[English] 日本語
Yorodumi
- PDB-5bwo: Crystal Structure of Human SIRT3 in Complex with a Palmitoyl H3K9... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bwo
TitleCrystal Structure of Human SIRT3 in Complex with a Palmitoyl H3K9 Peptide
Components
  • NAD-dependent protein deacetylase sirtuin-3, mitochondrial
  • Palmitoyl H3K9 Peptide
KeywordsPEPTIDE/HYDROLASE / Hydrolase / PEPTIDE-HYDROLASE complex
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 / nucleosomal DNA binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / aerobic respiration / euchromatin / Transcriptional activation of mitochondrial biogenesis / positive regulation of insulin secretion / negative regulation of ERK1 and ERK2 cascade / structural constituent of chromatin / nucleosome / transferase activity / positive regulation of cell growth / sequence-specific DNA binding / mitochondrial matrix / protein heterodimerization activity / enzyme binding / protein-containing complex / mitochondrion / 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 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PALMITIC ACID / Histone H3.3C / NAD-dependent protein deacetylase sirtuin-3, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.376 Å
AuthorsGai, W. / Jiang, H. / Liu, D.
CitationJournal: Febs Lett. / Year: 2016
Title: Crystal structures of SIRT3 reveal that the alpha 2-alpha 3 loop and alpha 3-helix affect the interaction with long-chain acyl lysine.
Authors: Gai, W. / Li, H. / Jiang, H. / Long, Y. / Liu, D.
History
DepositionJun 8, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Palmitoyl H3K9 Peptide
A: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8174
Polymers35,4962
Non-polymers3222
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.445, 54.636, 113.203
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein/peptide Palmitoyl H3K9 Peptide


Mass: 1093.194 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: Q6NXT2*PLUS
#2: Protein NAD-dependent protein deacetylase sirtuin-3, mitochondrial / hSIRT3 / Regulatory protein SIR2 homolog 3 / SIR2-like protein 3


Mass: 34402.445 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 118-399
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT3, SIR2L3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NTG7, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#3: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsThe 4th residue of the peptide that the author used for the cocrystallization was indeed a ...The 4th residue of the peptide that the author used for the cocrystallization was indeed a palmitoylated lysine. It is composed of residue LYS and PLM. In fact, the palmitoyl lysine was covered very well by the electron density on the 2Fo-Fc map.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 35.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2M Ammonium formate, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 21, 2015 / Details: M
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.37→50 Å / Num. obs: 11428 / % possible obs: 99.1 % / Redundancy: 7.79 % / Net I/σ(I): 15.2
Reflection shellResolution: 2.37→2.45 Å / Mean I/σ(I) obs: 6.3 / % possible all: 99.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PHENIX1.10.1_2155model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GLR

3glr


Resolution: 2.376→29.149 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1128 10 %RANDOM
Rwork0.2393 ---
obs0.2441 11282 99.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.376→29.149 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2215 0 18 104 2337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022288
X-RAY DIFFRACTIONf_angle_d0.5693109
X-RAY DIFFRACTIONf_dihedral_angle_d10.1591370
X-RAY DIFFRACTIONf_chiral_restr0.043349
X-RAY DIFFRACTIONf_plane_restr0.004403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3763-2.48440.29251370.25891228X-RAY DIFFRACTION98
2.4844-2.61530.29461390.27361249X-RAY DIFFRACTION99
2.6153-2.7790.30161370.27311250X-RAY DIFFRACTION99
2.779-2.99340.29951390.27171242X-RAY DIFFRACTION99
2.9934-3.29420.321390.27621260X-RAY DIFFRACTION99
3.2942-3.770.26321410.23871271X-RAY DIFFRACTION99
3.77-4.74650.29951430.20851289X-RAY DIFFRACTION99
4.7465-29.15110.26231530.21111365X-RAY DIFFRACTION99

+
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