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- PDB-2msy: Solution structure of Hox homeodomain -

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Basic information

Entry
Database: PDB / ID: 2msy
TitleSolution structure of Hox homeodomain
ComponentsHomeobox protein Hox-C9
KeywordsTRANSCRIPTION / homeodomain / transcription factor
Function / homology
Function and homology information


embryonic skeletal system morphogenesis / proximal/distal pattern formation / aggresome / anterior/posterior pattern specification / negative regulation of cell cycle / transcription repressor complex / sequence-specific double-stranded DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity ...embryonic skeletal system morphogenesis / proximal/distal pattern formation / aggresome / anterior/posterior pattern specification / negative regulation of cell cycle / transcription repressor complex / sequence-specific double-stranded DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
: / Hox9, N-terminal activation domain / Homeobox protein HXA9/HXB9/HXC9 / Hox9 activation region / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain ...: / Hox9, N-terminal activation domain / Homeobox protein HXA9/HXB9/HXC9 / Hox9 activation region / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Homeobox protein Hox-C9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsminimized average structure, model1
Model type detailsminimized average
AuthorsKim, H. / Park, S. / Han, J. / Lee, B.
CitationJournal: Biochim.Biophys.Acta / Year: 2015
Title: Structural insight into the interaction between the Hox and HMGB1 and understanding of the HMGB1-enhancing effect of Hox-DNA binding.
Authors: Kim, H.H. / Park, S.J. / Han, J.H. / Pathak, C. / Cheong, H.K. / Lee, B.J.
History
DepositionAug 11, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Other
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Homeobox protein Hox-C9


Theoretical massNumber of molelcules
Total (without water)8,6771
Polymers8,6771
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 lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Homeobox protein Hox-C9 / Homeobox protein Hox-3B


Mass: 8677.257 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 184-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HOXC9, HOX3B / Production host: Escherichia coli (E. coli) / References: UniProt: P31274

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY
1313D 1H-13C NOESY
1413D CBCA(CO)NH
1513D HNCA
1613D HNCO
1713D (H)CCH-TOCSY
1813D 1H-15N TOCSY
1913D HBHA(CO)NH

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] MES-1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: MES-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.05 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX9001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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