[English] 日本語
Yorodumi
- PDB-7jvu: Crystal structure of human histone deacetylase 8 (HDAC8) I45T mut... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jvu
TitleCrystal structure of human histone deacetylase 8 (HDAC8) I45T mutation complexed with SAHA
ComponentsHistone deacetylase 8
KeywordsHYDROLASE / Histone deacetylase / Cornelia de Lange Syndrome (CdLS)
Function / homology
Function and homology information


histone decrotonylase activity / histone H4K16 deacetylase activity, hydrolytic mechanism / histone H4K5 deacetylase activity, hydrolytic mechanism / histone H4K8 deacetylase activity, hydrolytic mechanism / histone H3K4 deacetylase activity, hydrolytic mechanism / histone H3K14 deacetylase activity, hydrolytic mechanism / histone H4K12 deacetylase activity, hydrolytic mechanism / histone deacetylase / histone H3K9 deacetylase activity, hydrolytic mechanism / regulation of telomere maintenance ...histone decrotonylase activity / histone H4K16 deacetylase activity, hydrolytic mechanism / histone H4K5 deacetylase activity, hydrolytic mechanism / histone H4K8 deacetylase activity, hydrolytic mechanism / histone H3K4 deacetylase activity, hydrolytic mechanism / histone H3K14 deacetylase activity, hydrolytic mechanism / histone H4K12 deacetylase activity, hydrolytic mechanism / histone deacetylase / histone H3K9 deacetylase activity, hydrolytic mechanism / regulation of telomere maintenance / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / mitotic sister chromatid cohesion / histone deacetylase activity / nuclear chromosome / Notch-HLH transcription pathway / histone deacetylase complex / negative regulation of protein ubiquitination / Hsp70 protein binding / Resolution of Sister Chromatid Cohesion / HDACs deacetylate histones / Hsp90 protein binding / regulation of protein stability / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Separation of Sister Chromatids / heterochromatin formation / chromatin organization / DNA-binding transcription factor binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Histone deacetylase / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily
Similarity search - Domain/homology
: / OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE / Histone deacetylase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5004765401 Å
AuthorsOsko, J.D. / Christianson, D.W. / Decroos, C. / Porter, N.J. / Lee, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM49758 United States
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Structural analysis of histone deacetylase 8 mutants associated with Cornelia de Lange Syndrome spectrum disorders.
Authors: Osko, J.D. / Porter, N.J. / Decroos, C. / Lee, M.S. / Watson, P.R. / Raible, S.E. / Krantz, I.D. / Deardorff, M.A. / Christianson, D.W.
History
DepositionAug 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone deacetylase 8
B: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,69017
Polymers86,4402
Non-polymers1,25015
Water11,440635
1
A: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8769
Polymers43,2201
Non-polymers6568
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8148
Polymers43,2201
Non-polymers5947
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.314, 84.118, 94.281
Angle α, β, γ (deg.)90.000, 99.064, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Histone deacetylase 8 / HD8


Mass: 43219.938 Da / Num. of mol.: 2 / Mutation: I45T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC8, HDACL1, CDA07 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BY41, histone deacetylase

-
Non-polymers , 5 types, 650 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-SHH / OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE / SAHA


Mass: 264.320 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N2O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 635 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.07 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 M imidazole, pH 7.0, 15% PEG35000, 4 mM TCEP / PH range: 7-8

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 15, 2015
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→55.91 Å / Num. obs: 131305 / % possible obs: 99.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 16.8670373583 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.034 / Net I/σ(I): 19.5
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 130929 / CC1/2: 0.757 / Rpim(I) all: 0.389 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3EWF

3ewf


Resolution: 1.5004765401→15.9951076656 Å / SU ML: 0.129063430768 / Cross valid method: FREE R-VALUE / σ(F): 1.33718454107 / Phase error: 19.0740531924
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.184587196948 6593 5.03690008709 %
Rwork0.164399381995 124301 -
obs0.165440737685 130894 99.8725784177 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.8636882906 Å2
Refinement stepCycle: LAST / Resolution: 1.5004765401→15.9951076656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5597 0 72 635 6304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00523781757195914
X-RAY DIFFRACTIONf_angle_d0.8052324292828038
X-RAY DIFFRACTIONf_chiral_restr0.0527454343713875
X-RAY DIFFRACTIONf_plane_restr0.0053862959911041
X-RAY DIFFRACTIONf_dihedral_angle_d7.121198346424700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5005-1.51750.2684836237022040.2516172539794083X-RAY DIFFRACTION98.2130584192
1.5175-1.53540.2722970553012050.240527634014157X-RAY DIFFRACTION99.9541704858
1.5354-1.55410.2740818746472090.2304206827184135X-RAY DIFFRACTION99.9769850403
1.5541-1.57370.2280021740292200.2196154945344134X-RAY DIFFRACTION99.9770378875
1.5737-1.59440.2207396934492350.2082248722254105X-RAY DIFFRACTION100
1.5944-1.61620.2496436010852310.210559364644144X-RAY DIFFRACTION99.9771480804
1.6162-1.63930.2282404153382170.1948472872734104X-RAY DIFFRACTION100
1.6393-1.66370.227739168412040.1948485259614173X-RAY DIFFRACTION99.954327472
1.6637-1.68970.203957012562110.1836541021934110X-RAY DIFFRACTION99.9768625636
1.6897-1.71740.2293339095392040.1809615087044187X-RAY DIFFRACTION100
1.7174-1.7470.1885923402892380.1766076171794123X-RAY DIFFRACTION100
1.747-1.77870.1950245791592240.1728881441094144X-RAY DIFFRACTION100
1.7787-1.81280.1890383452861950.1779543177634097X-RAY DIFFRACTION99.976706266
1.8128-1.84980.2202602079272220.1761204784644172X-RAY DIFFRACTION100
1.8498-1.890.2047649246422210.1708684702394133X-RAY DIFFRACTION100
1.89-1.93390.1980255305842000.1707404887974130X-RAY DIFFRACTION100
1.9339-1.98210.1968917596082060.1756250994254196X-RAY DIFFRACTION99.9772882126
1.9821-2.03560.188771103072090.1741624377944127X-RAY DIFFRACTION100
2.0356-2.09540.1967726123752360.1659901980314120X-RAY DIFFRACTION100
2.0954-2.16290.1899929123562300.1703559921774146X-RAY DIFFRACTION100
2.1629-2.240.1814114841432180.1650075195044145X-RAY DIFFRACTION100
2.24-2.32940.1862430718322250.1626404591494148X-RAY DIFFRACTION100
2.3294-2.43510.2034434481452210.162186132194146X-RAY DIFFRACTION100
2.4351-2.5630.1756987214952460.1623514071084148X-RAY DIFFRACTION99.9772468714
2.563-2.72280.1874206920222480.163088178584114X-RAY DIFFRACTION100
2.7228-2.93180.1800224630852290.1670592933194162X-RAY DIFFRACTION100
2.9318-3.22470.1872583685372320.1642327675854147X-RAY DIFFRACTION100
3.2247-3.68630.1790554233691920.154960767654205X-RAY DIFFRACTION100
3.6863-4.62570.1441170594542350.1306876553634181X-RAY DIFFRACTION100
4.6257-15.9950.1541580794932260.1448534894434185X-RAY DIFFRACTION98.262419247

+
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