[English] 日本語
Yorodumi
- PDB-4hd8: Crystal structure of human Sirt3 in complex with Fluor-de-Lys pep... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hd8
TitleCrystal structure of human Sirt3 in complex with Fluor-de-Lys peptide and piceatannol
Components
  • Fluor-de-Lys peptide
  • NAD-dependent protein deacetylase sirtuin-3, mitochondrial
KeywordsHYDROLASE/HYDROLASE INHIBITOR / NAD-dependent deacetylase / Sirtuin / mitochondrial / inhibitor complex / piceatannol / resveratrol-like compound / HYDROLASE-HYDROLASE INHIBITOR complex
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 / protein deacetylation / NAD-dependent histone deacetylase activity / 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 / protein deacetylation / NAD-dependent histone deacetylase activity / Regulation of FOXO transcriptional activity by acetylation / NAD+ binding / negative regulation of reactive oxygen species metabolic process / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / aerobic respiration / Transcriptional activation of mitochondrial biogenesis / positive regulation of insulin secretion / negative regulation of ERK1 and ERK2 cascade / transferase activity / sequence-specific DNA binding / mitochondrial matrix / enzyme binding / protein-containing complex / mitochondrion / zinc ion binding / nucleoplasm / 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 / 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
ISOPROPYL ALCOHOL / PICEATANNOL / NAD-dependent protein deacetylase sirtuin-3, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNguyen, G.T.T. / Gertz, M. / Steegborn, C.
CitationJournal: Plos One / Year: 2012
Title: A molecular mechanism for direct sirtuin activation by resveratrol.
Authors: Gertz, M. / Nguyen, G.T. / Fischer, F. / Suenkel, B. / Schlicker, C. / Franzel, B. / Tomaschewski, J. / Aladini, F. / Becker, C. / Wolters, D. / Steegborn, C.
History
DepositionOct 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: 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 / pdbx_struct_special_symmetry / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
F: Fluor-de-Lys peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6245
Polymers32,2542
Non-polymers3703
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.600, 114.600, 123.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-402-

PIT

-
Components

-
Protein / Protein/peptide , 2 types, 2 molecules AF

#1: Protein NAD-dependent protein deacetylase sirtuin-3, mitochondrial / hSIRT3 / Regulatory protein SIR2 homolog 3 / SIR2-like protein 3


Mass: 31484.219 Da / Num. of mol.: 1 / Fragment: UNP residues 116-399
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIR2L3, SIRT3 / Plasmid: pVFT3S / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Rosetta2
References: UniProt: Q9NTG7, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide Fluor-de-Lys peptide


Mass: 769.913 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: coumarin-modified tetra peptide

-
Non-polymers , 4 types, 105 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PIT / PICEATANNOL / 4-[(E)-2-(3,5-DIHYDROXYPHENYL)ETHENYL]BENZENE-1,2-DIOL


Mass: 244.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12O4
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 200 mM NaCl, 100 mM HEPES pH 7, 10% (v/v) isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Sep 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.3→38.7 Å / Num. all: 14077 / Num. obs: 14069 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 20
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 7 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 4.3 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→38.74 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.066 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.291 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2405 704 5 %RANDOM
Rwork0.1736 13365 --
obs0.1769 14069 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.45 Å2 / Biso mean: 31.3997 Å2 / Biso min: 11.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.31 Å2-0 Å2
2--0.31 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 2.3→38.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2102 0 23 102 2227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192203
X-RAY DIFFRACTIONr_angle_refined_deg1.8922.0063004
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3335269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.31222.73795
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.56815356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1681519
X-RAY DIFFRACTIONr_chiral_restr0.1110.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0221689
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 52 -
Rwork0.204 979 -
all-1031 -
obs--99.81 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more