondary structure propensities (SSP) were predicted from the assigned chemical shifts using the ncSPC webserver37 and showed a distinct propensity for helical structures within CIN85-PRM1 (Figure ​Figure33B). Torsion angles predicted using TALOS-N38 were consistent with a 310 helix formed by I224, K225, and L226. This was lost upon introduction of the R/A mutations (Figure ​Figure33B). We assigned the resonances of the free peptide in order to determine whether the helical structures within CIN85-PRM1 form upon binding or are already present in the free peptide but disrupted by the R/A mutations (Figures S8 and S9). We found no significant propensity for helix in the free peptide and the helical structure thus likely forms through a disorder-to-order transition upon binding to SH3C.
Protein: DP04156 (UniProt Q96B97)
Region: residues 228	to 232
Annotation: phosphorylation display site (Disorder function)
Evidence: author statement used in manual assertion
Supporting statements:
The serine residue at position 230 was shown to significantly weaken the CIN85-PRM1:SH3 association in its phosphorylated state (Figure ​Figure22B and Table 1). In addition, it was found to be highly phosphorylated in a multitude of phosphoproteomic studies (Figure S4).
Protein: DP04156 (UniProt Q96B97)
Region: residues 219	to 232
Annotation: self-inhibition (Disorder function)
Evidence: author statement used in manual assertion
Supporting statements:
The SH3C Domain in CIN851–333 Is Autoinhibited by Binding to CIN85-PRM1 Intramolecularly
The authors have already defined previously that residues 219-232 correspond to PRM1.
Protein: DP04157 (UniProt O00418)
Region: residues 562	to 597
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The region G562-G597 was found to be disordered with an average {1H}−15N NOE value of 0.35 ± 0.08.
Protein: DP04158 (UniProt Q9BX66)
Region: residues 851	to 867
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Our results showed that, in the free state, the residues of the
SH3a and SH3b domains exhibit quite uniform NOEs with an aver-
age of 0.70, whereas the residues of the linker region display much
lower (even negative) NOE values (Fig. 6D). Upon binding with
vin857, the residues in the linker region show no obvious change
in their NOE values, indicating that the 20-residue linker of the
tandem SH3 domains is still highly flexible even after binding with
vin857 and may not participate in the interaction of the SH3
domains with vin 857.
The plot of NOE values and Figure 4A indicates that the flexible linker is between residues 851-867.
Protein: DP04158 (UniProt Q9BX66)
Region: residues 851	to 867
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Our results showed that, in the free state, the residues of the
SH3a and SH3b domains exhibit quite uniform NOEs with an aver-
age of 0.70, whereas the residues of the linker region display much
lower (even negative) NOE values (Fig. 6D). Upon binding with
vin857, the residues in the linker region show no obvious change
in their NOE values, indicating that the 20-residue linker of the
tandem SH3 domains is still highly flexible even after binding with
vin857 and may not participate in the interaction of the SH3
domains with vin 857.
The plot of NOE values and Figure 4A indicates that the flexible linker is between residues 851-867.
Protein: DP04159 (UniProt A0A0H2ZJC1)
Region: residues 1	to 55
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
However, for SutA, the results of these analyses lend credence to the bioinformatics predictions and suggest that much of the protein outside a central α-helix is disordered. Residues 56–76 show the positive Cα and CO and negative Hα secondary chemical shifts associated with an α-helix structure (Wishart et al., 1991), and also show fast R2 relaxation rates and positive (1H-15N)NOE, suggesting that they are not disordered (Reddy & Rainey, 2010). RDCs for the helix region are also positive, as has been observed for α-helical regions of a partially denatured protein (Mohana-Borges et al., 2004). The short β-strand is less strongly supported, but secondary shifts for those residues are mostly of the appropriate sign for a β-strand (albeit of small magnitudes). In the N-tail, a small number of isolated residues have a positive NOE signal or secondary shifts that are not near zero, but in general, the residues of this region have the low R2, secondary shift, and RDC values that are characteristic of disorder.
Protein: DP04159 (UniProt A0A0H2ZJC1)
Region: residues 77	to 105
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
However, for SutA, the results of these analyses lend credence to the bioinformatics predictions and suggest that much of the protein outside a central α-helix is disordered. Residues 56–76 show the positive Cα and CO and negative Hα secondary chemical shifts associated with an α-helix structure (Wishart et al., 1991), and also show fast R2 relaxation rates and positive (1H-15N)NOE, suggesting that they are not disordered (Reddy & Rainey, 2010). RDCs for the helix region are also positive, as has been observed for α-helical regions of a partially denatured protein (Mohana-Borges et al., 2004). The short β-strand is less strongly supported, but secondary shifts for those residues are mostly of the appropriate sign for a β-strand (albeit of small magnitudes).
The C-tail has several residues that show somewhat higher R2 values and non-zero RDCs, suggestive of some degree of structure, but classic secondary structure elements are not apparent.
Protein: DP04159 (UniProt A0A0H2ZJC1)
Region: residues 77	to 105
Annotation: flexible C-terminal tail (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
However, for SutA, the results of these analyses lend credence to the bioinformatics predictions and suggest that much of the protein outside a central α-helix is disordered. Residues 56–76 show the positive Cα and CO and negative Hα secondary chemical shifts associated with an α-helix structure (Wishart et al., 1991), and also show fast R2 relaxation rates and positive (1H-15N)NOE, suggesting that they are not disordered (Reddy & Rainey, 2010). RDCs for the helix region are also positive, as has been observed for α-helical regions of a partially denatured protein (Mohana-Borges et al., 2004). The short β-strand is less strongly supported, but secondary shifts for those residues are mostly of the appropriate sign for a β-strand (albeit of small magnitudes).
The C-tail has several residues that show somewhat higher R2 values and non-zero RDCs, suggestive of some degree of structure, but classic secondary structure elements are not apparent.
Protein: DP04159 (UniProt A0A0H2ZJC1)
Region: residues 1	to 55
Annotation: flexible N-terminal tail (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
However, for SutA, the results of these analyses lend credence to the bioinformatics predictions and suggest that much of the protein outside a central α-helix is disordered. Residues 56–76 show the positive Cα and CO and negative Hα secondary chemical shifts associated with an α-helix structure (Wishart et al., 1991), and also show fast R2 relaxation rates and positive (1H-15N)NOE, suggesting that they are not disordered (Reddy & Rainey, 2010). RDCs for the helix region are also positive, as has been observed for α-helical regions of a partially denatured protein (Mohana-Borges et al., 2004). The short β-strand is less strongly supported, but secondary shifts for those residues are mostly of the appropriate sign for a β-strand (albeit of small magnitudes). In the N-tail, a small number of isolated residues have a positive NOE signal or secondary shifts that are not near zero, but in general, the residues of this region have the low R2, secondary shift, and RDC values that are characteristic of disorder.
Protein: DP04159 (UniProt A0A0H2ZJC1)
Region: residues 95	to 99
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We collected 15N HSQC spectra for these mixtures, as well as for SutA alone, using a Bruker 800 MHZ AV III HD spectrometer to help overcome difficulties introduced by the low concentration of β1 domain we could produce. While the peak positions for SutA alone and for the SutA+σS mixture were nearly identical, several SutA residues showed chemical shift perturbations in the β1 mixture, compared with the other two samples (Fig. 2C). Three of these residues, K95, D97 and K99, would be on the same side of an extended peptide chain in the C-tail, suggesting that this tail could directly interact with β1 in an extended conformation.
Protein: DP04159 (UniProt A0A0H2ZJC1)
Region: residues 1	to 55
Annotation: positive regulation of transcription, DNA-templated (Biological process)
Evidence: in vitro transcription assay evidence used in manual assertion
Supporting statements:
We found that WT SutA increased transcription by both holoenzymes in vitro, but the magnitude of the effect was much larger for EσS (up to 6 times the amount of transcript produced in the absence of SutA) than for Eσ70 (up to 1.7 times) (Fig. 3B and Supporting Information, Fig. S13). In both cases, the effect saturated at concentrations of SutA between 125 and 500 nM, but transcription increased more than 2-fold for EσS even at 31 nM, the lowest concentration tested. The acidic N-tail is strictly required for activation, as the ΔN mutant inhibited transcription in a dose-dependent manner.
Protein: DP04160 (UniProt Q0B311)
Region: residues 296	to 315
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The disordered termini of the PCP domain are highly mobile on the fast ps-ns timescale as indicated by low heteronuclear nuclear Overhauser effects (NOEs), transverse relaxation rates (R2), and high longitudinal relaxation rates (R1) for these regions compared to the structured core (Fig. 1d and Supplementary Fig. 13). The overall rotational diffusion13 is consistent with a monomeric state, with a compact folded core and disordered termini (Supplementary Materials and Methods). The dynamic, disordered nature of the terminal regions is further confirmed by the low predicted S2 parameters (Fig. 1d and Supplementary Fig. 14; S2 of 1 and 0 indicate complete rigidity and unrestricted motion, respectively), typical chemical shift values for a random coil and a lack of long-range NOEs.
Cross-references: PDB:5MTI
BMRB:34085
Protein: DP04160 (UniProt Q0B311)
Region: residues 296	to 315
Annotation: flexible C-terminal tail (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The disordered termini of the PCP domain are highly mobile on the fast ps-ns timescale as indicated by low heteronuclear nuclear Overhauser effects (NOEs), transverse relaxation rates (R2), and high longitudinal relaxation rates (R1) for these regions compared to the structured core (Fig. 1d and Supplementary Fig. 13). The overall rotational diffusion13 is consistent with a monomeric state, with a compact folded core and disordered termini (Supplementary Materials and Methods). The dynamic, disordered nature of the terminal regions is further confirmed by the low predicted S2 parameters (Fig. 1d and Supplementary Fig. 14; S2 of 1 and 0 indicate complete rigidity and unrestricted motion, respectively), typical chemical shift values for a random coil and a lack of long-range NOEs.
Cross-references: PDB:5MTI
BMRB:34085
Protein: DP04160 (UniProt Q0B311)
Region: residues 307	to 315
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In the NMR titrations of the Bamb_5917 holo-PCP domain with both full-length Bamb_5915 and its excised βHD domain the system is in slow to intermediate exchange14 (Supplementary Fig. 16). Higher than average local apparent association constants, Ka, in the titrations with the excised βHD domain identify a Short Linear Motif (SLiM; S307-R315)11 in the disordered C-terminus of Bamb_5917 as the major interaction site (Fig. 2a-b).
Residues boundaries of the partner's βHD domain could be identified from a supplementary table.
Cross-references: BMRB:27304
Protein: DP04161 (UniProt B7UM99)
Region: residues 198	to 233
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
For this integrative study, we used the protein constructs encompassing the residues 1-233 and 388-550 from the N-terminal and C-terminal cytosolic regions of EPEC O127:H6 Tir, respectively.
The corresponding SAXS-driven ab initio reconstruction highlights an elongated S-shaped core for the N-Tir dimer (Supplementary Fig. 6). This extended dimer is largely disordered but contains stable secondary structural elements.
Nevertheless, we found that the 52 kDa dimer has a [15N-1HN]-HSQC NMR spectrum at 5 °C characterised by intense signals and low chemical shift dispersion akin to an IDP (Fig. 2d). We assigned the resonances at 5 °C mostly to the first 80 and last 35 residues of the N-Tir, meaning that those regions are flexible in solution.
Protein: DP04161 (UniProt B7UM99)
Region: residues 1	to 80
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
 For this integrative study, we used the protein constructs encompassing the residues 1-233 and 388-550 from the N-terminal and C-terminal cytosolic regions of EPEC O127:H6 Tir, respectively (Fig. 1e, Supplementary Fig. 4, Supplementary Table 4)
Nevertheless, we found that the 52 kDa dimer has a [15N-1HN]-HSQC NMR spectrum at 5 °C characterised by intense signals and low chemical shift dispersion akin to an IDP (Fig. 2d). We assigned the resonances at 5 °C mostly to the first 80 and last 35 residues of the N-Tir, meaning that those regions are flexible in solution.
Protein: DP04161 (UniProt B7UM99)
Region: residues 388	to 550
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
We assessed the structural disorder propensity of EPEC O127:H6 N-Tir and C-Tir by multiple biophysical methods, including small-angle X-ray scattering (SAXS), circular dichroism (CD), and nuclear magnetic resonance (NMR).
For this integrative study, we used the protein constructs encompassing the residues 1-233 and 388-550 from the N-terminal and C-terminal cytosolic regions of EPEC O127:H6 Tir, respectively (Fig. 1e, Supplementary Fig. 4, Supplementary Table 4). 
Analytical SEC in combination with SAXS reveals a monomeric state for C-Tir in solution with an Rg of 38.8 ± 0.2 Å and a Dmax of 128.0 ± 5.0 Å (Supplementary Figure 6, Supplementary Table 5).
The SAXS-derived Kratky plot of C-Tir also shows characteristics of disordered or unfolded proteins, monotonically increasing without a well-defined maximum (Fig. 4a).
 Likewise, the asymmetric pair distance distribution function, P(r), obtained from the scattering data, is compatible with a highly flexible protein sampling pairwise distances far exceeding those expected for a globular protein of the same molecular weight59 (Supplementary Figure 6).
Protein: DP04161 (UniProt B7UM99)
Region: residues 388	to 550
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
We assessed the structural disorder propensity of EPEC O127:H6 N-Tir and C-Tir by multiple biophysical methods, including small-angle X-ray scattering (SAXS), circular dichroism (CD), and nuclear magnetic resonance (NMR).
 For this integrative study, we used the protein constructs encompassing the residues 1-233 and 388-550 from the N-terminal and C-terminal cytosolic regions of EPEC O127:H6 Tir, respectively (Fig. 1e, Supplementary Fig. 4, Supplementary Table 4).
The intrinsic disorder of C-Tir is also reflected in its CD and [15N-1HN]-HSQC NMR spectra. C-Tir’s CD profile has negative ellipticity at 200 nm and a shallow band in the 210–230 nm range (Fig. 4b), indicating a high content of random coil with minimal ordered structural elements60.
Protein: DP04161 (UniProt B7UM99)
Region: residues 198	to 233
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
 For this integrative study, we used the protein constructs encompassing the residues 1-233 and 388-550 from the N-terminal and C-terminal cytosolic regions of EPEC O127:H6 Tir, respectively (Fig. 1e, Supplementary Fig. 4, Supplementary Table 4)
Nevertheless, we found that the 52 kDa dimer has a [15N-1HN]-HSQC NMR spectrum at 5 °C characterised by intense signals and low chemical shift dispersion akin to an IDP (Fig. 2d). We assigned the resonances at 5 °C mostly to the first 80 and last 35 residues of the N-Tir, meaning that those regions are flexible in solution.
Protein: DP04161 (UniProt B7UM99)
Region: residues 452	to 456
Annotation: phosphorylation display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
To this end, we incubated C-Tir with the Src family PTK Fyn, and quantitatively monitored its phosphorylation by NMR72. The sensitivity of chemical shifts to changes caused by phosphorylation allowed us to identify four phosphorylated tyrosine sites along the disordered C-Tir modified by Fyn (i.e., Y454, Y474, Y483, Y511). Phosphorylation caused small but noticeable changes in the chemical shifts of the tyrosines and adjacent residues. The [15N-1HN]-HSQC spectrum displayed low amide proton dispersion, a diagnostic that the C-Tir remains disordered upon multisite phosphorylation.
Cross-references: BMRB:50759
Protein: DP04161 (UniProt B7UM99)
Region: residues 472	to 476
Annotation: phosphorylation display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
To this end, we incubated C-Tir with the Src family PTK Fyn, and quantitatively monitored its phosphorylation by NMR72. The sensitivity of chemical shifts to changes caused by phosphorylation allowed us to identify four phosphorylated tyrosine sites along the disordered C-Tir modified by Fyn (i.e., Y454, Y474, Y483, Y511). Phosphorylation caused small but noticeable changes in the chemical shifts of the tyrosines and adjacent residues. The [15N-1HN]-HSQC spectrum displayed low amide proton dispersion, a diagnostic that the C-Tir remains disordered upon multisite phosphorylation.
Cross-references: BMRB:50759
Protein: DP04161 (UniProt B7UM99)
Region: residues 481	to 485
Annotation: phosphorylation display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
To this end, we incubated C-Tir with the Src family PTK Fyn, and quantitatively monitored its phosphorylation by NMR72. The sensitivity of chemical shifts to changes caused by phosphorylation allowed us to identify four phosphorylated tyrosine sites along the disordered C-Tir modified by Fyn (i.e., Y454, Y474, Y483, Y511). Phosphorylation caused small but noticeable changes in the chemical shifts of the tyrosines and adjacent residues. The [15N-1HN]-HSQC spectrum displayed low amide proton dispersion, a diagnostic that the C-Tir remains disordered upon multisite phosphorylation.
Cross-references: BMRB:50759
Protein: DP04161 (UniProt B7UM99)
Region: residues 509	to 513
Annotation: phosphorylation display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
To this end, we incubated C-Tir with the Src family PTK Fyn, and quantitatively monitored its phosphorylation by NMR72. The sensitivity of chemical shifts to changes caused by phosphorylation allowed us to identify four phosphorylated tyrosine sites along the disordered C-Tir modified by Fyn (i.e., Y454, Y474, Y483, Y511). Phosphorylation caused small but noticeable changes in the chemical shifts of the tyrosines and adjacent residues. The [15N-1HN]-HSQC spectrum displayed low amide proton dispersion, a diagnostic that the C-Tir remains disordered upon multisite phosphorylation.
Cross-references: BMRB:50759
Protein: DP04161 (UniProt B7UM99)
Region: residues 388	to 550
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
For this integrative study, we used the protein constructs encompassing the residues 1-233 and 388-550 from the N-terminal and C-terminal cytosolic regions of EPEC O127:H6 Tir, respectively (Fig. 1e, Supplementary Fig. 4, Supplementary Table 4)
This construct’s 2D-[15N-1HN]-HSQC NMR spectrum displays a typical IDP fingerprint with low chemical shift dispersion61 (Fig. 4c).
Cross-references: BMRB:50758