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- PDB-2yrq: Solution structure of the tandem HMG box domain from Human High m... -

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Basic information

Entry
Database: PDB / ID: 2yrq
TitleSolution structure of the tandem HMG box domain from Human High mobility group protein B1
ComponentsHigh mobility group protein B1
KeywordsDNA BINDING PROTEIN / HMG box domain / DNA binding / Helix-turn-helix motif / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


regulation of tolerance induction / calcium-dependent protein kinase regulator activity / endodeoxyribonuclease activator activity / regulation of T cell mediated immune response to tumor cell / positive regulation of mismatch repair / negative regulation of apoptotic cell clearance / plasmacytoid dendritic cell activation / neutrophil clearance / negative regulation of RNA polymerase II transcription preinitiation complex assembly / T-helper 1 cell activation ...regulation of tolerance induction / calcium-dependent protein kinase regulator activity / endodeoxyribonuclease activator activity / regulation of T cell mediated immune response to tumor cell / positive regulation of mismatch repair / negative regulation of apoptotic cell clearance / plasmacytoid dendritic cell activation / neutrophil clearance / negative regulation of RNA polymerase II transcription preinitiation complex assembly / T-helper 1 cell activation / myeloid dendritic cell activation / positive regulation of toll-like receptor 2 signaling pathway / positive regulation of dendritic cell differentiation / positive regulation of toll-like receptor 9 signaling pathway / C-X-C chemokine binding / negative regulation of CD4-positive, alpha-beta T cell differentiation / Scavenging by Class B Receptors / DNA geometric change / positive regulation of toll-like receptor 4 signaling pathway / endothelial cell chemotaxis / RAGE receptor binding / endothelial cell proliferation / positive regulation of interleukin-1 production / V(D)J recombination / Regulation of TLR by endogenous ligand / inflammatory response to antigenic stimulus / bubble DNA binding / alphav-beta3 integrin-HMGB1 complex / Apoptosis induced DNA fragmentation / macrophage activation involved in immune response / positive regulation of monocyte chemotactic protein-1 production / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of monocyte chemotaxis / MyD88 deficiency (TLR2/4) / positive regulation of activated T cell proliferation / positive regulation of vascular endothelial cell proliferation / apoptotic cell clearance / positive regulation of DNA binding / DNA binding, bending / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / T-helper 1 cell differentiation / dendritic cell chemotaxis / supercoiled DNA binding / phosphatidylserine binding / positive regulation of wound healing / regulation of nucleotide-excision repair / positive regulation of sprouting angiogenesis / chemoattractant activity / transcription repressor complex / endoplasmic reticulum-Golgi intermediate compartment / negative regulation of type II interferon production / TRAF6 mediated NF-kB activation / DNA topological change / positive regulation of interferon-alpha production / negative regulation of blood vessel endothelial cell migration / positive regulation of interleukin-10 production / Advanced glycosylation endproduct receptor signaling / Pyroptosis / positive regulation of blood vessel endothelial cell migration / protein kinase activator activity / positive regulation of interleukin-12 production / four-way junction DNA binding / condensed chromosome / DNA polymerase binding / activation of innate immune response / positive regulation of interferon-beta production / positive regulation of autophagy / cytokine activity / positive regulation of interleukin-8 production / positive regulation of interleukin-1 beta production / lipopolysaccharide binding / positive regulation of non-canonical NF-kappaB signal transduction / base-excision repair / positive regulation of interleukin-6 production / TAK1-dependent IKK and NF-kappa-B activation / positive regulation of JNK cascade / integrin binding / double-strand break repair via nonhomologous end joining / neuron projection development / autophagy / double-strand break repair / positive regulation of tumor necrosis factor production / transcription corepressor activity / double-stranded RNA binding / cellular response to lipopolysaccharide / positive regulation of cytosolic calcium ion concentration / single-stranded DNA binding / ER-Phagosome pathway / double-stranded DNA binding / DNA recombination / secretory granule lumen / heterochromatin formation / DNA-binding transcription factor binding / ficolin-1-rich granule lumen / damaged DNA binding / positive regulation of viral entry into host cell / RNA polymerase II-specific DNA-binding transcription factor binding / early endosome / positive regulation of MAPK cascade
Similarity search - Function
HMG box A DNA-binding domain, conserved site / HMG box A DNA-binding domain signature. / : / High mobility group box domain / DNA Binding (I), subunit A / HMG-box domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain ...HMG box A DNA-binding domain, conserved site / HMG box A DNA-binding domain signature. / : / High mobility group box domain / DNA Binding (I), subunit A / HMG-box domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
High mobility group protein B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, restrained molecular dynamics
AuthorsTomizawa, T. / Koshiba, S. / Watanabe, S. / Harada, T. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the tandem HMG box domain from Human High mobility group protein B1
Authors: Tomizawa, T. / Koshiba, S. / Watanabe, S. / Harada, T. / Kigawa, T. / Yokoyama, S.
History
DepositionApr 2, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: High mobility group protein B1


Theoretical massNumber of molelcules
Total (without water)19,6751
Polymers19,6751
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations, structures with the lowest energy, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein High mobility group protein B1 / High mobility group protein 1 / HMG-1


Mass: 19674.662 Da / Num. of mol.: 1 / Fragment: HMG box domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: HMGB1 / Plasmid: P061030-05 / References: UniProt: P09429

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1.09mM HMG box domain U-15N,13C; 20mM d-Tris-HCl (pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 296 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3Brukercollection
NMRPipe20060524Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.9823Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics, restrained molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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