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- PDB-2vqo: Structure of HDAC4 catalytic domain with a gain-of-function muati... -

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Basic information

Entry
Database: PDB / ID: 2vqo
TitleStructure of HDAC4 catalytic domain with a gain-of-function muation bound to a trifluoromethylketone inhbitor
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 / peptidyl-lysine deacetylation / positive regulation of protein sumoylation / negative regulation of transcription by competitive promoter binding / histone deacetylase activity, hydrolytic mechanism / histone deacetylase / protein deacetylation / 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 / peptidyl-lysine deacetylation / positive regulation of protein sumoylation / negative regulation of transcription by competitive promoter binding / histone deacetylase activity, hydrolytic mechanism / histone deacetylase / protein deacetylation / cardiac muscle hypertrophy in response to stress / negative regulation of glycolytic process / SUMO transferase activity / protein lysine deacetylase activity / histone deacetylase activity / type I interferon-mediated signaling pathway / DNA-binding transcription activator activity / Notch-HLH transcription pathway / negative regulation of gene expression, epigenetic / potassium ion binding / B cell activation / histone deacetylase complex / RUNX3 regulates p14-ARF / protein sumoylation / transcription repressor complex / response to interleukin-1 / SUMOylation of chromatin organization proteins / B cell differentiation / epigenetic regulation of gene expression / SUMOylation of intracellular receptors / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / nervous system development / molecular adaptor activity / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / inflammatory response / 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 / cytoplasm / cytosol
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
: / Chem-TFG / Histone deacetylase 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 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 18, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 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_asym_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_asym_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

Downloads & links

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Assembly

Deposited unit
A: HISTONE DEACETYLASE 4
B: HISTONE DEACETYLASE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,29913
Polymers88,8772
Non-polymers1,42211
Water4,540252
1
A: HISTONE DEACETYLASE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1977
Polymers44,4381
Non-polymers7596
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: HISTONE DEACETYLASE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1016
Polymers44,4381
Non-polymers6635
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)86.092, 70.965, 88.331
Angle α, β, γ (deg.)90.00, 108.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein HISTONE DEACETYLASE 4 / HD4


Mass: 44438.301 Da / Num. of mol.: 2 / 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

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Non-polymers , 5 types, 263 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-TFG / 2,2,2-TRIFLUORO-1-{5-[(3-PHENYL-5,6-DIHYDROIMIDAZO[1,2-A]PYRAZIN-7(8H)-YL)CARBONYL]THIOPHEN-2-YL}ETHANE-1,1-DIOL


Mass: 423.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H16F3N3O3S
#5: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 669 TO ALA ENGINEERED RESIDUE IN CHAIN A, CYS 700 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, CYS 669 TO ALA ENGINEERED RESIDUE IN CHAIN A, CYS 700 TO ALA ENGINEERED RESIDUE IN CHAIN A, HIS 976 TO TYR ENGINEERED RESIDUE IN CHAIN B, CYS 669 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 700 TO ALA ENGINEERED RESIDUE IN CHAIN B, 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: 2.9 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 6.5
Details: 1.6M AMMONIUM SULPHATE, 0.1M MES PH 6.5, 10% DIOXANE, 1MM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.94
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. obs: 15329 / % possible obs: 97.5 % / Redundancy: 3 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.8
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 3 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.5 / % possible all: 97.5

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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: 2.15→40 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.024 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 23-34 AND 85-111 ARE NOT VISIBLE IN THE ELECTRON DENSITY MAPS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 2719 5.1 %RANDOM
Rwork0.21 ---
obs0.212 50970 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.02 Å2
Baniso -1Baniso -2Baniso -3
1-1.85 Å20 Å23.29 Å2
2---1.18 Å20 Å2
3---1.37 Å2
Refinement stepCycle: LAST / Resolution: 2.15→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5403 0 79 252 5734
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225669
X-RAY DIFFRACTIONr_bond_other_d0.0020.023726
X-RAY DIFFRACTIONr_angle_refined_deg1.0821.9727735
X-RAY DIFFRACTIONr_angle_other_deg0.8523.0019070
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5025739
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.92223.924237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88415885
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6091532
X-RAY DIFFRACTIONr_chiral_restr0.0570.2863
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026414
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021134
X-RAY DIFFRACTIONr_nbd_refined0.2120.21162
X-RAY DIFFRACTIONr_nbd_other0.1760.23781
X-RAY DIFFRACTIONr_nbtor_refined0.170.22717
X-RAY DIFFRACTIONr_nbtor_other0.0830.22755
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2227
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0810.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3010.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0940.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4031.53583
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.75825736
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.96732109
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5884.51981
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: 2.15→2.21 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.312 207
Rwork0.308 3758

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