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- PDB-1hme: STRUCTURE OF THE HMG BOX MOTIF IN THE B-DOMAIN OF HMG1 -

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Basic information

Entry
Database: PDB / ID: 1hme
TitleSTRUCTURE OF THE HMG BOX MOTIF IN THE B-DOMAIN OF HMG1
ComponentsHIGH MOBILITY GROUP PROTEIN FRAGMENT-B
KeywordsDNA-BINDING
Function / homology
Function and homology information


male-specific defense response to bacterium / Apoptosis induced DNA fragmentation / open form four-way junction DNA binding / crossed form four-way junction DNA binding / positive regulation of myeloid cell apoptotic process / non-sequence-specific DNA binding, bending / Pyroptosis / TAK1-dependent IKK and NF-kappa-B activation / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling ...male-specific defense response to bacterium / Apoptosis induced DNA fragmentation / open form four-way junction DNA binding / crossed form four-way junction DNA binding / positive regulation of myeloid cell apoptotic process / non-sequence-specific DNA binding, bending / Pyroptosis / TAK1-dependent IKK and NF-kappa-B activation / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / Regulation of TLR by endogenous ligand / regulation of tolerance induction / calcium-dependent protein kinase regulator activity / positive regulation of myeloid progenitor cell differentiation / 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 / negative regulation of RNA polymerase II transcription preinitiation complex assembly / myeloid dendritic cell activation / toll-like receptor 2 signaling pathway / T-helper 1 cell activation / T-helper 1 cell differentiation / positive regulation of myeloid cell differentiation / glycolipid binding / positive regulation of toll-like receptor 2 signaling pathway / positive regulation of macrophage inflammatory protein 1 alpha production / positive regulation of dendritic cell differentiation / C-X-C chemokine binding / positive regulation of toll-like receptor 9 signaling pathway / negative regulation of CD4-positive, alpha-beta T cell differentiation / bent DNA binding / neutrophil clearance / positive regulation of glycogen catabolic process / DNA geometric change / positive regulation of toll-like receptor 4 signaling pathway / endothelial cell chemotaxis / RAGE receptor binding / positive regulation of interleukin-1 production / eye development / bubble DNA binding / induction of positive chemotaxis / V(D)J recombination / alphav-beta3 integrin-HMGB1 complex / myeloid cell differentiation / myeloid progenitor cell differentiation / inflammatory response to antigenic stimulus / regulation of nucleotide-excision repair / myoblast proliferation / macrophage activation involved in immune response / positive regulation of monocyte chemotaxis / positive regulation of monocyte chemotactic protein-1 production / positive regulation of innate immune response / cellular response to interleukin-7 / endothelial cell proliferation / positive regulation of chemokine (C-X-C motif) ligand 2 production / glycogen catabolic process / apoptotic cell clearance / supercoiled DNA binding / positive regulation of vascular endothelial cell proliferation / positive regulation of mesenchymal cell proliferation / DNA binding, bending / Neutrophil degranulation / positive regulation of smooth muscle cell migration / MyD88-dependent toll-like receptor signaling pathway / toll-like receptor 4 signaling pathway / positive regulation of wound healing / phosphatidylserine binding / negative regulation of DNA replication / positive regulation of sprouting angiogenesis / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of activated T cell proliferation / negative regulation of type II interferon production / negative regulation of blood vessel endothelial cell migration / positive regulation of interferon-alpha production / positive regulation of interleukin-10 production / protein kinase activator activity / cellular response to interleukin-1 / positive regulation of blood vessel endothelial cell migration / response to type II interferon / positive regulation of myoblast differentiation / response to glucose / response to glucocorticoid / four-way junction DNA binding / condensed chromosome / DNA polymerase binding / positive regulation of interleukin-12 production / positive regulation of autophagy / transcription repressor complex / peptide binding / activation of innate immune response / positive regulation of mitotic cell cycle / positive regulation of interferon-beta production / positive regulation of interleukin-1 beta production / cytokine activity / positive regulation of interleukin-8 production / positive regulation of JNK cascade / lipopolysaccharide binding / lung development / positive regulation of non-canonical NF-kappaB signal transduction
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 speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR
AuthorsWeir, H.M. / Kraulis, P.J. / Hill, C.S. / Raine, A.R.C. / Laue, E.D. / Thomas, J.O.
CitationJournal: EMBO J. / Year: 1993
Title: Structure of the HMG box motif in the B-domain of HMG1.
Authors: Weir, H.M. / Kraulis, P.J. / Hill, C.S. / Raine, A.R. / Laue, E.D. / Thomas, J.O.
History
DepositionFeb 10, 1994Processing site: BNL
Revision 1.0May 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 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 FRAGMENT-B


Theoretical massNumber of molelcules
Total (without water)8,7911
Polymers8,7911
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)1 / -
Representative

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Components

#1: Protein HIGH MOBILITY GROUP PROTEIN FRAGMENT-B


Mass: 8791.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / References: UniProt: P63159

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

Software
NameVersionClassification
X-PLOR2model building
X-PLOR2refinement
X-PLOR2phasing
NMR softwareName: X-PLOR / Version: 2.1 / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers submitted total number: 1

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