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- PDB-2h8n: Structure of a glutamine-rich domain from histone deacetylase 4 -

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Basic information

Entry
Database: PDB / ID: 2h8n
TitleStructure of a glutamine-rich domain from histone deacetylase 4
ComponentsHistone deacetylase 4
KeywordsTRANSCRIPTION / alpha helix / polar zipper
Function / homology
Function and homology information


RUNX2 regulates chondrocyte maturation / response to denervation involved in regulation of muscle adaptation / negative regulation of myotube differentiation / peptidyl-lysine deacetylation / positive regulation of protein sumoylation / negative regulation of transcription by competitive promoter binding / regulation of protein binding / protein deacetylation / cardiac muscle hypertrophy in response to stress / histone deacetylase ...RUNX2 regulates chondrocyte maturation / response to denervation involved in regulation of muscle adaptation / negative regulation of myotube differentiation / peptidyl-lysine deacetylation / positive regulation of protein sumoylation / negative regulation of transcription by competitive promoter binding / regulation of protein binding / protein deacetylation / cardiac muscle hypertrophy in response to stress / histone deacetylase / protein lysine deacetylase activity / negative regulation of glycolytic process / SUMO transferase activity / histone deacetylase activity / negative regulation of gene expression, epigenetic / B cell activation / type I interferon-mediated signaling pathway / Notch-HLH transcription pathway / potassium ion binding / protein sumoylation / RUNX3 regulates p14-ARF / histone deacetylase complex / transcription repressor complex / SUMOylation of chromatin organization proteins / response to interleukin-1 / B cell differentiation / SUMOylation of intracellular receptors / negative regulation of DNA-binding transcription factor activity / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / positive regulation of DNA-binding transcription factor activity / nervous system development / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / molecular adaptor activity / nuclear speck / chromatin remodeling / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of cell population proliferation / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1550 / Histone deacetylase, glutamine rich N-terminal domain / Glutamine rich N terminal domain of histone deacetylase 4 / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1550 / Histone deacetylase, glutamine rich N-terminal domain / Glutamine rich N terminal domain of histone deacetylase 4 / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
Histone deacetylase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsGuo, L. / Han, A. / Bates, D.L. / Chen, L.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Crystal structure of a conserved N-terminal domain of histone deacetylase 4 reveals functional insights into glutamine-rich domains.
Authors: Guo, L. / Han, A. / Bates, D.L. / Cao, J. / Chen, L.
History
DepositionJun 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone deacetylase 4
B: Histone deacetylase 4
C: Histone deacetylase 4
D: Histone deacetylase 4


Theoretical massNumber of molelcules
Total (without water)54,6134
Polymers54,6134
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10050 Å2
ΔGint-69 kcal/mol
Surface area17790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.398, 60.451, 60.450
Angle α, β, γ (deg.)90.00, 108.74, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe tetramer in the asymmetric unit is the biological assembly, no crystallographic symmetry is invovled in the tetramer formation.

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Components

#1: Protein
Histone deacetylase 4 / / HD4


Mass: 13653.348 Da / Num. of mol.: 4 / Fragment: N-terminal glutamine-rich Domain, residues 62-129
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC4, KIAA0288 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta PlysS / References: UniProt: P56524

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.93987 Å3/Da / Density % sol: 58.161419 %
Description: THE REFLECTIONS IN THE STRUCTURE FACTOR FILE WERE SCALED TO 2.3A, THE STRUCTURE WAS REFINED TO 2.6A. ALTHOUGH THE DIFFRACTION WENT TO 2.3A, DUE TO SEVERE ANISOTROPIC EFFECT, USEFUL DATA WAS ONLY TO 2.6A.
Crystal growTemperature: 291 K / pH: 7.5
Details: 0.825M LITHIUM SULFATE, 55mM HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.1271
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 2, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 2.6→6 Å / Num. obs: 19701 / % possible obs: 99 % / Observed criterion σ(I): 2
Reflection shellResolution: 2.6→2.73 Å / % possible all: 99

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
ADSCdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→6 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.307 1702 RANDOM
Rwork0.281 --
obs0.283 16845 -
all-18241 -
Displacement parametersBiso mean: 93.34 Å2
Baniso -1Baniso -2Baniso -3
1-42.392 Å20 Å27.494 Å2
2---24.865 Å20 Å2
3----17.528 Å2
Refinement stepCycle: LAST / Resolution: 2.6→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 0 0 2328
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.8011.5
X-RAY DIFFRACTIONc_mcangle_it4.8222
X-RAY DIFFRACTIONc_scbond_it4.7972
X-RAY DIFFRACTIONc_scangle_it8.2112.5
Xplor fileSerial no: 1 / Param file: protein_rep.param

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