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- PDB-4kxq: Structure of NAD-dependent protein deacetylase sirtuin-1 (closed ... -

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Basic information

Entry
Database: PDB / ID: 4kxq
TitleStructure of NAD-dependent protein deacetylase sirtuin-1 (closed state, 1.85 A)
Components(NAD-dependent protein deacetylase sirtuin- ...) x 2
KeywordsHYDROLASE / deacetylase
Function / homology
Function and homology information


negative regulation of prostaglandin biosynthetic process / regulation of smooth muscle cell apoptotic process / maintenance of nucleus location / histone H3K deacetylase activity / NAD-dependent histone decrotonylase activity / negative regulation of attachment of mitotic spindle microtubules to kinetochore / negative regulation of cellular response to testosterone stimulus / protein depropionylation / NAD-dependent protein-lysine depropionylase activity / histone H3K14 deacetylase activity, NAD-dependent ...negative regulation of prostaglandin biosynthetic process / regulation of smooth muscle cell apoptotic process / maintenance of nucleus location / histone H3K deacetylase activity / NAD-dependent histone decrotonylase activity / negative regulation of attachment of mitotic spindle microtubules to kinetochore / negative regulation of cellular response to testosterone stimulus / protein depropionylation / NAD-dependent protein-lysine depropionylase activity / histone H3K14 deacetylase activity, NAD-dependent / eNoSc complex / regulation of peroxisome proliferator activated receptor signaling pathway / regulation of transcription by glucose / histone H4K12 deacetylase activity, hydrolytic mechanism / positive regulation of macrophage apoptotic process / negative regulation of triglyceride biosynthetic process / regulation of endodeoxyribonuclease activity / behavioral response to starvation / pyrimidine dimer repair by nucleotide-excision repair / triglyceride mobilization / keratin filament binding / HLH domain binding / regulation of lipid storage / Regulation of MITF-M dependent genes involved in metabolism / histone H3K9 deacetylase activity, NAD-dependent / leptin-mediated signaling pathway / negative regulation of peptidyl-lysine acetylation / histone H4K16 deacetylase activity, NAD-dependent / regulation of brown fat cell differentiation / deacetylase activity / positive regulation of smooth muscle cell differentiation / bHLH transcription factor binding / response to leptin / peptidyl-lysine acetylation / intracellular triglyceride homeostasis / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of androgen receptor signaling pathway / positive regulation of adaptive immune response / regulation of centrosome duplication / negative regulation of phosphorylation / rDNA heterochromatin / ovulation from ovarian follicle / regulation of bile acid biosynthetic process / single strand break repair / negative regulation of signal transduction by p53 class mediator / NAD-dependent protein lysine deacetylase activity / rDNA heterochromatin formation / protein acetyllysine N-acetyltransferase / negative regulation of protein acetylation / histone deacetylase activity, NAD-dependent / chromatin silencing complex / protein deacetylation / positive regulation of MHC class II biosynthetic process / UV-damage excision repair / DNA methylation-dependent constitutive heterochromatin formation / protein lysine deacetylase activity / negative regulation of TOR signaling / negative regulation of helicase activity / positive regulation of cAMP-dependent protein kinase activity / mitogen-activated protein kinase binding / Regulation of FOXO transcriptional activity by acetylation / nuclear inner membrane / positive regulation of macrophage cytokine production / positive regulation of double-strand break repair / stress-induced premature senescence / negative regulation of NF-kappaB transcription factor activity / histone deacetylase activity / muscle organ development / DNA repair-dependent chromatin remodeling / DNA synthesis involved in DNA repair / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of fat cell differentiation / : / intracellular glucose homeostasis / negative regulation of cellular senescence / negative regulation of DNA damage response, signal transduction by p53 class mediator / positive regulation of macroautophagy / macrophage differentiation / negative regulation of cell cycle / white fat cell differentiation / regulation of glucose metabolic process / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cholesterol efflux / NAD+ binding / Regulation of HSF1-mediated heat shock response / positive regulation of blood vessel endothelial cell migration / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / fatty acid homeostasis / Transcriptional and post-translational regulation of MITF-M expression and activity / heterochromatin / cellular response to glucose starvation / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / regulation of cellular response to heat / energy homeostasis / positive regulation of gluconeogenesis / regulation of mitotic cell cycle / positive regulation of endothelial cell proliferation / positive regulation of adipose tissue development
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 ...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 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5-DIPHOSPHORIBOSE / BETA-MERCAPTOETHANOL / NAD-dependent protein deacetylase sirtuin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.849 Å
AuthorsDavenport, A.M. / Huber, F.M. / Hoelz, A.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Structural and Functional Analysis of Human SIRT1.
Authors: Davenport, A.M. / Huber, F.M. / Hoelz, A.
History
DepositionMay 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references / Structure summary
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD-dependent protein deacetylase sirtuin-1
B: NAD-dependent protein deacetylase sirtuin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0586
Polymers35,2632
Non-polymers7954
Water5,405300
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-16 kcal/mol
Surface area15470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.714, 92.714, 97.745
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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NAD-dependent protein deacetylase sirtuin- ... , 2 types, 2 molecules AB

#1: Protein NAD-dependent protein deacetylase sirtuin-1 / SIRT1 / hSIRT1 / Regulatory protein SIR2 homolog 1 / SIR2-like protein 1 / hSIR2


Mass: 31833.107 Da / Num. of mol.: 1 / Fragment: deacetylase domain (UNP residues 234-510)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) RIL
References: UniProt: Q96EB6, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide NAD-dependent protein deacetylase sirtuin-1 / SIRT1 / hSIRT1 / Regulatory protein SIR2 homolog 1 / SIR2-like protein 1 / hSIR2


Mass: 3429.748 Da / Num. of mol.: 1 / Fragment: UNP residues 641-663
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) RIL / References: UniProt: Q96EB6

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Non-polymers , 5 types, 304 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#5: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 3.44 Å3/Da / Density % sol: 64.23 %
Crystal growpH: 7.4 / Details: 100 mM Tris, pH 7.4, 13% PEG20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.2821 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2013
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2821 Å / Relative weight: 1
ReflectionResolution: 1.849→50 Å / Num. obs: 41954 / Biso Wilson estimate: 34.23 Å2
Reflection shellHighest resolution: 1.849 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.849→46.357 Å / Occupancy max: 1 / Occupancy min: 0.35 / SU ML: 0.22 / σ(F): 1.35 / Phase error: 20.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1894 1924 4.76 %
Rwork0.1684 --
obs0.1695 41937 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.32 Å2 / Biso mean: 43.6853 Å2 / Biso min: 20.75 Å2
Refinement stepCycle: LAST / Resolution: 1.849→46.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2426 0 47 300 2773
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092596
X-RAY DIFFRACTIONf_angle_d1.2273523
X-RAY DIFFRACTIONf_chiral_restr0.068383
X-RAY DIFFRACTIONf_plane_restr0.006458
X-RAY DIFFRACTIONf_dihedral_angle_d13.771006
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.849-1.87280.35221380.294128172955
1.8728-1.89740.26441490.264328933042
1.8974-1.92340.30751420.265927962938
1.9234-1.95090.2981400.2427872927
1.9509-1.980.21621480.231928943042
1.98-2.0110.25231400.212927842924
2.011-2.0440.2791460.206228132959
2.044-2.07920.24971350.210328592994
2.0792-2.1170.21761360.205228432979
2.117-2.15770.22421460.192228062952
2.1577-2.20180.17811420.180328593001
2.2018-2.24960.1951440.187127872931
2.2496-2.3020.18471390.174528052944
2.302-2.35950.21971440.171128943038
2.3595-2.42330.2031400.159928052945
2.4233-2.49460.21541380.167328552993
2.4946-2.57510.17531480.159528342982
2.5751-2.66720.19861370.154628022939
2.6672-2.7740.19571480.165628392987
2.774-2.90020.20291380.168328292967
2.9002-3.05310.21111320.178628482980
3.0531-3.24430.21641360.180228522988
3.2443-3.49470.19961460.168828192965
3.4947-3.84620.17981500.161128412991
3.8462-4.40240.14541400.133228482988
4.4024-5.54510.13621360.134228202956
5.5451-46.37150.18291460.175628292975

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