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- PDB-5zgc: Crystal Structure of SIRT3 in complex with H4K16bhb peptide -

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Basic information

Entry
Database: PDB / ID: 5zgc
TitleCrystal Structure of SIRT3 in complex with H4K16bhb peptide
Components
  • Histone H4K16bhb peptide
  • 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 / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / aerobic respiration / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / Transcriptional activation of mitochondrial biogenesis / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / negative regulation of ERK1 and ERK2 cascade / DNA Damage/Telomere Stress Induced Senescence / positive regulation of insulin secretion / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Processing of DNA double-strand break ends / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / transferase activity / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / sequence-specific DNA binding / chromosome, telomeric region / mitochondrial matrix / Amyloid fiber formation / protein heterodimerization activity / enzyme binding / protein-containing complex / mitochondrion / DNA binding / RNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / 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 H4, conserved site ...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 H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone-fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone H4 / NAD-dependent protein deacetylase sirtuin-3, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLi, H. / Zhang, X.
CitationJournal: To be published
Title: Crystal Structure of SIRT3 in complex with H4K16bhb peptide
Authors: Li, H. / Zhang, X.
History
DepositionMar 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
B: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
C: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
D: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
E: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
F: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
G: Histone H4K16bhb peptide
H: Histone H4K16bhb peptide
I: Histone H4K16bhb peptide
J: Histone H4K16bhb peptide
K: Histone H4K16bhb peptide
L: Histone H4K16bhb peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,00617
Polymers190,67912
Non-polymers3275
Water1,09961
1
A: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
G: Histone H4K16bhb peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8453
Polymers31,7802
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
H: Histone H4K16bhb peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8453
Polymers31,7802
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
I: Histone H4K16bhb peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8453
Polymers31,7802
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
K: Histone H4K16bhb peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8453
Polymers31,7802
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
J: Histone H4K16bhb peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8453
Polymers31,7802
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
L: Histone H4K16bhb peptide


Theoretical massNumber of molelcules
Total (without water)31,7802
Polymers31,7802
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.512, 138.512, 242.876
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
NAD-dependent protein deacetylase sirtuin-3, mitochondrial / hSIRT3


Mass: 30495.225 Da / Num. of mol.: 6 / Fragment: UNP residues 121-394
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT3 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9NTG7, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide
Histone H4K16bhb peptide


Mass: 1284.535 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P62805*PLUS
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1M Bicine pH 9.0, 10% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 25, 2018 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 52894 / % possible obs: 99.6 % / Redundancy: 7.5 % / Biso Wilson estimate: 69.03 Å2 / Rpim(I) all: 0.039 / Net I/σ(I): 13.6
Reflection shellResolution: 2.9→2.97 Å / Rpim(I) all: 0.47

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Processing

Software
NameVersionClassification
PHENIX1.14_3247refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
Cootmodel building
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→43.157 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2798 2624 4.96 %0
Rwork0.2244 50270 --
obs0.2271 52894 99.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 179.09 Å2 / Biso mean: 72.3898 Å2 / Biso min: 24.46 Å2
Refinement stepCycle: final / Resolution: 2.9→43.157 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12363 0 5 61 12429
Biso mean--90 55.54 -
Num. residues----1572
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8996-2.95230.37281400.30852540268098
2.9523-3.00910.36671540.302126052759100
3.0091-3.07050.33321330.292726102743100
3.0705-3.13720.34921240.297525932717100
3.1372-3.21020.34441330.282326302763100
3.2102-3.29040.30061380.26562580271899
3.2904-3.37940.34971220.25826352757100
3.3794-3.47880.34461440.262626162760100
3.4788-3.5910.34571520.260226002752100
3.591-3.71930.34611440.252426212765100
3.7193-3.86810.29531690.239226082777100
3.8681-4.0440.29361400.218826392779100
4.044-4.25710.27921260.199126482774100
4.2571-4.52350.20541330.192926762809100
4.5235-4.87230.24071310.18342646277799
4.8723-5.36190.24111300.190526922822100
5.3619-6.13580.26861410.212527012842100
6.1358-7.72330.27571480.221227422890100
7.7233-43.16150.21731220.19912888301099

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