LiteFold/DisProt huggingface dataset:
Protein: DP00040 (UniProt P17096)
Region: residues 1	to 107
Annotation: molecular adaptor activity (Molecular function)
Evidence: immunodetection assay evidence used in manual assertion
Supporting statements:
A derivative of HMG I lacking amino acids 91 to 108, the acidic C-terminal domain, was also capable of reconstituting integration activity (Fig. ​(Fig.3B,3B, lane 4). Derivatives containing amino acids 9 to 75 or 50 to 91, either A/T hooks 1 plus 2 or 2 plus 3, also reconstituted activity (Fig. ​(Fig.3B,3B, lanes 6, 8, and 9). The 50–91 protein displayed the highest specific activity for reconstitution, retaining activity at 0.2 μg per reaction.
We also demonstrated that the HIV-1 long terminal repeats (LTRs) contain multiple DNA binding sites for HMG I(Y). Tests in vitro revealed that binding of HMG I(Y) apposed LTR DNAs in a manner that promoted intermolecular ligation of dilute DNA solutions. As with assays of PIC reconstitution, these assays of DNA condensation required multiple DNA binding domains in each HMG I(Y) monomer. Taken together, these studies strengthen the idea that HMG I(Y) acts as an architectural cofactor for retroviral cDNA integration complexes and suggest a model for its role.
The binding of HMGA to AT-rich sites in PICs retroviral cDNAs leads to the formation of integrase-cDNA complexes.
Protein: DP00040 (UniProt P17096)
Region: residues 1	to 107
Annotation: protein binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
Wild type HMG I, as well as 3 block alanine mutants (residues 21–26, 46–52, and 71–74) were found to bind p50 relatively well, although this interaction is abolished with the other alanine mutants (G59A, R60A, P61A4, K62A, and G63A) and GST as a control.
Protein: DP00040 (UniProt P17096)
Region: residues 70	to 80
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Third, analysis of 15 N relaxation data 12 for the 2:1 DNA to protein complex (Fig. 3a) delineated two distinct ordered domains comprising a longer DBD2 (residues 7- 22) and a shorter DBD3 (residues 33-41) separated by a highly flexible linker (residues 22- 32).
The flexible linker defined as 22-32 actually corresponds to region 70-80 in the UniProt numbering.
Protein: DP00040 (UniProt P17096)
Region: residues 1	to 107
Annotation: DNA binding (Molecular function)
Evidence: fluorescence recovery after photobleaching evidence used in manual assertion
Supporting statements:
We identified the first two of the three AT hooks as main players mediating DNA/chromatin binding.
AT-hook motifs I and II of HMGA1a are main mediators of DNA binding in vivo
Protein: DP00040 (UniProt P17096)
Region: residues 1	to 107
Annotation: RNA binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
EMSAs with 7SK L2 RNA revealed that HMGA1a 3xΔA/T shows not only a decreased DNA-binding activity but also a significantly reduced ability to interact with 7SK L2 RNA (Figure 2C). Furthermore, EMSAs of 7SK L2 RNA with HMGA1 versions containing mutations of each single A/T-hook motif (HMGA1a ΔA/T1, HMGA1a ΔA/T2 and HMGA1a ΔA/T3) identify the first A/T-hook motif of HMGA1a as the site of interaction with 7SK RNA (Figure 2C, upper panel), since the same reduction in binding affinity is observed with the single HMGA1a ΔA/T1 mutant as with the triple mutant.
Protein: DP00040 (UniProt P17096)
Region: residues 1	to 107
Annotation: RNA binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
HMGA1 co-purifies specifically with 7SK RNA
Protein: DP00040 (UniProt P17096)
Region: residues 1	to 107
Annotation: molecular function activator activity (Molecular function)
Evidence: RNAi evidence used in manual assertion
Supporting statements:
Importantly, albeit most genes are repressed in their expression by HMGA1, we also identified several genes that are positively regulated by HMGA1 and 7SK RNA (Figure 7A).
Protein: DP00040 (UniProt P17096)
Region: residues 1	to 107
Annotation: protein binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
Figure 1C shows that the HMG I antibody coprecipitates CBP (lane 2) and that the CBP antibody coprecipitates HMG I (lane 4).
Protein: DP00040 (UniProt P17096)
Region: residues 69	to 73
Annotation: acetylation display site (Disorder function)
Evidence: radioligand binding assay evidence used in manual assertion
Supporting statements:
Specifically, CBP preferentially acetylates Lys-65 whereas P/CAF preferentially acetylates Lys-71.
Protein: DP00040 (UniProt P17096)
Region: residues 63	to 67
Annotation: acetylation display site (Disorder function)
Evidence: radioligand binding assay evidence used in manual assertion
Supporting statements:
Specifically, CBP preferentially acetylates Lys-65 whereas P/CAF preferentially acetylates Lys-71.
Protein: DP00040 (UniProt P17096)
Region: residues 81	to 89
Annotation: DNA binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Here we present the crystal structure of the complex of a DNA oligonucleotide with the third AT-hook (DBD3 in ref. 10) of the HMGA1 protein. 
Cross-references: PDB:3uxw
Protein: DP00040 (UniProt P17096)
Region: residues 50	to 91
Annotation: transcription coactivator activity (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The structure reveals a new architectural minor groove binding motif which stabilizes B-DNA, thereby facilitating the binding of other transcription factors in the opposing major groove. 
 Hence, it seems likely that the principal architectural role of HMG-1 probably involves reversing and preventing intrinsic distortions in DNA conformation, including bending or kinking, by binding in the minor groove, thereby facilitating specific recognition of the opposing major groove by other transcriptional factors such as NF-KB.
Cross-references: PDB:2EZD
PDB:2EZF
PDB:2EZG
PDB:2EZE
Protein: DP00040 (UniProt P17096)
Region: residues 1	to 107
Annotation: transcription coactivator activity (Molecular function)
Evidence: anti-sense experiment evidence used in manual assertion
Supporting statements:
We further show that HMG-I and a novel related protein, HMG-R, also interact with other transcription factors. Using sense and antisense constructs of HMG-I/R in transient transfection assays with a retinoid responsive reporter, we also demonstrate that HMG-I/R is important for retinoid dependent transcriptional activity of RAR. These findings suggest a step wise mechanism by which RARs and other transcription factors can cause a targeted unfolding of compact chromatin as a first step in transcriptional activation, which would then be followed by recruitment of HAT activity and subsequent events.
Our data indicate that RARs and other transcription factors are capable of recruiting the H1 displacing activities of HMG-I/HMG-R in a targeted and ligand-dependent manner (Fig. 7). Since HMG-I protein has 19 putative acetylation sites (lysine residues), including two in the DNA binding AzT hook domain (Fig. 2B), the acetylation of HMG-I by CBP/p300 could potentially decrease its ability to displace H1. However, in accordance with its proposed role as a H1 displacement factor, either CBP or p300 (Fig. 5A) did not acetylate HMG-I 
In order to destabilize compact higher order chromatin structures and to liberate DNA from the nucleosome at the site of active transcription and facilitate RNA polymerase II complex assembly, both linker and chromosomal histones need to be released by transcription factors. Our model predicts that nuclear receptors and other transcription factors may recruit HMG-I/HMG-R and HATs in a targeted step wise manner, thereby unraveling linker and core histone assembly and facilitating the formation of transcriptionally competent DNA in the promoter regions of target genes.
We further show that HMG-I and HMG-R interact with RXR-α , PPAR-γ, c-Jun, and CBP, thus indicating recruitment of HMG-I/R by various transcription factors as a common mechanism for enhancer-dependent transcriptional activation. Finally, using transient transfections, we demonstrate that HMG-I/R is required for retinoid-dependent transactivation of a reporter construct by RAR, thus showing the functional consequences of RAR-HMG-I/R interactions.
Protein: DP00040 (UniProt P17096)
Region: residues 1	to 107
Annotation: protein binding (Molecular function)
Evidence: yeast 2-hybrid evidence used in manual assertion
Supporting statements:
 In this report, we show that RARs interact in a ligand-dependent manner with HMG-I, which is known to displace histone H1 from chromatin.
 HMG-I and HMG-R interact with RARγΔAB in yeast. 
HMG-I and HMG-R proteins interacted specifically with RARγΔAB in the presence but not in the absence of the RAR-specific agonist, TTNPB (15) (Fig. 2A), demonstrating the ligand dependence of RAR/HMG interaction. TTNPB-induced RARγΔΔB interaction with both HMG-I and HMG-R was dose-dependent (data not shown).
HMG-R is a variant of HMG-I with a deletion of 67 nucleotids, being identical in the first 65 AA but differing thereafter. This protein is not listed on UniProt
Protein: DP00040 (UniProt P17096)
Region: residues 1	to 107
Annotation: protein binding (Molecular function)
Evidence: beta-galactosidase reporter gene assay evidence used in manual assertion
Supporting statements:
To demonstrate that the full-length RARγ also interacts with HMG-I/HMG-R in a ligand-dependent manner in vivo, stably transformed RARγ (pAS2-RARγ) yeast cells were further transformed with pACT2-HMG-I/HMG-R and assayed for β-galactosidase activity in the  absence or presence of TTNPB. Full-length RARγ, by virtue of its intrinsic activation functions (2), elicited a low level of β-galactosidase activity in the presence of TTNPB, which was further induced approximately 25-fold in the presence of pACT2-HMG-I and pACT2-HMG-R (Fig. 3A). 
To determine the regions of RAR involved in interaction with HMG in vivo, pGBT-RARγ-DEF, pAS2-RARγΔAB, and pAS2-RARγ transformed yeast cells were used. pACT2-HMG-R interacted poorly with RARγDEF and RARγΔAB but interacted strongly with RARγ (Fig. 3D).
HMG-R is a variant of HMG-I with a deletion of 67 nucleotids, being identical in the first 65 AA but differing thereafter. This protein is not listed on UniProt
Full-length RARγ interacted with both HMG-I and HMG-R in a retinoid dose-dependent manner (Fig. 3E).
Protein: DP00042 (UniProt P02315)
Region: residues 1	to 70
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
All the  resonances are sharp  and  are readily  assigned to equivalent  residues of a given type. It is  the spectrum typical of a disordered protein.
Protein: DP00042 (UniProt P02315)
Region: residues 10	to 35
Annotation: nucleic acid binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The line widths in 0 M NaCl are somewhat  greater than in 500 mM NaCl however and this demonstrates that the H6 does interact with   the DNA under these conditions  but that bound H6 is in rapid  equilibrium with  free solution  H6.
The specific peak broadening observed  suggest that it is largely the N-terminal half of H6 that is involved in inter- actions with DNA. Since the single threonine at position 7 is not markedly  affected,  the interacting segment probably extends from around residue 10 to around residue 35.
Protein: DP00042 (UniProt P02315)
Region: residues 1	to 70
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Circular  dichroism  spectra of H6 obtained  under similar conditions support this conclusion : in the  absence of salt  the ellipticity at 222 nm is z -1000" and this   changes to - 2000° in 1 M NaCl at pH 7. On the basis of - 1000° for a random coil [21] and -30000° for a  full helical chain [22], -2000°   represents <4% helix or less than three  residues.
Protein: DP00043 (UniProt P02929)
Region: residues 103	to 151
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
TonB-CTD is monomeric with an unstructured N terminus (103-151) and a well structured C terminus (152-239).
Cross-references: PDB:1XX3
Protein: DP00044 (UniProt P02259)
Region: residues 1	to 21
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
This extensive digestion is thought to be a consequence of disordered chain regions, whilst the sequence  22- 100 shows resistance to digestion as a  result  of  being in a  com- pact folded form, i.e. peptide GH5 is a close approxi- mation to the compact region  of intact H5.
Protein: DP00044 (UniProt P02259)
Region: residues 99	to 109
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Thus of the 89 residues in the polypeptide chain, 5  residues at the N terminus and II residues at the C terminus are missing in the current model. 
Cross-references: PDB:1HST
Protein: DP00044 (UniProt P02259)
Region: residues 102	to 190
Annotation: disorder (Structural state)
Evidence: curator inference from database used in manual assertion
Supporting statements:
This poly-E region is inferred by the curator to be disordered, based on MobiDB-Lite and according to experimental evidence demonstrating that poly-E repeats display random-coil-like conformation (PMID:16949547)
Protein: DP00044 (UniProt P02259)
Region: residues 101	to 190
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
This extensive digestion is thought to be a consequence of disordered chain regions, whilst the sequence  22- 100 shows resistance to digestion as a  result  of  being in a  com- pact folded form, i.e. peptide GH5 is a close approxi- mation to the compact region  of intact H5.
Protein: DP00047 (UniProt P02687)
Region: residues 1	to 169
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In order to acquire insight into the structure of MBP, we have carried out circular dichroism (CD) experiments on the protein both in the lipid-free and in the lipid-bound form. Our data clearly show that lipid-free MBP is mainly disordered with only a small amount having alpha-helix and beta-sheet motifs.
Protein: DP00047 (UniProt P02687)
Region: residues 1	to 169
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
On the other hand, the lipid-bound form of MBP appears to have a consistent amount of ordered secondary structure.
In particular, the increase in the ordered α- and antiparallel β-structures on going from a polar (LF-MBP) to an apolar (LB-MBP) environment is quite evident. Such an increase corresponds to a loss of the random coil and, to a lesser extent, of the β-turn structures. The “other” type of contributions totally disappear in the LB-MBP spectrum. These results demonstrate that MBP assumes a more ordered conformation in the lipid-bound form.
Protein: DP00047 (UniProt P02687)
Region: residues 1	to 169
Annotation: lipid binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
On the other hand, the lipid-bound form of MBP appears to have a consistent amount of ordered secondary structure.
In particular, the increase in the ordered α- and antiparallel β-structures on going from a polar (LF-MBP) to an apolar (LB-MBP) environment is quite evident. Such an increase corresponds to a loss of the random coil and, to a lesser extent, of the β-turn structures. The “other” type of contributions totally disappear in the LB-MBP spectrum. These results demonstrate that MBP assumes a more ordered conformation in the lipid-bound form.
Protein: DP00047 (UniProt P02687)
Region: residues 1	to 169
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD far-UV spectrum of MBP shows a a large negative peak around 200 nm in aqueous solution, indicative of a disordered conformation of the protein in the unbound state.
In aqueous solution, MBP showed a random coil structure confirmed by its circular dichroism (CD) spectra.
The thermodynamically stable state of aqueous MBP is known to exhibit no secondary structure (15). The CD results also indicate that the protein sample used to examine interaction between MBP and TPI was of a random coil structure. More orderly structures have been ascribed to interactions with other molecules including lipids (22), particularly anionic lipids (25).
Protein: DP00047 (UniProt P02687)
Region: residues 1	to 169
Annotation: lipid binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Given that MBP is known to specifically interact with the membrane's lipid components, this study was designed to explore the effects of these lipids on the conformation of the protein by examining its interaction with the lipid triphosphoinositide (TPI).
Protein: DP00047 (UniProt P02687)
Region: residues 1	to 109
Annotation: lipid binding (Molecular function)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
The presence of the intrinsic lipids around MBP (LB-MBP, spectrum c) causes a further increase in the intensityof the fluorescence emission spectrum and a blue shift of7.5 nm of the maximum.
Protein: DP00048 (UniProt P03406)
Region: residues 58	to 77
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The  N-terminal  region  from  residue  58  to  the polyproline  motif,  and  the  loop  (residues  149–178)  connecting  strands  βC–βD  are  disordered  and  not  visible  in the electron-density map.
These results seem to support that the polyproline regionis partially disordered without a binding partner, suggesting it is intrinsically flexible.
Cross-references: PDB:1AVV
Protein: DP00048 (UniProt P03406)
Region: residues 149	to 178
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The  N-terminal  region  from  residue  58  to  the polyproline  motif,  and  the  loop  (residues  149–178)  connecting  strands  βC–βD  are  disordered  and  not  visible  in the electron-density map.
Cross-references: PDB:1AVV
Protein: DP00048 (UniProt P03406)
Region: residues 149	to 178
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
 The  N-terminal  region  from  residue  58  to  the polyproline  motif,  and  the  loop  (residues  149–178)  connecting  strands  βC–βD  are  disordered  and  not  visible  in the electron-density map. 
Cross-references: PDB:1AVZ
PDB:1AVV
Protein: DP00048 (UniProt P03406)
Region: residues 54	to 70
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Two regions of Nef core are disordered in the crystal and are not modeled: the N-terminal 16 residues and 29 residues in a large internal loop (residues 149–177) that is distant from the SH3-binding surface.
Cross-references: PDB:1EFN
Protein: DP00048 (UniProt P03406)
Region: residues 149	to 177
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Two regions of Nef core are disordered in the crystal and are not modeled: the N-terminal 16 residues and 29 residues in a large internal loop (residues 149–177) that is distant from the SH3-binding surface.
The disordered loop (residues 149–178) between βC and βD is indicated as a dotted line.
Cross-references: PDB:1EFN
Protein: DP00048 (UniProt P03406)
Region: residues 71	to 77
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Comparison of the bound and unbound Nef structures revealed that a proline-rich motif (Pro-x-x-Pro), which is implicated in SH3 binding, is partially disordered in the absence of the binding partner; this motif only fully adopts a left-handed polyproline type II helix conformation upon complex formation with the Fyn SH3 domain.
Cross-references: PDB:1AVZ
Protein: DP00048 (UniProt P03406)
Region: residues 71	to 77
Annotation: SH3 domain binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Comparison of the bound and unbound Nef structures revealed that a proline-rich motif (Pro-x-x-Pro), which is implicated in SH3 binding, is partially disordered in the absence of the binding partner; this motif only fully adopts a left-handed polyproline type II helix conformation upon complex formation with the Fyn SH3 domain.
It is the SH3 domain that restrains its flexibility and stabilizes the PPII helix conformation upon complex formation.
Cross-references: PDB:1AVZ
Protein: DP00048 (UniProt P03406)
Region: residues 71	to 77
Annotation: viral life cycle (Biological process)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Recent genetic and biochemical studies [20] have shown that Nef blocks a receptor-proximal event in the TCR/CD3 pathway, and that this effect is mediated by the interaction of Nef with a specific SH3 domain present in the TCR complex. Combined with these experiments, our structural data support the identification of Fyn SH3 as the candidate target of Nef in T cells and strengthen the hypothesis that the complex of Nef with the wild-type Fyn kinase forms in vivo. Aberrant TCR-mediated signaling may involve dysfunctional regulation of Fyn by Nef.
The interaction of Nef with the TCR machinery is likely to be critical for AIDS pathogenesis. The resulting alteration in the T-cell activation status and perturbations in TCR-mediated signaling may lead to an increase in virus production and contribute to the immune unresponsiveness of infected T cells.
Cross-references: PDB:1AVZ
PDB:1AVV
Protein: DP00048 (UniProt P03406)
Region: residues 71	to 77
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Residues 71–77 of Nef form a left-handed PP-II helix that spans the strictly conserved PxxP motif. The PP-II helix has side chains emanating in three directions, two of which are utilized for interactions with the SH3 domain (Figure 4).
Cross-references: PDB:1EFN
Protein: DP00049 (UniProt P70475)
Region: residues 487	to 606
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Proteolytic cleavage of NZF-1a in the absence of zinc initially produced multiple bands. By 60 min the protein was completely digested.
Protein: DP00049 (UniProt P70475)
Region: residues 487	to 606
Annotation: disorder to order (Structural transition)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
Titration of zinc(II) into the apoprotein led to dispersion of these resonances, indicative of structure formation.