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- PDB-4a69: Structure of HDAC3 bound to corepressor and inositol tetraphosphate -

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Basic information

Entry
Database: PDB / ID: 4a69
TitleStructure of HDAC3 bound to corepressor and inositol tetraphosphate
Components
  • HISTONE DEACETYLASE 3,
  • NUCLEAR RECEPTOR COREPRESSOR 2
KeywordsTRANSCRIPTION / HYDROLASE
Function / homology
Function and homology information


: / : / transcription corepressor binding => GO:0001222 / NAD-dependent histone H3K14 deacetylase activity / NR1D1 (REV-ERBA) represses gene expression / Loss of MECP2 binding ability to the NCoR/SMRT complex / p75NTR negatively regulates cell cycle via SC1 / negative regulation of androgen receptor signaling pathway / regulation of cellular ketone metabolic process / nuclear glucocorticoid receptor binding ...: / : / transcription corepressor binding => GO:0001222 / NAD-dependent histone H3K14 deacetylase activity / NR1D1 (REV-ERBA) represses gene expression / Loss of MECP2 binding ability to the NCoR/SMRT complex / p75NTR negatively regulates cell cycle via SC1 / negative regulation of androgen receptor signaling pathway / regulation of cellular ketone metabolic process / nuclear glucocorticoid receptor binding / protein deacetylation / negative regulation of JNK cascade / cellular response to fluid shear stress / histone deacetylase / protein lysine deacetylase activity / Notch binding / histone deacetylase activity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Notch-HLH transcription pathway / RUNX2 regulates osteoblast differentiation / Association of TriC/CCT with target proteins during biosynthesis / estrous cycle / transcription factor binding / histone deacetylase complex / regulation of lipid metabolic process / Regulation of MECP2 expression and activity / NF-kappaB binding / positive regulation of TOR signaling / spindle assembly / 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 / cyclin binding / SUMOylation of transcription cofactors / negative regulation of miRNA transcription / Regulation of PTEN gene transcription / positive regulation of protein ubiquitination / HDACs deacetylate histones / Downregulation of SMAD2/3:SMAD4 transcriptional activity / circadian regulation of gene expression / regulation of protein stability / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / PPARA activates gene expression / Cytoprotection by HMOX1 / mitotic spindle / 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 / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Nuclear Receptor transcription pathway / positive regulation of protein import into nucleus / circadian rhythm / histone deacetylase binding / transcription corepressor activity / Circadian Clock / response to estradiol / positive regulation of cold-induced thermogenesis / chromatin organization / nuclear body / positive regulation of protein phosphorylation / negative regulation of DNA-templated transcription / chromatin binding / chromatin / negative regulation of apoptotic process / Golgi apparatus / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
N-CoR, GPS2-interacting domain / G-protein pathway suppressor 2-interacting domain / Histone deacetylase / Histone deacetylase domain / SANT domain profile. / SANT domain / Myb domain / Arginase; Chain A / Myb-like DNA-binding domain / Histone deacetylase family ...N-CoR, GPS2-interacting domain / G-protein pathway suppressor 2-interacting domain / Histone deacetylase / 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 / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / D-MYO INOSITOL 1,4,5,6 TETRAKISPHOSPHATE / : / Histone deacetylase 3 / Nuclear receptor corepressor 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsWatson, P.J. / Fairall, L. / Santos, G.M. / Schwabe, J.W.R.
CitationJournal: Nature / Year: 2012
Title: Structure of Hdac3 Bound to Co-Repressor and Inositol Tetraphosphate.
Authors: Watson, P.J. / Fairall, L. / Santos, G.M. / Schwabe, J.W.R.
History
DepositionNov 1, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Other
Revision 1.2Dec 20, 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_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_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 3,
B: HISTONE DEACETYLASE 3,
C: NUCLEAR RECEPTOR COREPRESSOR 2
D: NUCLEAR RECEPTOR COREPRESSOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,22518
Polymers108,4514
Non-polymers1,77414
Water6,251347
1
A: HISTONE DEACETYLASE 3,
C: NUCLEAR RECEPTOR COREPRESSOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1139
Polymers54,2262
Non-polymers8877
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-57.1 kcal/mol
Surface area18270 Å2
MethodPISA
2
B: HISTONE DEACETYLASE 3,
D: NUCLEAR RECEPTOR COREPRESSOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1139
Polymers54,2262
Non-polymers8877
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-55.9 kcal/mol
Surface area18160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.447, 118.634, 190.707
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein HISTONE DEACETYLASE 3, / / HD3 / RPD3-2 / SMAP45 / HDAC3


Mass: 42916.484 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-376
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PCDNA3 / Cell line (production host): HEK293F / Production host: HOMO SAPIENS (human) / References: UniProt: O15379, histone deacetylase
#2: Protein NUCLEAR RECEPTOR COREPRESSOR 2 / N-COR2 / CTG REPEAT PROTEIN 26 / SMAP270 / SILENCING MEDIATOR OF RETINOIC ACID AND THYROID HORMONE ...N-COR2 / CTG REPEAT PROTEIN 26 / SMAP270 / SILENCING MEDIATOR OF RETINOIC ACID AND THYROID HORMONE RECEPTOR / SMRT / T3 RECEPTOR-ASSOCIATING FACTOR / TRAC / THYROID-\ / RETINOIC-ACID-RECEPTOR-ASSOCIATED COREPRESSOR


Mass: 11309.239 Da / Num. of mol.: 2 / Fragment: RESIDUES 389-480
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PCDNA3 / Cell line (production host): HEK293F / Production host: HOMO SAPIENS (human) / References: UniProt: Q9Y618

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Non-polymers , 6 types, 361 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-I0P / D-MYO INOSITOL 1,4,5,6 TETRAKISPHOSPHATE


Mass: 500.075 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H16O18P4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O

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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: 2.43 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1 M HEPES PH 7.5 0.2 M NACL 10 % V/V PROPAN-2-OL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778
DetectorType: PILATUS 2D HYBRID ARRAY / Detector: PIXEL / Date: May 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.06→28.93 Å / Num. obs: 49237 / % possible obs: 85.9 % / Observed criterion σ(I): 2.7 / Redundancy: 2.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.9
Reflection shellResolution: 2.06→2.17 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.7 / % possible all: 68.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EW8

3ew8


Resolution: 2.06→95.35 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.675 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.26 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.23617 2631 5.1 %RANDOM
Rwork0.18702 ---
obs0.18955 49237 85.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.739 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å20 Å2
2---0.67 Å20 Å2
3---1.66 Å2
Refinement stepCycle: LAST / Resolution: 2.06→95.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7095 0 94 347 7536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.027373
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2611.9549988
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6145871
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39723.867375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.219151190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8391536
X-RAY DIFFRACTIONr_chiral_restr0.0860.21045
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215690
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.061→2.115 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 144 -
Rwork0.233 2536 -
obs--60.98 %

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