[English] 日本語
Yorodumi
- PDB-4a69: Structure of HDAC3 bound to corepressor and inositol tetraphosphate -

+
Open data


ID or keywords:

Loading...

-
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


protein decrotonylase activity / positive regulation of ferroptosis / cornified envelope assembly / : / negative regulation of cardiac muscle cell differentiation / protein de-2-hydroxyisobutyrylase activity / Loss of MECP2 binding ability to the NCoR/SMRT complex / protein lysine delactylase activity / positive regulation of type B pancreatic cell apoptotic process / p75NTR negatively regulates cell cycle via SC1 ...protein decrotonylase activity / positive regulation of ferroptosis / cornified envelope assembly / : / negative regulation of cardiac muscle cell differentiation / protein de-2-hydroxyisobutyrylase activity / Loss of MECP2 binding ability to the NCoR/SMRT complex / protein lysine delactylase activity / positive regulation of type B pancreatic cell apoptotic process / p75NTR negatively regulates cell cycle via SC1 / random inactivation of X chromosome / histone decrotonylase activity / negative regulation of interleukin-1 production / regulation of ketone metabolic process / nuclear glucocorticoid receptor binding / negative regulation of androgen receptor signaling pathway / histone deacetylase activity, hydrolytic mechanism / histone deacetylase / protein deacetylation / cellular response to fluid shear stress / STAT3 nuclear events downstream of ALK signaling / negative regulation of protein export from nucleus / Notch binding / neural precursor cell proliferation / protein lysine deacetylase activity / negative regulation of JNK cascade / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / cellular response to parathyroid hormone stimulus / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / histone deacetylase activity / response to dexamethasone / Notch-HLH transcription pathway / DNA repair-dependent chromatin remodeling / ubiquitin-specific protease binding / RUNX2 regulates osteoblast differentiation / Association of TriC/CCT with target proteins during biosynthesis / establishment of mitotic spindle orientation / histone deacetylase complex / Regulation of MECP2 expression and activity / negative regulation of tumor necrosis factor production / regulation of multicellular organism growth / positive regulation of TOR signaling / NF-kappaB binding / establishment of skin barrier / estrous cycle / nuclear retinoid X receptor binding / spindle assembly / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / lactation / Regulation of lipid metabolism by PPARalpha / transcription repressor complex / cyclin binding / SUMOylation of transcription cofactors / regulation of mitotic cell cycle / negative regulation of miRNA transcription / cerebellum development / epigenetic regulation of gene expression / positive regulation of protein ubiquitination / Regulation of PTEN gene transcription / transcription corepressor binding / HDACs deacetylate histones / response to nutrient levels / Downregulation of SMAD2/3:SMAD4 transcriptional activity / enzyme activator activity / circadian regulation of gene expression / Heme signaling / cellular response to mechanical stimulus / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / regulation of circadian rhythm / regulation of protein stability / chromatin DNA binding / Nuclear Receptor transcription pathway / NOTCH1 Intracellular Domain Regulates Transcription / Transcriptional regulation of white adipocyte differentiation / positive regulation of protein import into nucleus / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / nuclear matrix / positive regulation of protein phosphorylation / HCMV Early Events / mitotic spindle / : / transcription corepressor activity / response to estradiol / positive regulation of neuron apoptotic process / positive regulation of cold-induced thermogenesis / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / GTPase binding / DNA-binding transcription factor binding / in utero embryonic development / transcription by RNA polymerase II / nuclear body / response to xenobiotic stimulus / negative regulation of DNA-templated transcription / chromatin binding
Similarity search - Function
N-CoR, GPS2-interacting domain / : / G-protein pathway suppressor 2-interacting domain / Histone deacetylase / Histone deacetylase domain / SANT domain profile. / Arginase; Chain A / Myb domain / SANT domain / : ...N-CoR, GPS2-interacting domain / : / G-protein pathway suppressor 2-interacting domain / Histone deacetylase / Histone deacetylase domain / SANT domain profile. / Arginase; Chain A / Myb domain / SANT domain / : / Myb-like DNA-binding domain / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / Homeodomain-like / SANT/Myb domain / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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


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


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more