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- PDB-5zoo: Crystal structure of histone deacetylase 4 (HDAC4) in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5zoo
TitleCrystal structure of histone deacetylase 4 (HDAC4) in complex with a SMRT corepressor SP1 fragment
Components
  • Histone deacetylase 4
  • SMRT corepressor SP1 fragment
KeywordsHYDROLASE / protein-peptide complex
Function / homology
Function and homology information


RUNX2 regulates chondrocyte maturation / Loss of MECP2 binding ability to the NCoR/SMRT complex / response to denervation involved in regulation of muscle adaptation / negative regulation of myotube differentiation / peptidyl-lysine deacetylation / negative regulation of androgen receptor signaling pathway / regulation of cellular ketone metabolic process / nuclear glucocorticoid receptor binding / positive regulation of protein sumoylation / negative regulation of transcription by competitive promoter binding ...RUNX2 regulates chondrocyte maturation / Loss of MECP2 binding ability to the NCoR/SMRT complex / response to denervation involved in regulation of muscle adaptation / negative regulation of myotube differentiation / peptidyl-lysine deacetylation / negative regulation of androgen receptor signaling pathway / regulation of cellular ketone metabolic process / nuclear glucocorticoid receptor binding / 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 / Notch binding / negative regulation of glycolytic process / SUMO transferase activity / histone deacetylase activity / negative regulation of gene expression, epigenetic / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / B cell activation / type I interferon-mediated signaling pathway / Notch-HLH transcription pathway / potassium ion binding / protein sumoylation / histone deacetylase complex / RUNX3 regulates p14-ARF / estrous cycle / Regulation of MECP2 expression and activity / nuclear retinoid X receptor binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to organonitrogen compound / transcription repressor complex / lactation / Regulation of lipid metabolism by PPARalpha / cerebellum development / SUMOylation of chromatin organization proteins / response to interleukin-1 / B cell differentiation / SUMOylation of transcription cofactors / negative regulation of miRNA transcription / HDACs deacetylate histones / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SUMOylation of intracellular receptors / negative regulation of DNA-binding transcription factor activity / PPARA activates gene expression / Cytoprotection by HMOX1 / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / nuclear matrix / Transcriptional regulation of white adipocyte differentiation / HCMV Early Events / Nuclear Receptor transcription pathway / histone deacetylase binding / transcription corepressor activity / positive regulation of DNA-binding transcription factor activity / response to estradiol / nervous system development / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / molecular adaptor activity / nuclear body / nuclear speck / chromatin remodeling / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin 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 / DNA binding / zinc ion binding / nucleoplasm / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Histone deacetylase, glutamine rich N-terminal domain / Glutamine rich N terminal domain of histone deacetylase 4 / : / N-CoR, GPS2-interacting domain / G-protein pathway suppressor 2-interacting domain / Histone deacetylase domain / SANT domain profile. / SANT domain / Myb domain / Arginase; Chain A ...Histone deacetylase, glutamine rich N-terminal domain / Glutamine rich N terminal domain of histone deacetylase 4 / : / N-CoR, GPS2-interacting domain / G-protein pathway suppressor 2-interacting domain / Histone deacetylase domain / SANT domain profile. / SANT domain / Myb domain / Arginase; Chain A / Myb-like DNA-binding domain / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Ureohydrolase domain superfamily / Homeobox-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Histone deacetylase 4 / Nuclear receptor corepressor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPark, S.Y. / Hwang, H.J. / Kim, J.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)2017R1D1A3B03032278, 2017R1D1A1B03034080, 2014R1A4A1003642 Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structural basis of the specific interaction of SMRT corepressor with histone deacetylase 4.
Authors: Park, S.Y. / Kim, G.S. / Hwang, H.J. / Nam, T.H. / Park, H.S. / Song, J. / Jang, T.H. / Lee, Y.C. / Kim, J.S.
History
DepositionApr 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Apr 24, 2019Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: Histone deacetylase 4
A: SMRT corepressor SP1 fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1966
Polymers44,9872
Non-polymers2094
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-46 kcal/mol
Surface area15800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.424, 131.424, 67.770
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11G-1382-

HOH

21G-1407-

HOH

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Components

#1: Protein Histone deacetylase 4 / / HD4


Mass: 43399.152 Da / Num. of mol.: 1 / Fragment: UNP residues 652-1052 / Mutation: H976Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC4, KIAA0288 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P56524, histone deacetylase
#2: Protein/peptide SMRT corepressor SP1 fragment


Mass: 1587.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y618*PLUS
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe alanine (chain G, 1) is remaining amino acid after TEV digestion to remove expression tag.

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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: 3.92 Å3/Da / Density % sol: 68.63 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 7.5 / Details: PEG 3350, iso-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 5, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.846→29.565 Å / Num. obs: 57039 / % possible obs: 98.4 % / Redundancy: 3.2 % / Biso Wilson estimate: 24.19 Å2 / Rsym value: 0.138 / Net I/σ(I): 12
Reflection shellResolution: 1.85→1.88 Å / Rsym value: 0.45

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VQW

2vqw


Resolution: 1.85→9.989 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1753 2260 4 %
Rwork0.1554 --
obs0.1562 56436 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→9.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3031 0 4 279 3314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043101
X-RAY DIFFRACTIONf_angle_d0.7054210
X-RAY DIFFRACTIONf_dihedral_angle_d13.0471833
X-RAY DIFFRACTIONf_chiral_restr0.047470
X-RAY DIFFRACTIONf_plane_restr0.004552
Refinement TLS params.Method: refined / Origin x: 56.4793 Å / Origin y: -17.636 Å / Origin z: 2.1535 Å
111213212223313233
T0.2423 Å20.0193 Å20.0028 Å2-0.1297 Å2-0.0029 Å2--0.1536 Å2
L0.5227 °2-0.0468 °2-0.048 °2-1.1631 °2-0.0403 °2--1.1254 °2
S0.0217 Å °-0.0037 Å °0.0717 Å °0.0308 Å °0.0072 Å °0.0265 Å °-0.2123 Å °-0.0498 Å °-0.0223 Å °
Refinement TLS groupSelection details: all

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