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- PDB-1hsm: THE STRUCTURE OF THE HMG BOX AND ITS INTERACTION WITH DNA -

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Basic information

Entry
Database: PDB / ID: 1hsm
TitleTHE STRUCTURE OF THE HMG BOX AND ITS INTERACTION WITH DNA
ComponentsHIGH MOBILITY GROUP PROTEIN 1High-mobility group
KeywordsDNA-BINDING
Function / homology
Function and homology information


regulation of T cell mediated immune response to tumor cell / negative regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of toll-like receptor 9 signaling pathway / neutrophil clearance / positive regulation of DNA ligation / apoptotic cell clearance / endoplasmic reticulum-Golgi intermediate compartment / condensed chromosome / autophagy / chemotaxis ...regulation of T cell mediated immune response to tumor cell / negative regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of toll-like receptor 9 signaling pathway / neutrophil clearance / positive regulation of DNA ligation / apoptotic cell clearance / endoplasmic reticulum-Golgi intermediate compartment / condensed chromosome / autophagy / chemotaxis / DNA recombination / adaptive immune response / endosome / inflammatory response / DNA repair / innate immune response / DNA binding / extracellular region / nucleus / plasma membrane
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 / High mobility group box domain superfamily ...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
BETA-MERCAPTOETHANOL / High mobility group protein B1
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodSOLUTION NMR
AuthorsRead, C.M. / Cary, P.D. / Crane-Robinson, C. / Driscoll, P.C. / Carillo, M.O.M. / Norman, D.G.
Citation
Journal: To be Published
Title: The Structure of the Hmg Box and its Interaction with DNA
Authors: Read, C.M. / Cary, P.D. / Crane-Robinson, C. / Driscoll, P.C. / Carillo, M.O.M. / Norman, D.G.
#1: Journal: Nucleic Acids Res. / Year: 1993
Title: Solution Structure of a DNA-Binding Domain from Hmg1
Authors: Read, C.M. / Cary, P.D. / Crane-Robinson, C. / Driscoll, P.C. / Norman, D.G.
History
DepositionNov 17, 1994Processing site: BNL
Revision 1.0Feb 7, 1995Provider: 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 / struct_conn / struct_site
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_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIGH MOBILITY GROUP PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9212
Polymers8,8431
Non-polymers781
Water0
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 1 / High-mobility group


Mass: 8843.149 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: INSERT DERIVED BY PCR / Plasmid: PGEX-2T GENE: INSERT DERIVED BY PCR / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 ALPHA / References: UniProt: P07156
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS

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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-PLOR3model building
X-PLOR3refinement
X-PLOR3phasing
NMR software
NameVersionDeveloperClassification
SIMULATED ANNEALINGNILGESrefinement
X-PLOR3BRUNGERrefinement
NMR ensembleConformers submitted total number: 1

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