[English] 日本語
Yorodumi
- PDB-8hly: Crystal structure of SIRT3 in complex with H3K23la peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8hly
TitleCrystal structure of SIRT3 in complex with H3K23la peptide
Components
  • H3K23la peptide
  • NAD-dependent protein deacetylase sirtuin-3, mitochondrial
KeywordsHYDROLASE / SIRT3 / Lysine lactylation eraser
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 / protein deacetylation / NAD-dependent histone deacetylase activity / 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 / protein deacetylation / NAD-dependent histone deacetylase activity / 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 / transferase activity / sequence-specific DNA binding / mitochondrial matrix / enzyme binding / protein-containing complex / mitochondrion / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Sirtuin, catalytic core small domain superfamily / Sirtuin family / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
(2S)-2-HYDROXYPROPANOIC ACID / NAD-dependent protein deacetylase sirtuin-3, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhuming, F. / Hao, Q.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC) Hong Kong
CitationJournal: Iscience / Year: 2023
Title: Identification of SIRT3 as an eraser of H4K16la.
Authors: Fan, Z. / Liu, Z. / Zhang, N. / Wei, W. / Cheng, K. / Sun, H. / Hao, Q.
History
DepositionDec 1, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
B: H3K23la peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3668
Polymers31,8722
Non-polymers4946
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-6 kcal/mol
Surface area12440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.043, 84.763, 89.187
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, 2 molecules AB

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


Mass: 31253.010 Da / Num. of mol.: 1
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, protein acetyllysine N-acetyltransferase
#2: Protein/peptide H3K23la peptide


Mass: 618.726 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: residues 21-26 of histone H3, with lactylated Lys-23
Source: (synth.) Homo sapiens (human)

-
Non-polymers , 5 types, 175 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn
#6: Chemical ChemComp-2OP / (2S)-2-HYDROXYPROPANOIC ACID


Mass: 90.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M BIS-TRIS pH at 6.5, 28% (w/v) Polyethylene glycol monomethyl ether 2000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97847 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97847 Å / Relative weight: 1
ReflectionResolution: 1.998→44.593 Å / Num. obs: 25433 / % possible obs: 95.93 % / Redundancy: 1.5 % / Biso Wilson estimate: 22.99 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.03378 / Rpim(I) all: 0.03378 / Rrim(I) all: 0.04777 / Net I/σ(I): 15.12
Reflection shellResolution: 1.998→2.07 Å / Redundancy: 1 % / Rmerge(I) obs: 0.07989 / Mean I/σ(I) obs: 3.48 / Num. unique obs: 1294 / CC1/2: 1 / CC star: 1 / Rpim(I) all: 0.07989 / Rrim(I) all: 0.113 / % possible all: 72.33

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→44.59 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2026 2561 10.07 %
Rwork0.1559 --
obs0.1605 25433 77.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→44.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2165 0 28 169 2362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042254
X-RAY DIFFRACTIONf_angle_d0.7143062
X-RAY DIFFRACTIONf_dihedral_angle_d5.821311
X-RAY DIFFRACTIONf_chiral_restr0.045346
X-RAY DIFFRACTIONf_plane_restr0.007398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.2599660.2144575X-RAY DIFFRACTION35
2.04-2.080.2511820.2116689X-RAY DIFFRACTION42
2.08-2.120.2287760.1874755X-RAY DIFFRACTION46
2.12-2.170.22971010.1987843X-RAY DIFFRACTION51
2.17-2.230.2311000.1694929X-RAY DIFFRACTION56
2.23-2.290.22151000.1591988X-RAY DIFFRACTION60
2.29-2.350.21541270.15681097X-RAY DIFFRACTION66
2.35-2.430.2151330.14591161X-RAY DIFFRACTION72
2.43-2.520.18831570.14091352X-RAY DIFFRACTION82
2.52-2.620.19121580.14681437X-RAY DIFFRACTION88
2.62-2.740.2181660.14181606X-RAY DIFFRACTION96
2.74-2.880.20661840.15181596X-RAY DIFFRACTION99
2.88-3.060.18661790.14351664X-RAY DIFFRACTION100
3.06-3.30.19411950.1481636X-RAY DIFFRACTION100
3.3-3.630.18151850.13881640X-RAY DIFFRACTION100
3.63-4.150.17251730.13391647X-RAY DIFFRACTION100
4.15-5.230.18881860.14391619X-RAY DIFFRACTION100
5.24-44.590.23831930.20971638X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -4.8497 Å / Origin y: -18.3698 Å / Origin z: 19.6547 Å
111213212223313233
T0.1454 Å2-0.0012 Å20.0041 Å2-0.1528 Å2-0.0268 Å2--0.1846 Å2
L0.7805 °2-0.3428 °20.4894 °2-0.817 °2-0.7951 °2--2.3439 °2
S-0.0716 Å °-0.103 Å °0.0701 Å °0.1111 Å °0.0337 Å °0.0018 Å °-0.168 Å °0.0094 Å °0.0449 Å °
Refinement TLS groupSelection details: all

+
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://pdbjlvh1.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