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- PDB-2vqv: Structure of HDAC4 catalytic domain with a gain-of-function mutat... -

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Basic information

Entry
Database: PDB / ID: 2vqv
TitleStructure of HDAC4 catalytic domain with a gain-of-function mutation bound to a hydroxamic acid inhibitor
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 / histone deacetylase complex / potassium ion binding / B cell activation / protein sumoylation / RUNX3 regulates p14-ARF / transcription repressor complex / response to interleukin-1 / epigenetic regulation of gene expression / SUMOylation of chromatin organization proteins / B cell differentiation / 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 / DNA-binding transcription factor binding / molecular adaptor activity / 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 / 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
Chem-HA3 / : / Histone deacetylase 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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 1.0Jul 22, 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 / struct_ncs_dom_lim / struct_site
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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)90,28514
Polymers88,8772
Non-polymers1,40812
Water905
1
A: HISTONE DEACETYLASE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0466
Polymers44,4381
Non-polymers6085
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HISTONE DEACETYLASE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2398
Polymers44,4381
Non-polymers8007
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.524, 70.766, 89.011
Angle α, β, γ (deg.)90.00, 108.57, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 1 / Auth seq-ID: 9 - 402 / Label seq-ID: 9 - 402

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (-0.29, -0.011, 0.957), (-0.009, -1, -0.014), (0.957, -0.013, 0.29)
Vector: -1.26025, 5.86855, 1.18469)

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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, 17 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / 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-HA3 / N-hydroxy-5-[(3-phenyl-5,6-dihydroimidazo[1,2-a]pyrazin-7(8H)-yl)carbonyl]thiophene-2-carboxamide


Mass: 368.410 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H16N4O3S
#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.: 5 / 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
Sequence detailsFIRST THREE RESIDUES OF THE SEQUENCE (GAM) COME FROM CLONING ARTEFACT.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1M MES PH 6.5, 1.6M AMMONIUM SULPHATE, 10% DIOXANE 1MM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. obs: 12577 / % possible obs: 98.2 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 6.7
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2 / % possible all: 99.5

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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: 3.3→30 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.846 / SU B: 28.082 / SU ML: 0.473 / Cross valid method: THROUGHOUT / ESU R Free: 0.615 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. MISSING RESIDUES DUE TO LACK OF ELECTRON DENSITY IN BOTH CHAINS A AND B INCLUDE 21-33 AND 84-114.
RfactorNum. reflection% reflectionSelection details
Rfree0.265 650 4.9 %RANDOM
Rwork0.234 ---
obs0.235 12576 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.45 Å2
Baniso -1Baniso -2Baniso -3
1-4.15 Å20 Å21.94 Å2
2---4.1 Å20 Å2
3---1.19 Å2
Refinement stepCycle: LAST / Resolution: 3.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5323 0 78 5 5406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225510
X-RAY DIFFRACTIONr_bond_other_d0.0020.023596
X-RAY DIFFRACTIONr_angle_refined_deg1.0871.9717491
X-RAY DIFFRACTIONr_angle_other_deg0.8523.0018727
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8615704
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.38123.778225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.55915837
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5871531
X-RAY DIFFRACTIONr_chiral_restr0.0530.2836
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026218
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021105
X-RAY DIFFRACTIONr_nbd_refined0.2270.21331
X-RAY DIFFRACTIONr_nbd_other0.180.23703
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22690
X-RAY DIFFRACTIONr_nbtor_other0.0850.22838
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2104
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2420.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3181.53506
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.60925590
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.74532026
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.3284.51901
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 4343 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.010.05
2Btight positional0.010.05
1Atight thermal0.060.5
2Btight thermal0.060.5
LS refinement shellResolution: 3.3→3.38 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.363 44
Rwork0.306 962

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