LiteFold/DisProt huggingface dataset:
Protein: DP02913 (UniProt P04004)
Region: residues 1	to 130
Annotation: molecular adaptor activity (Molecular function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
Our prior work using hydrodynamic methods with PAI-1 and full-length vitronectin demonstrated that there is a 2:1 (PAI-1:vitronectin) stoichiometry of interaction that leads to assembly of higher-order oligomeric complexes via a prominent intermediate containing four PAI-1 and two vitronectin molecules.
Calculated structures for the PAI-1:SMBIDD complex suggest that the IDD provides an interaction surface outside of the primary PAI-1-binding site located within the SMB domain; this binding is proposed to lead to the assembly of higher-order structures of vitronectin and PAI-1 commonly found in tissues.
Protein: DP02913 (UniProt P04004)
Region: residues 1	to 130
Annotation: protein binding (Molecular function)
Evidence: small-angle neutron scattering evidence used in manual assertion
Supporting statements:
Analysis of the SANS data using the Ensemble Optimization Method confirms that the SMBIDD adopts a more compact configuration when bound to PAI-1. Calculated structures for the PAI-1:SMBIDD complex suggest that the IDD provides an interaction surface outside of the primary PAI-1-binding site located within the SMB domain
Protein: DP02913 (UniProt P04004)
Region: residues 1	to 130
Annotation: disorder to order (Structural transition)
Evidence: small-angle neutron scattering evidence used in manual assertion
Supporting statements:
Analysis of the SANS data using the Ensemble Optimization Method confirms that the SMBIDD adopts a more compact configuration when bound to PAI-1. 
We compared the Rg values for free vs. bound SMB-IDD and observed that PAI-1 binding yields a shift in the Rg range for the SMB-IDD to predominantly lower values, consistent with a solution structure for the IDD that is restricted in conformation upon binding
In a series of SANS experiments to test for structural changes in the SMB-IDD, it was observed that PAI-1 binding led to structural reorganization of the IDD into a more compact structure. This result localizes an additional binding site for PAI-1 to the linker region in vitronectin.
Protein: DP02913 (UniProt P04004)
Region: residues 1	to 71
Annotation: protein binding (Molecular function)
Evidence: fluorescence polarization evidence used in manual assertion
Supporting statements:
To localize the putative binding site, we constructed a truncated form of vitronectin containing 71 amino acids from the N-terminus, including the SMB domain and an additional 24 amino acids from the IDD region. This portion of the IDD is rich in acidic amino acids, which are hypothesized to be complementary to several basic residues identified within an extensive vitronectin-binding site mapped on PAI-1 (Schar, Jensen, Christensen, Blouse, Andreasen, Peterson. J Biol Chem. 2008;283:10297-10309). Steady-state and stopped-flow fluorescence measurements demonstrate that the truncated form of vitronectin exhibits the same rapid biphasic association as full-length vitronectin and that the IDD hosts the elusive second PAI-1 binding site that lies external to the SMB domain of vitronectin.
Protein: DP02913 (UniProt P04004)
Region: residues 59	to 70
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Dashed lines indicate disordered residues in the reactive center loop (RCL) of PAI-1 and residues leading to the RGD sequence of somatomedin B.
The final model includes residues 6–337 and 348–379 of PAI-1 and 3–39 of SMB.
In a complex with PAI-1, the RGD sequence (residues 45–47 of the somatomedin B domain, Fig. 1b,c) will be positioned close to PAI-1, together with the rest of the large vitronectin molecule, leaving insufficient room for the RGD sequence to bind to integrins in the manner seen in the recent crystal structure of the integrin–RGD ligand complex
The numbering of the IDR that includes the RGD motif (64-66) of vitronectin, correspond to region 59-70 of the associated UniProt sequence, since PDB:1OC0 spans residues 20-70 of the protein.
Cross-references: PDB:1OC0
Protein: DP02913 (UniProt P04004)
Region: residues 22	to 58
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The interaction of the plasma protein vitronectin with plasminogen activator inhibitor-1 (PAI-1) is central to human health. Vitronectin binding extends the lifetime of active PAI-1, which controls hemostasis by inhibiting fibrinolysis and has also been implicated in angiogenesis. The PAI-1–vitronectin binding interaction also affects cell adhesion and motility. For these reasons, elevated PAI-1 activities are associated both with coronary thrombosis and with a poor prognosis in many cancers. Here we show the crystal structure at a resolution of 2.3 Å of the complex of the somatomedin B domain of vitronectin with PAI-1. The structure of the complex explains how vitronectin binds to and stabilizes the active conformation of PAI-1. It also explains the tissue effects of PAI-1, as PAI-1 competes for and sterically blocks the interaction of vitronectin with cell surface receptors and integrins.
Cross-references: PDB:1OC0
Protein: DP02913 (UniProt P04004)
Region: residues 22	to 58
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The interaction of the plasma protein vitronectin with plasminogen activator inhibitor-1 (PAI-1) is central to human health. Vitronectin binding extends the lifetime of active PAI-1, which controls hemostasis by inhibiting fibrinolysis and has also been implicated in angiogenesis. The PAI-1–vitronectin binding interaction also affects cell adhesion and motility. For these reasons, elevated PAI-1 activities are associated both with coronary thrombosis and with a poor prognosis in many cancers. Here we show the crystal structure at a resolution of 2.3 Å of the complex of the somatomedin B domain of vitronectin with PAI-1. The structure of the complex explains how vitronectin binds to and stabilizes the active conformation of PAI-1. It also explains the tissue effects of PAI-1, as PAI-1 competes for and sterically blocks the interaction of vitronectin with cell surface receptors and integrins.
Cross-references: PDB:1OC0
Protein: DP02913 (UniProt P04004)
Region: residues 22	to 58
Annotation: molecular function regulator (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The interaction of the plasma protein vitronectin with plasminogen activator inhibitor-1 (PAI-1) is central to human health. Vitronectin binding extends the lifetime of active PAI-1, which controls hemostasis by inhibiting fibrinolysis and has also been implicated in angiogenesis. The PAI-1–vitronectin binding interaction also affects cell adhesion and motility. For these reasons, elevated PAI-1 activities are associated both with coronary thrombosis and with a poor prognosis in many cancers. Here we show the crystal structure at a resolution of 2.3 Å of the complex of the somatomedin B domain of vitronectin with PAI-1. The structure of the complex explains how vitronectin binds to and stabilizes the active conformation of PAI-1. It also explains the tissue effects of PAI-1, as PAI-1 competes for and sterically blocks the interaction of vitronectin with cell surface receptors and integrins.
Protein: DP02915 (UniProt P48443)
Region: residues 2	to 127
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The obtained  CD  spectrum  of AB_hRXG is  typical for proteins  containing  disordered  regions (Figure 4A). It is characterized by a deep minimum at 200 nm and a lack of distinct minima at 208 nm and 222 nm, with only a shallow minimum at 222 nm, which suggests the existence of  some secondary structure.
Protein: DP02915 (UniProt P48443)
Region: residues 2	to 127
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
The remarkably bigger experimental Rs in comparison to the theoretical value places AB_hRXG on the  log (Rs)  versus  log (M)  plot  in the  area for IDPs with  PMG-like  properties (Figure 5B).
Protein: DP02915 (UniProt P48443)
Region: residues 2	to 127
Annotation: pre-molten globule (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
The remarkably bigger experimental Rs in comparison to the theoretical value places AB_hRXG on the  log (Rs)  versus  log (M)  plot  in the  area for IDPs with  PMG-like  properties (Figure 5B).
Protein: DP02915 (UniProt P48443)
Region: residues 2	to 127
Annotation: pre-molten globule (Structural state)
Evidence: analytical ultracentrifugation evidence used in manual assertion
Supporting statements:
The estimated molecular mass (13 490 Da, 13 260 Da and 13108  Da)  was  close  to the  theoretical  value  (14054Da)  and the  c(s)  distribution obtained for different protein concentration overlaps, indicating that AB_hRXG is a monomer with a highly  extended  conformation. The  obtained  Stokes  radii  (Rs)  for the different concentrations  of AB_hRXG (28.6  Å)  were in good  agreement  with the SEC  data  (27.5  Å).
The calculated f/f0ratio for AB_hRXG is 1.8 (Table 2), which indicates an extended conformation and again classifies AB_hRXGto the PMG-like IDPs.
Protein: DP02915 (UniProt P48443)
Region: residues 2	to 127
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
AB_hRXG in the absence of osmolyte appearedto be very sensitive to trypsin (Figure 7;  lines  6,  10  and  14)  and  proteinase  K  digestion
Protein: DP02915 (UniProt P48443)
Region: residues 2	to 127
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: microscopy evidence used in manual assertion
Supporting statements:
Taken  together,  the  data  show  that  AB_hRXG exhibits the ability  to  promote the formation of LLPS and that the process is concentration-and temperature-dependent.
To observe the formation of liquid droplets, a concentration of around 3 mg/ml and higher was needed.
Protein: DP02916 (UniProt Q14444)
Region: residues 607	to 709
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
To address these questions, we first reconstituted a model biomolecular condensate containing the intrinsically disordered C-terminal regions of FMRP (445–632, hereafter referredto as FMRP) and CAPRIN1 (607–709, hereafter referred to as CAPRIN1) for biophysical studies.
Figure 2  Solution-state NMR spectra of [13C,15N]CAPRIN1 inFMRP or pFMRP condensed phases. Disordered nature inferred from figure by the annotator.
Protein: DP02916 (UniProt Q14444)
Region: residues 607	to 709
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: fluorescence microscopy evidence used in manual assertion
Supporting statements:
Phosphorylation acts as switch for FMRP-CAPRIN1 co–phase separation and a determinant of subcompartmentalization with RNA.(A) Phase diagram for FMRP andpYCAPRIN1 co–phase separation
Phase diagram for co–phaseseparation of pFMRP and CAPRIN1. Teal dots represent conditions with observable droplet formation.
The Tyr residues in these regions of CAPRIN1 are known to be phosphorylated in vivo (22), which is suggestive of their regulatory function. When we Tyr-phosphorylated CAPRIN1 in vitro (pYCAPRIN1;fig. S3, C and D), we found that pYCAPRIN1co–phase-separates with FMRP but not with pFMRP
Overlay of CON spectra of [13C,15N]CAPRIN1 in FMRP (green) or in pFMRP (purple) condensed phases. (C) Examples of reduced intensities or small CSPs of arginine (1, 2) and aromatic (3) residues from the CON spectra
Protein: DP02916 (UniProt Q14444)
Region: residues 607	to 709
Annotation: protein binding (Molecular function)
Evidence: fluorescence resonance energy transfer evidence used in manual assertion
Supporting statements:
 CAPRIN1 binds pFMRP with a medium(~5) and high (~9) number of phosphorylation sites with apparent affinities of 16.1 ± 4.4mMand 5.8 ± 0.4mM, respectively. Error bars denote SD. (C) Phase diagram for co–phaseseparation of pFMRP and CAPRIN1
Protein: DP02916 (UniProt Q14444)
Region: residues 607	to 709
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
Using isothermal titration calorimetry (ITC), we detected no FMRP-CAPRIN1 interaction; however,after in vitro phosphorylation of FMRP (pFMRP;fig. S3, A and B) by casein kinase II (CK2), a known kinase that Ser/Thr-phosphorylates FMRP in vivo (22,23), we observed an effective 1 micromolar CAPRIN1-pFMRP binding affinity.
Protein: DP02917 (UniProt Q02521)
Region: residues 10	to 185
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Size exclusion chromatography of scSpp2(10–185) resulted in an apparent molecular mass of approximately 65 kDa, roughly three times higher than the calculated molecular mass of scSpp2(10–185). In contrast, multiangle light scattering identified this truncated Spp2 as a monomer, indicating that the protein behaves like a partially or fully unfolded protein.
Protein: DP02917 (UniProt Q02521)
Region: residues 10	to 150
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In addition, CD measurements were performed with scSpp2(10–150) as well as with the further truncated version scSpp2(100–150) containing only the G-patch region. The CD spectra clearly show the absence of stable secondary structure elements for both samples
Protein: DP02917 (UniProt Q02521)
Region: residues 10	to 185
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
To study the properties of scSpp2 in more detail, a heteronuclear singular quantum coherence (HSQC) NMR spectrum of 15N-labeled scSpp2(10–185) was recorded (Fig. 1C). The NMR spectrum was of high quality with a narrow distribution of the cross peaks around 8 ppm of the 1H frequency, which is typical for the spectra of intrinsically disordered proteins.
Protein: DP02917 (UniProt Q02521)
Region: residues 100	to 150
Annotation: protein binding (Molecular function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
Authors performed and infer information on binding using a homologous protein!
Binding experiments of different truncated versions of ctSpp2G-patch show that this N-terminal helix is sufficient for binding to the DEAH-box ATPase and thus likely displays the major anchor point of the G-patch motif.
In particular, glycines 223, 226, and 230 of ctSpp2 exhibit conformations allowed only for glycine residues, and mutation to serine strongly weakens the binding of the ctSpp2G-patch to ctPrp2 (SI Appendix, Fig. S7).
Protein: DP02917 (UniProt Q02521)
Region: residues 100	to 150
Annotation: molecular function activator activity (Molecular function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
The Prp2-specific cofactor Spp2 belongs to the family of G-patch–containing proteins. The name-giving glycine-rich patch (G-patch) consists of at least six conserved glycines and was first identified in RNA-associated proteins by bioinformatic analysis (20).
Spp2, which stimulates only the RNA-dependent ATPase activity of isolated Prp2 and not any helicase activity (24). Actually, no helicase activity could be observed for isolated Prp2 or the Prp2-Spp2 complex within the spliceosome (25, 26).
Protein: DP02917 (UniProt Q02521)
Region: residues 100	to 110
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Spp2G-patch is unfolded in solution and only transiently samples an α-helical conformation in its N-terminal part. This N-terminal amphipathic helix stably binds Prp2 mainly via hydrophobic interactions with a conserved hydrophobic patch at the winged-helix (WH) domain. The C-terminal part binds to the RecA2 domain and can adopt two alternative conformations.
In all crystal forms of the ctPrp2-ctSpp2211–254 complex, the N-terminal residues 212 to 222 of the G-patch domain form an amphipathic α-helix that is bound to the WH domain (Fig. 2A). The α-helix is terminated by a sharp kink, followed by a region exhibiting an extended conformation reaching the β-hairpin of the RecA2 domain. The C-terminal part of the ctSpp2 G-patch adopts two alternative conformations in the five different crystal structures.
The transition was observed for a homologous protein!
Protein: DP02918 (UniProt P17947)
Region: residues 118	to 165
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In 1:1-bound ΔN165, whose resonances were well resolved, 88 of the 95 assigned residues overlapped with ΔN117, with all PEST residues clustered around 8.2 ± 0.2 parts per million (ppm) on the 1H dimension, a chemical shift characteristic of disordered structures.
Protein: DP02918 (UniProt P17947)
Region: residues 1	to 168
Annotation: disorder (Structural state)
Evidence: author statement used in manual assertion
Supporting statements:
The remaining ~170 and 12 residues that flank N- and C-terminally, respectively, are intrinsically disordered sequences. The extended N-terminal IDR consists of an acidic transactivation domain (human residues 1 to 80), a Q-rich domain (residues 81 to 116), and a highly negatively charged PEST domain (residues 117 to 165), all of which are characteristic disordered regions in eukaryotic factors (9).
The DNA binding (ETS) domain of PU.1 represents its only structured domain, whose 1:1 complex with cognate DNA (Fig. 1A) is structurally conserved in this family of transcription factors.
Protein: DP02918 (UniProt P17947)
Region: residues 258	to 270
Annotation: disorder (Structural state)
Evidence: author statement used in manual assertion
Supporting statements:
The remaining ~170 and 12 residues that flank N- and C-terminally, respectively, are intrinsically disordered sequences. The extended N-terminal IDR consists of an acidic transactivation domain (human residues 1 to 80), a Q-rich domain (residues 81 to 116), and a highly negatively charged PEST domain (residues 117 to 165), all of which are characteristic disordered regions in eukaryotic factors (9).
The DNA binding (ETS) domain of PU.1 represents its only structured domain, whose 1:1 complex with cognate DNA (Fig. 1A) is structurally conserved in this family of transcription factors.
Protein: DP02918 (UniProt P17947)
Region: residues 118	to 165
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
To gain insight into the conformational structure of the free PU.1 dimer, we interrogated ΔN165 and ΔN117 by circular dichroism (CD) and NMR spectroscopy. At an identically low concentration (25 μM), a net contribution of coil content due to the PEST domain was apparent (Fig. 3C).
Protein: DP02919 (UniProt Q9SQK3)
Region: residues 40	to 112
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The crystal structure of the STT hetero-dimer complex from Arabidopsis was determined at 2.2 A˚ resolution (Table S1 ). Because the IDRs of STT1 and STT2 are highly mobile, residues 40–112 of STT1 and residues 37–231 of STT2 could not be accurately modeled into the electron density.
Protein: DP02919 (UniProt Q9SQK3)
Region: residues 40	to 112
Annotation: protein binding (Molecular function)
Evidence: bait-prey hybrid interaction evidence used in manual assertion
Supporting statements:
Moreover, deletion of IDRs of either STT1 or STT2 substantially impacts binding of OE23 to the STT complex as revealed by pull-down assays.
Protein: DP02919 (UniProt Q9SQK3)
Region: residues 40	to 112
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
the STT complex was able to bind the LMNG-solubilized synthetic transit peptide of OE23 (KD =8 mM) at an approximately 1:1 protein: peptide ratio
ITC-based titration assays also demonstrated that deletion of the IDRs of either STT1 or STT2 substantially impaired binding of cpTat transit peptide to the STT complex, showing an 20-fold and 10-fold higher KD, respectively
Protein: DP02919 (UniProt Q9SQK3)
Region: residues 40	to 112
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: microscopy evidence used in manual assertion
Supporting statements:
Our results showed that 0.5 mM in vitro-translated OE23 precursor could also induce the STTs (2.5 mM) phase separation (Figure 4B).
Substitution of the residues of the LTP binding motif within the STTs prevented phase separation (Figure S4A). Thus, besides formation of STT oligomers, the STTs-LTP binding reaction is also required for this phase separation.
Protein: DP02920 (UniProt Q05753)
Region: residues 37	to 231
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The crystal structure of the STT hetero-dimer complex from Arabidopsis was determined at 2.2 A˚ resolution (Table S1 ). Because the IDRs of STT1 and STT2 are highly mobile, residues 40–112 of STT1 and residues 37–231 of STT2 could not be accurately modeled into the electron density.
Protein: DP02920 (UniProt Q05753)
Region: residues 37	to 231
Annotation: protein binding (Molecular function)
Evidence: bait-prey hybrid interaction evidence used in manual assertion
Supporting statements:
Moreover, deletion of IDRs of either STT1 or STT2 substantially impacts binding of OE23 to the STT complex as revealed by pull-down assays
Protein: DP02920 (UniProt Q05753)
Region: residues 37	to 231
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
the STT complex was able to bind the LMNG-solubilized synthetic transit peptide of OE23 (KD = 8 mM) at an approximately 1:1 protein: peptide ratio. 
ITC-based titration assays also demonstrated that deletion of the IDRs of either STT1 or STT2 substantially impaired binding of cpTat transit peptide to the STT complex, showing an 20-fold and 10-fold higher KD, respectively
Protein: DP02920 (UniProt Q05753)
Region: residues 37	to 231
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: microscopy evidence used in manual assertion
Supporting statements:
Our results showed that 0.5 mM in vitro-translated OE23 precursor could also induce the STTs (2.5 mM) phase separation (Figure 4B).
Substitution of the residues of the LTP binding motif within the STTs prevented phase separation (Figure S4A). Thus, besides formation of STT oligomers, the STTs-LTP binding reaction is also required for this phase separation.