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- PDB-1aab: NMR STRUCTURE OF RAT HMG1 HMGA FRAGMENT -

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Entry
Database: PDB / ID: 1aab
TitleNMR STRUCTURE OF RAT HMG1 HMGA FRAGMENT
ComponentsHIGH MOBILITY GROUP PROTEIN
KeywordsDNA-BINDING / HMG-BOX
Function / homology
Function and homology information


male-specific defense response to bacterium / Apoptosis induced DNA fragmentation / open form four-way junction DNA binding / calcium-dependent protein kinase regulator activity / positive regulation of myeloid progenitor cell differentiation / crossed form four-way junction DNA binding / positive regulation of myeloid cell apoptotic process / Pyroptosis / TAK1-dependent IKK and NF-kappa-B activation / TRAF6 mediated NF-kB activation ...male-specific defense response to bacterium / Apoptosis induced DNA fragmentation / open form four-way junction DNA binding / calcium-dependent protein kinase regulator activity / positive regulation of myeloid progenitor cell differentiation / crossed form four-way junction DNA binding / positive regulation of myeloid cell apoptotic process / Pyroptosis / TAK1-dependent IKK and NF-kappa-B activation / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / plasmacytoid dendritic cell activation / Regulation of TLR by endogenous ligand / regulation of tolerance induction / positive regulation of mismatch repair / regulation of T cell mediated immune response to tumor cell / negative regulation of apoptotic cell clearance / negative regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of myeloid cell differentiation / myeloid dendritic cell activation / positive regulation of toll-like receptor 2 signaling pathway / T-helper 1 cell activation / T-helper 1 cell differentiation / glycolipid binding / positive regulation of dendritic cell differentiation / positive regulation of macrophage inflammatory protein 1 alpha production / C-X-C chemokine binding / negative regulation of CD4-positive, alpha-beta T cell differentiation / positive regulation of toll-like receptor 9 signaling pathway / bent DNA binding / positive regulation of glycogen catabolic process / neutrophil clearance / positive regulation of toll-like receptor 4 signaling pathway / DNA geometric change / endothelial cell chemotaxis / RAGE receptor binding / eye development / positive regulation of interleukin-1 production / bubble DNA binding / induction of positive chemotaxis / V(D)J recombination / myeloid cell differentiation / alphav-beta3 integrin-HMGB1 complex / myeloid progenitor cell differentiation / regulation of nucleotide-excision repair / macrophage activation involved in immune response / inflammatory response to antigenic stimulus / 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 / glycogen catabolic process / positive regulation of chemokine (C-X-C motif) ligand 2 production / apoptotic cell clearance / myoblast proliferation / supercoiled DNA binding / positive regulation of vascular endothelial cell proliferation / DNA binding, bending / positive regulation of mesenchymal cell proliferation / Neutrophil degranulation / positive regulation of wound healing / positive regulation of smooth muscle cell migration / phosphatidylserine binding / positive regulation of sprouting angiogenesis / negative regulation of DNA replication / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of activated T cell proliferation / positive regulation of interferon-alpha production / negative regulation of type II interferon production / negative regulation of blood vessel endothelial cell migration / positive regulation of interleukin-10 production / protein kinase activator activity / cellular response to interleukin-1 / response to type II interferon / positive regulation of blood vessel endothelial cell migration / positive regulation of myoblast differentiation / response to glucose / response to glucocorticoid / four-way junction DNA binding / condensed chromosome / DNA polymerase binding / positive regulation of autophagy / transcription repressor complex / positive regulation of interleukin-12 production / positive regulation of mitotic cell cycle / activation of innate immune response / peptide binding / positive regulation of interferon-beta production / positive regulation of interleukin-1 beta production / cytokine activity / positive regulation of interleukin-8 production / response to insulin / positive regulation of JNK cascade / lipopolysaccharide binding / lung development / positive regulation of non-canonical NF-kappaB signal transduction / cell morphogenesis / base-excision repair / positive regulation of neuron projection development
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
AuthorsHardman, C.H. / Broadhurst, R.W. / Raine, A.R.C. / Grasser, K.D. / Thomas, J.O. / Laue, E.D.
Citation
Journal: Biochemistry / Year: 1995
Title: Structure of the A-domain of HMG1 and its interaction with DNA as studied by heteronuclear three- and four-dimensional NMR spectroscopy.
Authors: Hardman, C.H. / Broadhurst, R.W. / Raine, A.R. / Grasser, K.D. / Thomas, J.O. / Laue, E.D.
#1: Journal: To be Published
Title: Backbone Dynamics of the a Domain of Hmg1 as Studied by 15N NMR Spectroscopy
Authors: Broadhurst, R.W. / Hardman, C.H. / Thomas, J.O. / Laue, E.D.
History
DepositionOct 28, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: HIGH MOBILITY GROUP PROTEIN


Theoretical massNumber of molelcules
Total (without water)9,6891
Polymers9,6891
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)33 / -
Representative

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Components

#1: Protein HIGH MOBILITY GROUP PROTEIN / HMGA DNA-BINDING HMG-BOX DOMAIN A OF RAT HMG1


Mass: 9689.119 Da / Num. of mol.: 1 / Fragment: FRAGMENT A (RESIDUES 1 - 83) / Mutation: C22S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: SPRAGUE-DAWLEY / Tissue: LIVER / Plasmid: PT7-HMGACS / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / 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

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR softwareName: X-PLOR / Version: 3.1 / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers submitted total number: 33

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