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- PDB-4ig9: Structure of NAD-dependent protein deacetylase sirtuin-1 (open st... -

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Basic information

Entry
Database: PDB / ID: 4ig9
TitleStructure of NAD-dependent protein deacetylase sirtuin-1 (open state, 2.64 A)
Components(NAD-dependent protein deacetylase sirtuin-1) 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 / eNoSc complex / histone H4K12 deacetylase activity / 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 ...negative regulation of prostaglandin biosynthetic process / regulation of smooth muscle cell apoptotic process / maintenance of nucleus location / eNoSc complex / histone H4K12 deacetylase activity / 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 / protein-propionyllysine depropionylase activity / regulation of peroxisome proliferator activated receptor signaling pathway / regulation of transcription by glucose / regulation of protein serine/threonine kinase activity / positive regulation of macrophage apoptotic process / NAD-dependent histone H3K14 deacetylase activity / negative regulation of triglyceride biosynthetic process / regulation of endodeoxyribonuclease activity / triglyceride mobilization / behavioral response to starvation / pyrimidine dimer repair by nucleotide-excision repair / HLH domain binding / regulation of lipid storage / keratin filament binding / leptin-mediated signaling pathway / NAD-dependent histone H3K9 deacetylase activity / negative regulation of peptidyl-lysine acetylation / NAD-dependent histone H4K16 deacetylase activity / regulation of brown fat cell differentiation / deacetylase activity / positive regulation of smooth muscle cell differentiation / bHLH transcription factor binding / response to leptin / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / intracellular triglyceride homeostasis / peptidyl-lysine acetylation / negative regulation of androgen receptor signaling pathway / positive regulation of adaptive immune response / regulation of centrosome duplication / rDNA heterochromatin / ovulation from ovarian follicle / single strand break repair / negative regulation of cAMP-dependent protein kinase activity / regulation of bile acid biosynthetic process / NAD-dependent protein lysine deacetylase activity / rDNA heterochromatin formation / protein acetyllysine N-acetyltransferase / negative regulation of protein acetylation / chromatin silencing complex / negative regulation of phosphorylation / DNA methylation-dependent heterochromatin formation / protein deacetylation / NAD-dependent histone deacetylase activity / positive regulation of MHC class II biosynthetic process / UV-damage excision repair / protein lysine deacetylase activity / positive regulation of cAMP-dependent protein kinase activity / negative regulation of TOR signaling / negative regulation of helicase activity / positive regulation of macrophage cytokine production / mitogen-activated protein kinase binding / positive regulation of double-strand break repair / Regulation of FOXO transcriptional activity by acetylation / DNA repair-dependent chromatin remodeling / nuclear inner membrane / muscle organ development / stress-induced premature senescence / histone deacetylase activity / 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 NF-kappaB transcription factor activity / 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 cysteine-type endopeptidase activity involved in apoptotic process / macrophage differentiation / positive regulation of macroautophagy / negative regulation of cell cycle / white fat cell differentiation / regulation of glucose metabolic process / NAD+ binding / Regulation of HSF1-mediated heat shock response / positive regulation of cholesterol efflux / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of blood vessel endothelial cell migration / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / fatty acid homeostasis / heterochromatin / cellular response to glucose starvation / heterochromatin formation / energy homeostasis / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of cellular response to heat / positive regulation of insulin receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / positive regulation of gluconeogenesis / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / positive regulation of endothelial cell proliferation / regulation of mitotic cell cycle
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 / Rossmann fold ...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
NAD-dependent protein deacetylase sirtuin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.64 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
DepositionDec 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Feb 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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
C: NAD-dependent protein deacetylase sirtuin-1
D: NAD-dependent protein deacetylase sirtuin-1
E: NAD-dependent protein deacetylase sirtuin-1
F: NAD-dependent protein deacetylase sirtuin-1
G: NAD-dependent protein deacetylase sirtuin-1
H: NAD-dependent protein deacetylase sirtuin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,77312
Polymers141,5128
Non-polymers2624
Water82946
1
A: NAD-dependent protein deacetylase sirtuin-1
B: NAD-dependent protein deacetylase sirtuin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4433
Polymers35,3782
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: NAD-dependent protein deacetylase sirtuin-1
D: NAD-dependent protein deacetylase sirtuin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4433
Polymers35,3782
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: NAD-dependent protein deacetylase sirtuin-1
F: NAD-dependent protein deacetylase sirtuin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4433
Polymers35,3782
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: NAD-dependent protein deacetylase sirtuin-1
H: NAD-dependent protein deacetylase sirtuin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4433
Polymers35,3782
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.781, 115.781, 350.511
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
NAD-dependent protein deacetylase sirtuin-1 / hSIRT1 / Regulatory protein SIR2 homolog 1 / SIR2-like protein 1 / hSIR2 / SirtT1 75 kDa fragment / 75SirT1


Mass: 31833.107 Da / Num. of mol.: 4 / Fragment: UNP residues 234-510
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIR2L1, SIRT1 / Production host: Escherichia coli (E. coli)
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


Mass: 3544.836 Da / Num. of mol.: 4 / Fragment: UNP residues 641-665
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIR2L1, SIRT1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96EB6
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 46 / 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: 4.15 Å3/Da / Density % sol: 70.36 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 20 mM TRIS-HCl, 10 % PEG 20,000, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.2676 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2676 Å / Relative weight: 1
ReflectionResolution: 2.64→20 Å / Num. obs: 68583 / % possible obs: 97.1 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.64-2.747.80.943192.8
2.74-2.857.80.712195
2.85-2.987.40.531196.2
2.98-3.148.10.355197.3
3.14-3.348.20.238197.7
3.34-3.597.90.151197.8
3.59-3.957.90.096197.9
3.95-4.528.20.063198.6
4.52-5.678.10.054199
5.67-207.90.048198.3

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.64→19.941 Å / Occupancy max: 1 / Occupancy min: 0.38 / SU ML: 0.38 / σ(F): 1.34 / Phase error: 30.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2628 1996 2.92 %
Rwork0.2273 --
obs0.2283 68400 96.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.1737 Å2
Refinement stepCycle: LAST / Resolution: 2.64→19.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9235 0 4 46 9285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029612
X-RAY DIFFRACTIONf_angle_d0.6313017
X-RAY DIFFRACTIONf_dihedral_angle_d11.1393710
X-RAY DIFFRACTIONf_chiral_restr0.0441417
X-RAY DIFFRACTIONf_plane_restr0.0041712
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.70870.36511290.31044311X-RAY DIFFRACTION91
2.7087-2.78170.34841370.31024536X-RAY DIFFRACTION94
2.7817-2.86340.35671370.29734597X-RAY DIFFRACTION96
2.8634-2.95550.31341410.2884659X-RAY DIFFRACTION96
2.9555-3.06080.31561390.28824649X-RAY DIFFRACTION96
3.0608-3.18280.30841430.28324729X-RAY DIFFRACTION98
3.1828-3.32710.31891410.28344724X-RAY DIFFRACTION97
3.3271-3.50160.31011430.26274764X-RAY DIFFRACTION98
3.5016-3.71970.27051440.25454760X-RAY DIFFRACTION98
3.7197-4.00470.26311450.23544807X-RAY DIFFRACTION98
4.0047-4.40380.24571450.20784837X-RAY DIFFRACTION99
4.4038-5.03210.2371480.18294920X-RAY DIFFRACTION99
5.0321-6.30640.24861500.22184972X-RAY DIFFRACTION99
6.3064-19.94140.20731540.18385139X-RAY DIFFRACTION98

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