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- PDB-4x3o: Sirt2 in complex with a myristoyl peptide -

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Basic information

Entry
Database: PDB / ID: 4x3o
TitleSirt2 in complex with a myristoyl peptide
Components
  • NAD-dependent protein deacetylase sirtuin-2
  • peptide PRO-LYS-LYS-THR-GLY
KeywordsHYDROLASE/PEPTIDE / complex / Sirt2 / myristoyl peptide / HYDROLASE-PEPTIDE complex
Function / homology
Function and homology information


cellular response to caloric restriction / negative regulation of oligodendrocyte progenitor proliferation / cellular lipid catabolic process / negative regulation of striated muscle tissue development / NAD-dependent histone H4K16 deacetylase activity / positive regulation of meiotic nuclear division / positive regulation of attachment of spindle microtubules to kinetochore / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / paranodal junction ...cellular response to caloric restriction / negative regulation of oligodendrocyte progenitor proliferation / cellular lipid catabolic process / negative regulation of striated muscle tissue development / NAD-dependent histone H4K16 deacetylase activity / positive regulation of meiotic nuclear division / positive regulation of attachment of spindle microtubules to kinetochore / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / paranodal junction / tubulin deacetylation / lateral loop / NLRP3 inflammasome complex assembly / peptidyl-lysine deacetylation / mitotic nuclear membrane reassembly / negative regulation of NLRP3 inflammasome complex assembly / tubulin deacetylase activity / regulation of exit from mitosis / paranode region of axon / NAD-dependent protein lysine deacetylase activity / Schmidt-Lanterman incisure / positive regulation of fatty acid biosynthetic process / myelination in peripheral nervous system / rDNA heterochromatin formation / protein acetyllysine N-acetyltransferase / chromatin silencing complex / regulation of phosphorylation / Initiation of Nuclear Envelope (NE) Reformation / protein deacetylation / NAD-dependent histone deacetylase activity / juxtaparanode region of axon / positive regulation of oocyte maturation / protein lysine deacetylase activity / meiotic spindle / response to redox state / regulation of myelination / histone acetyltransferase binding / histone deacetylase activity / negative regulation of fat cell differentiation / negative regulation of peptidyl-threonine phosphorylation / positive regulation of execution phase of apoptosis / glial cell projection / positive regulation of cell division / NAD+ ADP-ribosyltransferase activity / NAD+ binding / subtelomeric heterochromatin formation / negative regulation of reactive oxygen species metabolic process / positive regulation of DNA binding / heterochromatin / heterochromatin formation / epigenetic regulation of gene expression / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / cellular response to epinephrine stimulus / substantia nigra development / centriole / negative regulation of autophagy / meiotic cell cycle / ubiquitin binding / negative regulation of protein catabolic process / mitotic spindle / autophagy / histone deacetylase binding / spindle / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / myelin sheath / chromosome / midbody / cellular response to oxidative stress / growth cone / cellular response to hypoxia / perikaryon / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA-binding transcription factor binding / microtubule / chromosome, telomeric region / regulation of cell cycle / cell division / innate immune response / negative regulation of DNA-templated transcription / centrosome / chromatin binding / nucleolus / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / zinc ion binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Sirtuin, class I / 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 ...Sirtuin, class I / 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
Chem-3Y0 / NAD-dependent protein deacetylase sirtuin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsWang, Y. / Zhang, W.Z. / Hao, Q.
CitationJournal: Cell Chem Biol / Year: 2017
Title: Deacylation Mechanism by SIRT2 Revealed in the 1'-SH-2'-O-Myristoyl Intermediate Structure.
Authors: Wang, Y. / Fung, Y.M.E. / Zhang, W. / He, B. / Chung, M.W.H. / Jin, J. / Hu, J. / Lin, H. / Hao, Q.
History
DepositionDec 1, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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_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-2
C: peptide PRO-LYS-LYS-THR-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8846
Polymers34,9362
Non-polymers9474
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-6 kcal/mol
Surface area14290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.433, 77.594, 56.249
Angle α, β, γ (deg.)90.000, 97.220, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AC

#1: Protein NAD-dependent protein deacetylase sirtuin-2 / Regulatory protein SIR2 homolog 2 / SIR2-like protein 2


Mass: 34404.691 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 52-355
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT2, SIR2L, SIR2L2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IXJ6, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide peptide PRO-LYS-LYS-THR-GLY


Mass: 531.645 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-3Y0 / [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R,4R,5R)-3-oxidanyl-5-sulfanyl-4-tridecoxy-oxolan-2-yl]methyl hydrogen phosphate


Mass: 757.727 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H49N5O13P2S
#6: 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: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 3350, 0.1M HEPES, 5% Glycerol / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97906 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97906 Å / Relative weight: 1
ReflectionResolution: 1.5→55.8 Å / Num. obs: 51055 / % possible obs: 99.7 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.039 / Rrim(I) all: 0.079 / Χ2: 0.851 / Net I/av σ(I): 16.736 / Net I/σ(I): 12.9 / Num. measured all: 208519
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.534.10.50624880.8530.2850.5830.875100
1.53-1.554.10.44825650.8710.2530.5160.90999.9
1.55-1.584.10.34325210.9280.1930.3950.906100
1.58-1.624.10.30825590.9390.1730.3540.926100
1.62-1.654.10.2625510.9450.1470.30.919100
1.65-1.694.10.23225220.960.130.2670.9100
1.69-1.734.10.19825410.9660.1110.2280.935100
1.73-1.784.10.16425400.9690.0920.1890.899100
1.78-1.834.10.13325390.980.0740.1530.86299.9
1.83-1.894.10.11325420.9820.0620.1290.887100
1.89-1.964.10.09825510.9840.0540.1120.81999.9
1.96-2.044.20.08225300.9880.0450.0940.8100
2.04-2.134.10.07225390.990.0390.0820.75100
2.13-2.244.10.06725570.990.0370.0770.70899.9
2.24-2.384.10.06525430.990.0360.0740.726100
2.38-2.564.10.06925520.9880.0390.080.867100
2.56-2.824.10.07325510.9880.0410.0841.085100
2.82-3.234.10.07125690.9880.040.0821.075100
3.23-4.0740.05325620.9910.0310.0610.62499.6
4.07-5040.0525010.9890.030.0590.53295.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.287 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.1566 2479 5 %RANDOM
Rwork0.1211 ---
obs0.1229 46767 96.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.43 Å2 / Biso mean: 18.811 Å2 / Biso min: 6.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.06 Å2
2--0.02 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2407 0 58 300 2765
Biso mean--17.36 35.39 -
Num. residues----303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192684
X-RAY DIFFRACTIONr_bond_other_d0.0020.022542
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.9983636
X-RAY DIFFRACTIONr_angle_other_deg0.95635910
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8455334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.94623.814118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.37415477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3351517
X-RAY DIFFRACTIONr_chiral_restr0.090.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213010
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02605
X-RAY DIFFRACTIONr_mcbond_it1.5041.5311294
X-RAY DIFFRACTIONr_mcbond_other1.4981.5281293
X-RAY DIFFRACTIONr_mcangle_it1.9562.2941639
X-RAY DIFFRACTIONr_rigid_bond_restr1.26135226
X-RAY DIFFRACTIONr_sphericity_free39.6586
X-RAY DIFFRACTIONr_sphericity_bonded11.58555367
LS refinement shellResolution: 1.499→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.213 154 -
Rwork0.159 2608 -
all-2762 -
obs--74.11 %
Refinement TLS params.Method: refined / Origin x: 5.9915 Å / Origin y: 6.2592 Å / Origin z: 20.6993 Å
111213212223313233
T0.0033 Å2-0.0003 Å20.0025 Å2-0.0003 Å2-0.0005 Å2--0.0024 Å2
L0.0104 °2-0.0031 °2-0.012 °2-0.0238 °2-0.0109 °2--0.0308 °2
S-0.0006 Å °0.001 Å °-0.002 Å °-0.0001 Å °0.0006 Å °0.0014 Å °-0 Å °-0.0006 Å °-0 Å °

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