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- PDB-5btr: Crystal structure of SIRT1 in complex with resveratrol and an AMC... -

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Basic information

Entry
Database: PDB / ID: 5btr
TitleCrystal structure of SIRT1 in complex with resveratrol and an AMC-containing peptide
Components
  • AMC-containing peptide
  • NAD-dependent protein deacetylase sirtuin-1
KeywordsHYDROLASE/SUBSTRATE / Deacetylase / Human Sirtuin 1 / N-terminal domain / Catalytic domain / C-terminal domain / Resveratrol / Substrate / HYDROLASE-SUBSTRATE complex
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 / response to leptin / bHLH transcription factor binding / 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 / DNA methylation-dependent heterochromatin formation / negative regulation of phosphorylation / chromatin silencing complex / NAD-dependent histone deacetylase activity / protein deacetylation / positive regulation of MHC class II biosynthetic process / UV-damage excision repair / protein lysine deacetylase activity / negative regulation of helicase activity / positive regulation of cAMP-dependent protein kinase activity / negative regulation of TOR signaling / positive regulation of macrophage cytokine production / mitogen-activated protein kinase binding / positive regulation of double-strand break repair / DNA repair-dependent chromatin remodeling / Regulation of FOXO transcriptional activity by acetylation / nuclear inner membrane / muscle organ development / stress-induced premature senescence / histone deacetylase activity / DNA synthesis involved in DNA repair / negative regulation of fat cell differentiation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of NF-kappaB transcription factor activity / 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 / positive regulation of macroautophagy / macrophage differentiation / 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 / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of blood vessel endothelial cell migration / fatty acid homeostasis / heterochromatin / cellular response to glucose starvation / heterochromatin formation / energy homeostasis / regulation of cellular response to heat / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of canonical NF-kappaB signal transduction / positive regulation of insulin receptor signaling pathway / positive regulation of gluconeogenesis / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / 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 / 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
RESVERATROL / NAD-dependent protein deacetylase sirtuin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsCao, D. / Wang, M. / Qiu, X. / Liu, D. / Jiang, H. / Yang, N. / Xu, R.M.
Funding support China, 6items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2012CB910702 China
National Natural Science Foundation of China31430018 China
National Natural Science Foundation of China31210103914 China
Strategic Priority Research Program of Chinese Academy of SciencesXDB08010100 China
Key Research Program of Chinese Academy of SciencesKJZD-EW-L05 China
National Key New Drug Creation and Manufacturing Program of China2014ZX09507002 China
CitationJournal: Genes Dev. / Year: 2015
Title: Structural basis for allosteric, substrate-dependent stimulation of SIRT1 activity by resveratrol
Authors: Cao, D. / Wang, M. / Qiu, X. / Liu, D. / Jiang, H. / Yang, N. / Xu, R.M.
History
DepositionJun 3, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Other
Revision 1.2Oct 18, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.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: AMC-containing peptide
E: AMC-containing peptide
F: AMC-containing peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,75918
Polymers137,5096
Non-polymers2,25012
Water19811
1
A: NAD-dependent protein deacetylase sirtuin-1
D: AMC-containing peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5866
Polymers45,8362
Non-polymers7504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NAD-dependent protein deacetylase sirtuin-1
E: AMC-containing peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5866
Polymers45,8362
Non-polymers7504
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NAD-dependent protein deacetylase sirtuin-1
F: AMC-containing peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5866
Polymers45,8362
Non-polymers7504
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.890, 133.890, 106.707
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
32

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A
211CHAIN B
311CHAIN C
112CHAIN A
212CHAIN B
312CHAIN C

NCS ensembles :
ID
1
2

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Components

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


Mass: 45040.375 Da / Num. of mol.: 3 / Fragment: UNP residues 143-512 and 641-665 / Mutation: C253S, C268S, C501S, C502S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT1, SIR2L1 / Plasmid: pET-28a smt3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q96EB6, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide AMC-containing peptide


Mass: 795.951 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-STL / RESVERATROL / Resveratrol


Mass: 228.243 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C14H12O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.69 Å3/Da / Density % sol: 66.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.9M sodium malonate, 0.5% Jeffamin M-600, 0.1M HEPES, pH 7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 31197 / % possible obs: 99.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 102.9 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 11
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
3.2-3.314.30.7172.331051.137100
3.31-3.454.20.45831161.16100
3.45-3.64.30.30530931.2100
3.6-3.794.20.18731151.225100
3.79-4.034.20.12330991.18100
4.03-4.344.20.08831331.089100
4.34-4.784.20.07231101.053100
4.78-5.474.10.07431330.972100
5.47-6.894.10.06731341.184100
6.89-5040.04831591.03498.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I5I

4i5i


Resolution: 3.2→44.63 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.26 / Stereochemistry target values: ML
Details: SINCE FRAGMENTS (RESIDUES 157-173) OF CHAINS A/B/C ARE DISORDERED AND THE THREE N-TERMIANL FRAGMENTS 143-156 OF THE THREE CHAINS ARE CLOSED TO EACH OTHER, AUTHOR CANNOT IDENTIFY THE CORRECT ...Details: SINCE FRAGMENTS (RESIDUES 157-173) OF CHAINS A/B/C ARE DISORDERED AND THE THREE N-TERMIANL FRAGMENTS 143-156 OF THE THREE CHAINS ARE CLOSED TO EACH OTHER, AUTHOR CANNOT IDENTIFY THE CORRECT CHAIN IDS OF THE N-TERMINAL FRAGMENTS.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1602 5.14 %Random selection
Rwork0.207 ---
obs0.209 31154 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 99.83 Å2
Refinement stepCycle: LAST / Resolution: 3.2→44.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8633 0 156 11 8800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069015
X-RAY DIFFRACTIONf_angle_d0.97912232
X-RAY DIFFRACTIONf_dihedral_angle_d14.6593416
X-RAY DIFFRACTIONf_chiral_restr0.0421328
X-RAY DIFFRACTIONf_plane_restr0.0051582
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A4956X-RAY DIFFRACTIONPOSITIONAL
12B4956X-RAY DIFFRACTIONPOSITIONAL
13C4956X-RAY DIFFRACTIONPOSITIONAL
21A165X-RAY DIFFRACTIONPOSITIONAL
22B165X-RAY DIFFRACTIONPOSITIONAL
23C165X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.30340.31951290.30042673X-RAY DIFFRACTION100
3.3034-3.42140.30531470.27592682X-RAY DIFFRACTION100
3.4214-3.55830.29441520.25432682X-RAY DIFFRACTION100
3.5583-3.72020.27941520.22572674X-RAY DIFFRACTION100
3.7202-3.91620.24991510.20292656X-RAY DIFFRACTION100
3.9162-4.16140.25941540.20452673X-RAY DIFFRACTION100
4.1614-4.48250.22971390.18462704X-RAY DIFFRACTION100
4.4825-4.9330.21441440.18382690X-RAY DIFFRACTION100
4.933-5.64570.27141560.20452684X-RAY DIFFRACTION100
5.6457-7.10830.28551410.24042725X-RAY DIFFRACTION100
7.1083-44.63430.21921370.18142709X-RAY DIFFRACTION98

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