[English] 日本語
Yorodumi
- PDB-8eqi: Crystal Structure of Danio rerio histone deacetylase 6 catalytic ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8eqi
TitleCrystal Structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with cyclopeptide des4.2.0
Components
  • Cyclopeptide des4.2.0
  • Hdac6 protein
KeywordsHYDROLASE/INHIBITOR / Hydrolase / histone deacetylase / inhibitor / metallohydrolase / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


negative regulation of cellular component organization / positive regulation of cellular component organization / regulation of biological quality / tubulin deacetylase activity / mitochondrion localization / swimming behavior / definitive hemopoiesis / regulation of microtubule-based process / protein lysine deacetylase activity / potassium ion binding ...negative regulation of cellular component organization / positive regulation of cellular component organization / regulation of biological quality / tubulin deacetylase activity / mitochondrion localization / swimming behavior / definitive hemopoiesis / regulation of microtubule-based process / protein lysine deacetylase activity / potassium ion binding / response to stress / hematopoietic progenitor cell differentiation / transferase activity / chromatin organization / actin binding / angiogenesis / perikaryon / axon / dendrite / centrosome / zinc ion binding / nucleus / cytoplasm
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 / Ureohydrolase domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
: / Protein deacetylase HDAC6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWatson, P.R. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM49758 United States
CitationJournal: Acs Chem.Biol. / Year: 2023
Title: Macrocyclic Octapeptide Binding and Inferences on Protein Substrate Binding to Histone Deacetylase 6.
Authors: Watson, P.R. / Gupta, S. / Hosseinzadeh, P. / Brown, B.P. / Baker, D. / Christianson, D.W.
History
DepositionOct 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.details
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hdac6 protein
B: Hdac6 protein
F: Cyclopeptide des4.2.0
G: Cyclopeptide des4.2.0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,88810
Polymers82,6014
Non-polymers2876
Water5,278293
1
A: Hdac6 protein
F: Cyclopeptide des4.2.0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4445
Polymers41,3012
Non-polymers1443
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-42 kcal/mol
Surface area12790 Å2
MethodPISA
2
B: Hdac6 protein
G: Cyclopeptide des4.2.0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4445
Polymers41,3012
Non-polymers1443
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-43 kcal/mol
Surface area13100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.450, 92.030, 153.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Hdac6 protein / Histone Deacetylase 6


Mass: 40285.484 Da / Num. of mol.: 2 / Fragment: catalytic domain 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: hdac6 / Production host: Escherichia coli (E. coli) / References: UniProt: A7YT55
#2: Protein/peptide Cyclopeptide des4.2.0


Mass: 1015.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 39.098 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100nL of 10mg/mL HDAC6 with 100nL precipitant (0.2 M ammonium tartrate dibasic pH 7.0, 20% w/v polyethylene glycol 3,350) followed by 25 nL of precipitant solution containing crystal seeds ...Details: 100nL of 10mg/mL HDAC6 with 100nL precipitant (0.2 M ammonium tartrate dibasic pH 7.0, 20% w/v polyethylene glycol 3,350) followed by 25 nL of precipitant solution containing crystal seeds of the HDAC6 complex with octapeptide inhibitor des4.3.1

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→78.89 Å / Num. obs: 111093 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 14.16 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.256 / Rpim(I) all: 0.115 / Net I/σ(I): 9.1
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 1.037 / Num. unique obs: 10837 / CC1/2: 0.61 / Rpim(I) all: 0.471

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
Zanudadata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB: 5EEM

5eem


Resolution: 2→78.89 Å / SU ML: 0.1997 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.2824
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2721 2820 5.08 %
Rwork0.2355 52713 -
obs0.2374 55533 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.16 Å2
Refinement stepCycle: LAST / Resolution: 2→78.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5398 0 144 293 5835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00735675
X-RAY DIFFRACTIONf_angle_d0.93097707
X-RAY DIFFRACTIONf_chiral_restr0.0542847
X-RAY DIFFRACTIONf_plane_restr0.00951004
X-RAY DIFFRACTIONf_dihedral_angle_d21.6986780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.28861500.26062556X-RAY DIFFRACTION99.52
2.03-2.070.29511460.24772575X-RAY DIFFRACTION99.67
2.07-2.110.3251300.24422608X-RAY DIFFRACTION99.78
2.11-2.150.28181290.25312640X-RAY DIFFRACTION99.57
2.15-2.20.30761330.23872589X-RAY DIFFRACTION99.63
2.2-2.250.29441500.23792593X-RAY DIFFRACTION99.75
2.25-2.310.26511390.2352621X-RAY DIFFRACTION99.64
2.31-2.370.28021450.23312596X-RAY DIFFRACTION99.85
2.37-2.440.29371360.23072617X-RAY DIFFRACTION99.75
2.44-2.520.26121300.23232629X-RAY DIFFRACTION99.64
2.52-2.610.25321250.23072642X-RAY DIFFRACTION99.75
2.61-2.710.26821350.23832640X-RAY DIFFRACTION99.82
2.71-2.840.28911380.24312622X-RAY DIFFRACTION99.86
2.84-2.990.32421360.24052628X-RAY DIFFRACTION99.78
2.99-3.170.30571480.24842657X-RAY DIFFRACTION99.79
3.17-3.420.22061350.24982657X-RAY DIFFRACTION99.79
3.42-3.760.28121360.22992654X-RAY DIFFRACTION99.75
3.76-4.310.25581520.20662674X-RAY DIFFRACTION99.86
4.31-5.430.20071610.21292715X-RAY DIFFRACTION99.65
5.43-78.890.28111660.24872800X-RAY DIFFRACTION98.64

+
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