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- PDB-9jv3: Structure of Human HDAC2 -

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Basic information

Entry
Database: PDB / ID: 9jv3
TitleStructure of Human HDAC2
ComponentsHistone deacetylase 2
KeywordsTRANSCRIPTION / Histone deacetylase 2
Function / homology
Function and homology information


positive regulation of male mating behavior / protein de-2-hydroxyisobutyrylase activity / protein lysine delactylase activity / negative regulation of dendritic spine development / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / histone decrotonylase activity / fungiform papilla formation / behavioral response to ethanol / NuRD complex ...positive regulation of male mating behavior / protein de-2-hydroxyisobutyrylase activity / protein lysine delactylase activity / negative regulation of dendritic spine development / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / histone decrotonylase activity / fungiform papilla formation / behavioral response to ethanol / NuRD complex / positive regulation of interleukin-1 production / regulation of cell fate specification / negative regulation of transcription by competitive promoter binding / EGR2 and SOX10-mediated initiation of Schwann cell myelination / negative regulation of stem cell population maintenance / histone deacetylase activity, hydrolytic mechanism / ESC/E(Z) complex / histone deacetylase / regulation of stem cell differentiation / cardiac muscle hypertrophy / cellular response to dopamine / STAT3 nuclear events downstream of ALK signaling / response to caffeine / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / embryonic digit morphogenesis / histone deacetylase activity / positive regulation of intracellular estrogen receptor signaling pathway / Notch-HLH transcription pathway / Sin3-type complex / eyelid development in camera-type eye / odontogenesis of dentin-containing tooth / positive regulation of stem cell population maintenance / dendrite development / response to amyloid-beta / RNA Polymerase I Transcription Initiation / histone deacetylase complex / positive regulation of oligodendrocyte differentiation / positive regulation of proteolysis / Regulation of MECP2 expression and activity / progesterone receptor signaling pathway / hair follicle placode formation / response to hyperoxia / NF-kappaB binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / cellular response to transforming growth factor beta stimulus / positive regulation of epithelial to mesenchymal transition / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / MECP2 regulates neuronal receptors and channels / Regulation of TP53 Activity through Acetylation / cellular response to retinoic acid / heat shock protein binding / SUMOylation of chromatin organization proteins / negative regulation of cell migration / response to amphetamine / Regulation of PTEN gene transcription / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / transcription coregulator binding / Regulation of endogenous retroelements by KRAB-ZFP proteins / response to nicotine / response to cocaine / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / promoter-specific chromatin binding / circadian regulation of gene expression / negative regulation of transforming growth factor beta receptor signaling pathway / NoRC negatively regulates rRNA expression / NOTCH1 Intracellular Domain Regulates Transcription / protein modification process / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / cellular response to hydrogen peroxide / positive regulation of tumor necrosis factor production / heterochromatin formation / negative regulation of neuron projection development / cellular response to heat / Factors involved in megakaryocyte development and platelet production / histone binding / response to lipopolysaccharide / Potential therapeutics for SARS / RNA polymerase II-specific DNA-binding transcription factor binding / chromosome, telomeric region / chromatin remodeling / response to xenobiotic stimulus / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / chromatin binding / negative regulation of apoptotic process / chromatin / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Histone deacetylase / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Histone deacetylase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsTojo, T. / Itoh, Y. / Kurohara, T. / Li, Y. / Singh, R. / Narozny, R. / Wiel, A. / Miyake, Y. / Yamashita, Y. / Kusakabe, K. ...Tojo, T. / Itoh, Y. / Kurohara, T. / Li, Y. / Singh, R. / Narozny, R. / Wiel, A. / Miyake, Y. / Yamashita, Y. / Kusakabe, K. / Uchida, S. / Suzuki, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Discovery of an HDAC2-selective inhibitor based on enzyme-inhibitor binding thermodynamics and kinetics, and its potential as a therapeutic drug for neurological disorders
Authors: Tojo, T. / Itoh, Y. / Kurohara, T. / Li, Y. / Singh, R. / Narozny, R. / Wiel, A. / Miyake, Y. / Yamashita, Y. / Kusakabe, K. / Uchida, S. / Suzuki, T.
History
DepositionOct 8, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone deacetylase 2
B: Histone deacetylase 2
C: Histone deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,50134
Polymers137,9943
Non-polymers2,50731
Water5,423301
1
A: Histone deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,75411
Polymers45,9981
Non-polymers75610
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,14313
Polymers45,9981
Non-polymers1,14512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histone deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,60410
Polymers45,9981
Non-polymers6069
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.024, 97.584, 138.967
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Histone deacetylase 2 / HD2 / Protein deacylase HDAC2


Mass: 45997.965 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q92769, histone deacetylase, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

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Non-polymers , 8 types, 332 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M CHES pH 9.5, 35-38% (v/v) PEG 600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.57→79.91 Å / Num. obs: 39492 / % possible obs: 97.4 % / Redundancy: 3.3 % / Rrim(I) all: 0.1 / Net I/σ(I): 11.9
Reflection shellResolution: 2.57→2.82 Å / Num. unique obs: 9527 / Rrim(I) all: 0.53

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in house model

Resolution: 2.57→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.894 / SU B: 13.036 / SU ML: 0.282 / Cross valid method: THROUGHOUT / ESU R: 1.081 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25647 953 2.4 %RANDOM
Rwork0.1815 ---
obs0.18336 38538 97.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 60.168 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å2-0 Å20 Å2
2--2.45 Å2-0 Å2
3----1.09 Å2
Refinement stepCycle: 1 / Resolution: 2.57→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8855 0 145 301 9301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0199135
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.241.95712242
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.86851103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.96423.695433
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.534151460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1691547
X-RAY DIFFRACTIONr_chiral_restr0.0870.21264
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216956
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2385.9534442
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.748.9255512
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.1386.1974693
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.83981.56214099
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: 2.57→2.637 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 66 -
Rwork0.247 2820 -
obs--98.1 %

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