[English] 日本語
Yorodumi
- PDB-5z93: Crystal Structure of SIRT3 in complex with H3K9bhb peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5z93
TitleCrystal Structure of SIRT3 in complex with H3K9bhb peptide
Components
  • Gene for histone H3 (germline gene)
  • NAD-dependent protein deacetylase sirtuin-3, mitochondrial
KeywordsHYDROLASE / Rossmann fold
Function / homology
Function and homology information


positive regulation of catalase activity / positive regulation of ceramide biosynthetic process / peptidyl-lysine deacetylation / positive regulation of superoxide dismutase activity / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / protein deacetylation / Regulation of FOXO transcriptional activity by acetylation / NAD+ binding ...positive regulation of catalase activity / positive regulation of ceramide biosynthetic process / peptidyl-lysine deacetylation / positive regulation of superoxide dismutase activity / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / protein deacetylation / Regulation of FOXO transcriptional activity by acetylation / NAD+ binding / negative regulation of reactive oxygen species metabolic process / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / aerobic respiration / Transcriptional activation of mitochondrial biogenesis / positive regulation of insulin secretion / negative regulation of ERK1 and ERK2 cascade / structural constituent of chromatin / nucleosome / transferase activity / sequence-specific DNA binding / mitochondrial matrix / enzyme binding / protein-containing complex / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily / Histone H3 signature 1. ...SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily / Histone H3 signature 1. / Histone H3/CENP-A / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NAD-dependent protein deacetylase sirtuin-3, mitochondrial / Gene for histone H3 (germline gene)
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.945 Å
AuthorsZhang, X. / Li, H.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: To Be Published
Title: Crystal Structure of SIRT3 in complex with H3K9bhb peptide
Authors: Zhang, X. / Li, H.
History
DepositionFeb 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
B: Gene for histone H3 (germline gene)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5573
Polymers32,4912
Non-polymers651
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-4 kcal/mol
Surface area13020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.361, 86.025, 88.431
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein NAD-dependent protein deacetylase sirtuin-3, mitochondrial / hSIRT3 / Regulatory protein SIR2 homolog 3 / SIR2-like protein 3


Mass: 31427.162 Da / Num. of mol.: 1 / Fragment: UNP residues 117-399
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT3, SIR2L3 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9NTG7, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide Gene for histone H3 (germline gene)


Mass: 1064.195 Da / Num. of mol.: 1 / Fragment: UNP residues 7-16 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: V9H1G0
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 1.95 Å3/Da / Density % sol: 37.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M MES pH 6.5, 25% PEG 1000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.945→50 Å / Num. obs: 19211 / % possible obs: 99.2 % / Redundancy: 6.2 % / Net I/σ(I): 24.7
Reflection shellResolution: 1.95→1.98 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.945→31.214 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2098 1944 10.12 %
Rwork0.1608 --
obs0.166 19211 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.945→31.214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2204 0 1 222 2427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062258
X-RAY DIFFRACTIONf_angle_d0.8293072
X-RAY DIFFRACTIONf_dihedral_angle_d17.8491358
X-RAY DIFFRACTIONf_chiral_restr0.052348
X-RAY DIFFRACTIONf_plane_restr0.006401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9452-1.99390.26971190.2041150X-RAY DIFFRACTION94
1.9939-2.04780.2471180.18571238X-RAY DIFFRACTION100
2.0478-2.1080.27841100.1821238X-RAY DIFFRACTION100
2.108-2.17610.25081510.1851201X-RAY DIFFRACTION100
2.1761-2.25380.23621290.17371233X-RAY DIFFRACTION99
2.2538-2.3440.24351520.1711205X-RAY DIFFRACTION100
2.344-2.45070.25091510.1661220X-RAY DIFFRACTION100
2.4507-2.57980.2381560.17341216X-RAY DIFFRACTION99
2.5798-2.74130.24311250.17121239X-RAY DIFFRACTION100
2.7413-2.95290.23631270.18471257X-RAY DIFFRACTION100
2.9529-3.24970.22361390.16861244X-RAY DIFFRACTION99
3.2497-3.71930.19731400.15371248X-RAY DIFFRACTION98
3.7193-4.68340.16331600.12571243X-RAY DIFFRACTION99
4.6834-31.21770.18711670.15631335X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1640.01120.13370.35080.12730.15890.034-0.05110.0492-0.00060.0163-0.19480.08820.11960.00010.23620.025-0.00660.29210.00060.24084.2759-30.710134.8077
20.21250.0559-0.20510.0118-0.04550.1892-0.48820.0868-0.0718-0.65960.21560.7832-0.3471-1.0039-0.02010.46260.0836-0.11220.3875-0.03150.3482-10.7653-11.661823.299
30.42710.13880.17320.3014-0.18460.22980.0464-0.16730.33030.15550.02970.2312-0.2431-0.45780.00010.29710.02720.00960.2805-0.02470.2809-17.523-7.93810.3145
40.1428-0.010.22870.2745-0.35290.5021-0.0573-0.02550.01650.0125-0.0425-0.1031-0.20450.0859-0.00010.2273-0.0097-0.00070.2241-0.0010.24691.8889-16.207817.7239
50.524-0.28240.42750.5965-0.18230.7897-0.0270.01220.0319-0.09570.0081-0.02360.0958-0.008300.19520.013-0.00430.2216-0.00710.2076-4.5463-18.19089.6194
60.56210.258-0.12580.6187-0.45630.4435-0.0864-0.19630.00940.0843-0.00940.14690.036-0.130500.22670.0148-0.00080.2495-0.01130.2656-5.4887-28.307632.1036
70.0575-0.07770.00590.1007-0.01470.001-0.41080.30010.61640.40220.2199-1.0606-0.26230.16490.00370.6832-0.1882-0.07160.51780.05960.563310.3591-8.687832.6897
80.06590.05980.08620.21020.0580.10030.3038-0.1941-0.09040.4677-0.0928-0.0540.1473-0.3255-0.00310.24220.0143-0.01360.3441-0.00940.2859-13.7527-25.997811.3682
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 122 through 144 )
2X-RAY DIFFRACTION2chain 'A' and (resid 145 through 161 )
3X-RAY DIFFRACTION3chain 'A' and (resid 162 through 199 )
4X-RAY DIFFRACTION4chain 'A' and (resid 200 through 261 )
5X-RAY DIFFRACTION5chain 'A' and (resid 262 through 327 )
6X-RAY DIFFRACTION6chain 'A' and (resid 328 through 379 )
7X-RAY DIFFRACTION7chain 'A' and (resid 380 through 395 )
8X-RAY DIFFRACTION8chain 'B' and (resid 7 through 13 )

+
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