[English] 日本語
Yorodumi
- PDB-3phd: Crystal structure of human HDAC6 in complex with ubiquitin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3phd
TitleCrystal structure of human HDAC6 in complex with ubiquitin
Components
  • Histone deacetylase 6
  • Polyubiquitin
KeywordsPROTEIN BINDING / HDAC6 / ubiquitin / 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 / negative regulation of aggrephagy / negative regulation of protein-containing complex disassembly / response to misfolded protein / positive regulation of protein oligomerization / type 2 mitophagy / aggresome assembly / : ...negative regulation of hydrogen peroxide metabolic process / cellular response to topologically incorrect protein / polyubiquitinated misfolded protein transport / negative regulation of aggrephagy / negative regulation of protein-containing complex disassembly / response to misfolded protein / positive regulation of protein oligomerization / type 2 mitophagy / aggresome assembly / : / : / protein modification process => GO:0036211 / : / regulation of autophagy of mitochondrion / peroxidase inhibitor activity / Cargo trafficking to the periciliary membrane / deacetylase activity / Transcriptional regulation by RUNX2 / tubulin deacetylase activity / positive regulation of type 2 mitophagy / tubulin deacetylation / lysosome localization / ATPase inhibitor activity / cilium disassembly / misfolded protein binding / positive regulation of intracellular estrogen receptor signaling pathway / aggresome / cytoplasmic ubiquitin ligase complex / regulation of androgen receptor signaling pathway / protein deacetylation / Transferases; Acyltransferases; Aminoacyltransferases / histone deacetylase activity / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / mitochondrion transport along microtubule / positive regulation of protein monoubiquitination / microtubule associated complex / Notch-HLH transcription pathway / negative regulation of gene expression, epigenetic / axonal transport of mitochondrion / RUNX2 regulates osteoblast differentiation / regulation of microtubule-based movement / histone deacetylase complex / cell leading edge / positive regulation of epithelial cell migration / protein quality control for misfolded or incompletely synthesized proteins / dynein complex binding / negative regulation of proteolysis / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Eukaryotic Translation Termination / HSF1 activation / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / Viral mRNA Translation / polyubiquitin modification-dependent protein binding / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / negative regulation of protein-containing complex assembly / GTP hydrolysis and joining of the 60S ribosomal subunit / alpha-tubulin binding / L13a-mediated translational silencing of Ceruloplasmin expression / cilium assembly / Major pathway of rRNA processing in the nucleolus and cytosol / beta-tubulin binding / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / regulation of macroautophagy / multivesicular body / axon cytoplasm / neuron projection morphogenesis / inclusion body / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / regulation of neuron apoptotic process / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Prevention of phagosomal-lysosomal fusion / regulation of mitochondrial membrane potential / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / positive regulation of protein ubiquitination / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A
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) / Herpes Virus-1 ...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 / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-B / Ubiquitin-60S ribosomal protein L40 / Protein deacetylase HDAC6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDong, A. / Qui, W. / Ravichandran, M. / Schuetz, A. / Loppnau, P. / Li, F. / Mackenzie, F. / Kozieradzki, I. / Ouyang, H. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Protein Aggregates Are Recruited to Aggresome by Histone Deacetylase 6 via Unanchored Ubiquitin C Termini.
Authors: Ouyang, H. / Ali, Y.O. / Ravichandran, M. / Dong, A. / Qiu, W. / Mackenzie, F. / Dhe-Paganon, S. / Arrowsmith, C.H. / Zhai, R.G.
History
DepositionNov 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Database references
Revision 1.3Nov 23, 2011Group: Database references
Revision 1.4Feb 8, 2012Group: Database references
Revision 1.5Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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 6
B: Histone deacetylase 6
C: Histone deacetylase 6
D: Histone deacetylase 6
E: Polyubiquitin
F: Polyubiquitin
G: Polyubiquitin
H: Polyubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,18720
Polymers82,4028
Non-polymers78512
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.748, 133.748, 118.768
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein
Histone deacetylase 6 / HD6


Mass: 12023.739 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC6, KIAA0901, JM21 / Plasmid: PET15-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 ROSETTA-R3 / References: UniProt: Q9UBN7, histone deacetylase
#2: Protein
Polyubiquitin


Mass: 8576.831 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB, UBA52, UBCEP2, UBC, RPS27A, UBA80, UBCEP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62988, UniProt: P0CG47*PLUS
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.22 Å3/Da / Density % sol: 61.84 %
Crystal growTemperature: 297 K / pH: 5.6
Details: 15% PEG 3350, 0.1M Ammonium Sulphate, 0.1M Bis-Tris, pH 5.6, temperature 297K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 22204 / Num. obs: 22204 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.2 % / Biso Wilson estimate: 92.68 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 45.8
Reflection shellResolution: 3→3.05 Å / Rmerge(I) obs: 0.767 / Mean I/σ(I) obs: 4.7 / % possible all: 100

-
Processing

Software
NameVersionClassification
Blu-IceGUI (SSRL)data collection
MOLREP9.2phasing
BUSTER2.8.0refinement
Coot0.6model building
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3C5K

3c5k


Resolution: 3→32.72 Å / Cor.coef. Fo:Fc: 0.9073 / Cor.coef. Fo:Fc free: 0.8561 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2648 463 2.09 %RANDOM
Rwork0.2346 ---
all0.2352 22135 --
obs0.2352 22135 --
Displacement parametersBiso mean: 72.86 Å2
Baniso -1Baniso -2Baniso -3
1--3.4578 Å20 Å20 Å2
2---3.4578 Å20 Å2
3---6.9157 Å2
Refine analyzeLuzzati coordinate error obs: 0.422 Å
Refinement stepCycle: LAST / Resolution: 3→32.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3307 0 12 2 3321
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0134002
X-RAY DIFFRACTIONt_angle_deg1.1246482
X-RAY DIFFRACTIONt_dihedral_angle_d9502
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes552
X-RAY DIFFRACTIONt_gen_planes5305
X-RAY DIFFRACTIONt_it340020
X-RAY DIFFRACTIONt_nbd65
X-RAY DIFFRACTIONt_omega_torsion3.88
X-RAY DIFFRACTIONt_other_torsion19.83
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4515
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact36604
LS refinement shellResolution: 3→3.15 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2907 71 2.45 %
Rwork0.2585 2823 -
all0.2593 2894 -

+
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