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- PDB-3c5k: Crystal structure of human HDAC6 zinc finger domain -

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Basic information

Entry
Database: PDB / ID: 3c5k
TitleCrystal structure of human HDAC6 zinc finger domain
ComponentsHistone deacetylase 6
KeywordsHYDROLASE / HDAC6 / Zinc finger / Actin-binding / Chromatin regulator / Cytoplasm / Metal-binding / Nucleus / Phosphoprotein / Repressor / Transcription / Transcription regulation / Ubl conjugation / Zinc-finger / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


negative regulation of hydrogen peroxide metabolic process / cellular response to topologically incorrect protein / polyubiquitinated misfolded protein transport / positive regulation of cellular response to oxidative stress / negative regulation of aggrephagy / positive regulation of cholangiocyte proliferation / response to misfolded protein / positive regulation of protein oligomerization / negative regulation of axon extension involved in axon guidance / type 2 mitophagy ...negative regulation of hydrogen peroxide metabolic process / cellular response to topologically incorrect protein / polyubiquitinated misfolded protein transport / positive regulation of cellular response to oxidative stress / negative regulation of aggrephagy / positive regulation of cholangiocyte proliferation / response to misfolded protein / positive regulation of protein oligomerization / negative regulation of axon extension involved in axon guidance / type 2 mitophagy / positive regulation of RIG-I signaling pathway / negative regulation of protein-containing complex disassembly / peroxidase inhibitor activity / regulation of establishment of protein localization / erythrocyte enucleation / regulation of autophagy of mitochondrion / protein-containing complex disassembly / tubulin deacetylation / Cilium Assembly / regulation of microtubule-based movement / collateral sprouting / tubulin deacetylase activity / Transcriptional regulation by RUNX2 / histone deacetylase activity, hydrolytic mechanism / lysosome localization / negative regulation of microtubule depolymerization / ATPase inhibitor activity / positive regulation of dendrite morphogenesis / cilium disassembly / misfolded protein binding / positive regulation of type 2 mitophagy / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / dendritic spine morphogenesis / protein deacetylation / aggresome assembly / regulation of androgen receptor signaling pathway / regulation of mitochondrion organization / cellular response to misfolded protein / Transferases; Acyltransferases; Aminoacyltransferases / regulation of fat cell differentiation / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / microtubule associated complex / aggresome / cellular response to parathyroid hormone stimulus / response to corticosterone / histone deacetylase activity / positive regulation of intracellular estrogen receptor signaling pathway / response to dexamethasone / Notch-HLH transcription pathway / negative regulation of gene expression, epigenetic / axonal transport of mitochondrion / dynein complex binding / cell leading edge / RUNX2 regulates osteoblast differentiation / response to immobilization stress / protein quality control for misfolded or incompletely synthesized proteins / histone deacetylase complex / positive regulation of epithelial cell migration / cilium assembly / polyubiquitin modification-dependent protein binding / alpha-tubulin binding / regulation of macroautophagy / HSF1 activation / beta-tubulin binding / negative regulation of protein-containing complex assembly / inclusion body / multivesicular body / negative regulation of proteolysis / axon cytoplasm / antiviral innate immune response / response to amphetamine / positive regulation of synaptic transmission, glutamatergic / actin filament organization / epigenetic regulation of gene expression / ubiquitin binding / transcription corepressor binding / intracellular protein transport / Hsp90 protein binding / Late endosomal microautophagy / protein destabilization / beta-catenin binding / regulation of protein stability / caveola / NOTCH1 Intracellular Domain Regulates Transcription / tau protein binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / cellular response to hydrogen peroxide / epidermal growth factor receptor signaling pathway / Chaperone Mediated Autophagy / protein polyubiquitination / Aggrephagy / actin binding / cellular response to heat / microtubule binding / perikaryon / microtubule / regulation of autophagy
Similarity search - Function
Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Zinc/RING finger domain, C3HC4 (zinc finger) ...Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Ureohydrolase domain superfamily / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein deacetylase HDAC6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsDong, A. / Ravichandran, M. / Schuetz, A. / Loppnau, P. / Li, Y. / MacKenzie, F. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. ...Dong, A. / Ravichandran, M. / Schuetz, A. / Loppnau, P. / Li, Y. / MacKenzie, F. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Dhe-Paganon, S. / Min, J. / Ouyang, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of Human HDAC6 zinc finger domain.
Authors: Dong, A. / Ravichandran, M. / Schuetz, A. / Loppnau, P. / Li, Y. / MacKenzie, F. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Dhe- ...Authors: Dong, A. / Ravichandran, M. / Schuetz, A. / Loppnau, P. / Li, Y. / MacKenzie, F. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Dhe-Paganon, S. / Min, J. / Ouyang, H.
History
DepositionJan 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3644
Polymers12,1681
Non-polymers1963
Water2,810156
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.500, 45.109, 55.759
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Histone deacetylase 6 / HD6


Mass: 12167.869 Da / Num. of mol.: 1 / Fragment: Residues 1109-1215
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC6 / Plasmid: pET15-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta-R3 / References: UniProt: Q9UBN7
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.09 Å3/Da / Density % sol: 41.23 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 3.5M Na formate, 100mM Bis-tris propane pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.26 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 26, 2008 / Details: Si(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.26 Å / Relative weight: 1
ReflectionResolution: 1.55→100 Å / Num. all: 15138 / Num. obs: 15138 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 13.3
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 6 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 5.84 / Num. unique all: 1206 / Rsym value: 0.201 / % possible all: 80.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.55→35.07 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.422 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.134 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The Friedel pairs were used in phasing. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Programs ARP/wARP 6.1.1, COOT 0.3.3 have also been used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.22663 486 4.8 %RANDOM
Rwork0.17332 ---
all0.1759 9546 --
obs0.1759 9546 65.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.927 Å2
Baniso -1Baniso -2Baniso -3
1--2.01 Å20 Å20 Å2
2--1.68 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.55→35.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms840 0 3 156 999
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021872
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1511.9161197
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1225107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23624.10339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.75915117
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.831151
X-RAY DIFFRACTIONr_chiral_restr0.0990.2125
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02690
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1870.2407
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2595
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.296
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0230.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.260
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6041.5548
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0432872
X-RAY DIFFRACTIONr_scbond_it1.53375
X-RAY DIFFRACTIONr_scangle_it2.2574.5325
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.186 23 -
Rwork0.199 386 -
obs--37.32 %

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