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- PDB-2vqw: Structure of inhibitor-free HDAC4 catalytic domain (with gain-of-... -

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Basic information

Entry
Database: PDB / ID: 2vqw
TitleStructure of inhibitor-free HDAC4 catalytic domain (with gain-of- function mutation His332Tyr)
ComponentsHISTONE DEACETYLASE 4
KeywordsHYDROLASE / INHIBITOR / REPRESSOR / CHROMATIN / COILED COIL / HISTONE DEACETYLASE / TRANSCRIPTION REGULATION / UBL CONJUGATION / CHROMATIN REGULATOR / POLYMORPHISM / TRANSCRIPTION / PHOSPHOPROTEIN / HDAC / ZINC / HDACI / NUCLEUS / CYTOPLASM
Function / homology
Function and homology information


RUNX2 regulates chondrocyte maturation / response to denervation involved in regulation of muscle adaptation / negative regulation of myotube differentiation / regulation of protein binding / peptidyl-lysine deacetylation / positive regulation of protein sumoylation / negative regulation of transcription by competitive promoter binding / protein deacetylation / histone deacetylase / cardiac muscle hypertrophy in response to stress ...RUNX2 regulates chondrocyte maturation / response to denervation involved in regulation of muscle adaptation / negative regulation of myotube differentiation / regulation of protein binding / peptidyl-lysine deacetylation / positive regulation of protein sumoylation / negative regulation of transcription by competitive promoter binding / protein deacetylation / histone deacetylase / cardiac muscle hypertrophy in response to stress / protein lysine deacetylase activity / negative regulation of glycolytic process / SUMO transferase activity / histone deacetylase activity / type I interferon-mediated signaling pathway / negative regulation of gene expression, epigenetic / Notch-HLH transcription pathway / B cell activation / potassium ion binding / histone deacetylase complex / RUNX3 regulates p14-ARF / protein sumoylation / transcription repressor complex / response to interleukin-1 / SUMOylation of chromatin organization proteins / B cell differentiation / positive regulation of DNA-binding transcription factor activity / SUMOylation of intracellular receptors / negative regulation of DNA-binding transcription factor activity / NOTCH1 Intracellular Domain Regulates Transcription / histone deacetylase binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / nervous system development / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / molecular adaptor activity / nuclear speck / inflammatory response / chromatin remodeling / 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
Histone deacetylase, glutamine rich N-terminal domain / Glutamine rich N terminal domain of histone deacetylase 4 / : / Histone deacetylase domain / Arginase; Chain A / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily ...Histone deacetylase, glutamine rich N-terminal domain / Glutamine rich N terminal domain of histone deacetylase 4 / : / Histone deacetylase domain / Arginase; Chain A / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Histone deacetylase 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBottomley, M.J. / Lo Surdo, P. / Di Giovine, P. / Cirillo, A. / Scarpelli, R. / Ferrigno, F. / Jones, P. / Neddermann, P. / De Francesco, R. / Steinkuhler, C. ...Bottomley, M.J. / Lo Surdo, P. / Di Giovine, P. / Cirillo, A. / Scarpelli, R. / Ferrigno, F. / Jones, P. / Neddermann, P. / De Francesco, R. / Steinkuhler, C. / Gallinari, P. / Carfi, A.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural and Functional Analysis of the Human Hdac4 Catalytic Domain Reveals a Regulatory Structural Zinc-Binding Domain.
Authors: Bottomley, M.J. / Lo Surdo, P. / Di Giovine, P. / Cirillo, A. / Scarpelli, R. / Ferrigno, F. / Jones, P. / Neddermann, P. / De Francesco, R. / Steinkuhler, C. / Gallinari, P. / Carfi, A.
History
DepositionMar 19, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: HISTONE DEACETYLASE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7115
Polymers44,5021
Non-polymers2094
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)137.911, 137.911, 69.519
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein HISTONE DEACETYLASE 4 / HD4


Mass: 44502.430 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 648-1057 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM-11 (OBTAINED FROM EMBL-HEIDELBERG) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P56524, histone deacetylase
#2: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Compound detailsENGINEERED RESIDUE IN CHAIN G, HIS 976 TO TYR

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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: 4.9 Å3/Da / Density % sol: 71 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1M HEPES PH 7.5, 18% PEG 10000, 1MM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 3→60 Å / Num. obs: 15460 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 14.3
Reflection shellResolution: 3→3.48 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VQJ

2vqj


Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.923 / SU B: 17.23 / SU ML: 0.314 / Cross valid method: THROUGHOUT / ESU R: 0.702 / ESU R Free: 0.356 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.261 756 5 %RANDOM
Rwork0.233 ---
obs0.234 14460 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 83.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.51 Å22.25 Å20 Å2
2--4.51 Å20 Å2
3----6.76 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2868 0 4 0 2872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0212936
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0331.9533991
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3265380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.93623.79124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.23715449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7971517
X-RAY DIFFRACTIONr_chiral_restr0.070.2450
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022248
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.21432
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.21999
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.274
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0980.26
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.224
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2981.51892
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.55223024
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.48631055
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.8234.5967
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 56 -
Rwork0.334 1035 -
obs--100 %

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