[English] 日本語
Yorodumi
- PDB-5dc8: Crystal structure of H142A-Y306F HDAC8 in complex with a tetrapep... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dc8
TitleCrystal structure of H142A-Y306F HDAC8 in complex with a tetrapeptide substrate
Components
  • Fluor-de-Lys tetrapeptide assay substrate
  • Histone deacetylase 8
KeywordsHYDROLASE / histone deacetylase 8 / arginase fold / deacetylase / enzyme-substrate complex
Function / homology
Function and homology information


histone decrotonylase activity / histone deacetylase activity, hydrolytic mechanism / histone deacetylase / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / regulation of telomere maintenance / mitotic sister chromatid cohesion / histone deacetylase activity / nuclear chromosome / Notch-HLH transcription pathway ...histone decrotonylase activity / histone deacetylase activity, hydrolytic mechanism / histone deacetylase / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / regulation of telomere maintenance / mitotic sister chromatid cohesion / histone deacetylase activity / nuclear chromosome / Notch-HLH transcription pathway / histone deacetylase complex / Hsp70 protein binding / negative regulation of protein ubiquitination / 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 domain / Arginase; Chain A / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Histone deacetylase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsDecroos, C. / Lee, M.S. / Christianson, D.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM49758 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM40602 United States
CitationJournal: Biochemistry / Year: 2016
Title: General Base-General Acid Catalysis in Human Histone Deacetylase 8.
Authors: Gantt, S.M. / Decroos, C. / Lee, M.S. / Gullett, L.E. / Bowman, C.M. / Christianson, D.W. / Fierke, C.A.
History
DepositionAug 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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_conn_type
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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_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_conn_type.id
Revision 1.5Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone deacetylase 8
B: Histone deacetylase 8
C: Fluor-de-Lys tetrapeptide assay substrate
D: Fluor-de-Lys tetrapeptide assay substrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,44312
Polymers87,9724
Non-polymers4718
Water14,952830
1
A: Histone deacetylase 8
C: Fluor-de-Lys tetrapeptide assay substrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2226
Polymers43,9862
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-40 kcal/mol
Surface area14430 Å2
MethodPISA
2
B: Histone deacetylase 8
D: Fluor-de-Lys tetrapeptide assay substrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2226
Polymers43,9862
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-40 kcal/mol
Surface area14830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.800, 97.887, 104.612
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein Histone deacetylase 8 / HD8


Mass: 43148.926 Da / Num. of mol.: 2 / Mutation: H142A, Y306F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC8, HDACL1, CDA07 / Plasmid: pHD2-Xa-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BY41, histone deacetylase
#2: Protein/peptide Fluor-de-Lys tetrapeptide assay substrate


Mass: 836.980 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 4 types, 838 molecules

#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: obtained synthetically / Formula: K
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 830 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris (pH 8.0), 10% (w/v) PEG 35000, and 4 mM TCEP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 20, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.3→49 Å / Num. obs: 208317 / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.8
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.855 / Mean I/σ(I) obs: 2.7 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIXdev_1833refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EWF

3ewf


Resolution: 1.3→49 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 12.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1489 10474 5.03 %
Rwork0.1282 --
obs0.1293 208197 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5742 0 18 830 6590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086743
X-RAY DIFFRACTIONf_angle_d1.269251
X-RAY DIFFRACTIONf_dihedral_angle_d12.1662524
X-RAY DIFFRACTIONf_chiral_restr0.084979
X-RAY DIFFRACTIONf_plane_restr0.0071236
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.31370.22763380.19746045X-RAY DIFFRACTION93
1.3137-1.32920.23033380.18446527X-RAY DIFFRACTION100
1.3292-1.34540.1973770.17366545X-RAY DIFFRACTION100
1.3454-1.36240.19943450.16376569X-RAY DIFFRACTION100
1.3624-1.38040.20913410.16276557X-RAY DIFFRACTION100
1.3804-1.39930.19983880.16056502X-RAY DIFFRACTION100
1.3993-1.41930.17953710.14866530X-RAY DIFFRACTION100
1.4193-1.44050.16583180.13766579X-RAY DIFFRACTION100
1.4405-1.4630.16053550.12766557X-RAY DIFFRACTION100
1.463-1.4870.13783340.11386548X-RAY DIFFRACTION100
1.487-1.51260.14223640.10846514X-RAY DIFFRACTION100
1.5126-1.54010.13473620.10216595X-RAY DIFFRACTION100
1.5401-1.56970.14543590.1056554X-RAY DIFFRACTION100
1.5697-1.60180.13413470.10516565X-RAY DIFFRACTION100
1.6018-1.63660.15153440.1046576X-RAY DIFFRACTION100
1.6366-1.67470.1363260.09886601X-RAY DIFFRACTION100
1.6747-1.71660.12563490.10386598X-RAY DIFFRACTION100
1.7166-1.7630.12583520.10826586X-RAY DIFFRACTION100
1.763-1.81480.13673480.10766580X-RAY DIFFRACTION100
1.8148-1.87340.1343300.11016601X-RAY DIFFRACTION100
1.8734-1.94040.13243730.11216610X-RAY DIFFRACTION100
1.9404-2.01810.1343690.11836618X-RAY DIFFRACTION100
2.0181-2.10990.14793240.12116593X-RAY DIFFRACTION100
2.1099-2.22120.13273530.12456624X-RAY DIFFRACTION100
2.2212-2.36030.14743150.13266689X-RAY DIFFRACTION100
2.3603-2.54260.15933570.13376652X-RAY DIFFRACTION100
2.5426-2.79840.15013420.14046706X-RAY DIFFRACTION100
2.7984-3.20330.15713560.14016693X-RAY DIFFRACTION100
3.2033-4.03550.14693620.12636782X-RAY DIFFRACTION100
4.0355-48.97830.14573370.13847027X-RAY DIFFRACTION100

+
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