[English] 日本語
Yorodumi
- PDB-3te6: Crystal Structure of the S. cerevisiae Sir3 AAA+ domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3te6
TitleCrystal Structure of the S. cerevisiae Sir3 AAA+ domain
ComponentsRegulatory protein SIR3
KeywordsGENE REGULATION / Heterochromatin / Gene Silencing / SIR Complex / HMR / HML / Telomere / AAA+ domain / structural / Sir4 / Sir3 / Sir2 / Nucleus
Function / homology
Function and homology information


establishment of protein-containing complex localization to telomere / nuclear-transcribed mRNA catabolic process, non-stop decay / telomere tethering at nuclear periphery / chromatin silencing complex / silent mating-type cassette heterochromatin formation / subtelomeric heterochromatin formation / nucleosome binding / heterochromatin / heterochromatin formation / double-strand break repair via nonhomologous end joining ...establishment of protein-containing complex localization to telomere / nuclear-transcribed mRNA catabolic process, non-stop decay / telomere tethering at nuclear periphery / chromatin silencing complex / silent mating-type cassette heterochromatin formation / subtelomeric heterochromatin formation / nucleosome binding / heterochromatin / heterochromatin formation / double-strand break repair via nonhomologous end joining / single-stranded DNA binding / double-stranded DNA binding / chromosome, telomeric region / nucleic acid binding / chromatin binding / nucleolus / mitochondrion / identical protein binding
Similarity search - Function
AAA lid domain / AAA lid domain / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / P-loop containing nucleotide triphosphate hydrolases ...AAA lid domain / AAA lid domain / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Regulatory protein SIR3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8001 Å
AuthorsHassler, M. / Ladurner, A.G.
CitationJournal: Genes Dev. / Year: 2011
Title: Structural basis for the role of the Sir3 AAA+ domain in silencing: interaction with Sir4 and unmethylated histone H3K79.
Authors: Ehrentraut, S. / Hassler, M. / Oppikofer, M. / Kueng, S. / Weber, J.M. / Mueller, J.W. / Gasser, S.M. / Ladurner, A.G. / Ehrenhofer-Murray, A.E.
History
DepositionAug 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2011Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Regulatory protein SIR3
B: Regulatory protein SIR3


Theoretical massNumber of molelcules
Total (without water)73,5112
Polymers73,5112
Non-polymers00
Water724
1
A: Regulatory protein SIR3


Theoretical massNumber of molelcules
Total (without water)36,7551
Polymers36,7551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Regulatory protein SIR3


Theoretical massNumber of molelcules
Total (without water)36,7551
Polymers36,7551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.590, 47.019, 127.852
Angle α, β, γ (deg.)90.00, 95.38, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Regulatory protein SIR3 / Silent information regulator 3


Mass: 36755.445 Da / Num. of mol.: 2 / Fragment: AAA+ domain (UNP Residues 530-845)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SIR3, CMT1, MAR2, STE8, YLR442C, L9753.10 / Plasmid: pET41 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P06701
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.65 Å3/Da / Density % sol: 66.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2 M ammonium sulfate, 2% (w/v) PEG 400, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 30, 2009 / Details: toroidal focusing mirror
RadiationMonochromator: single crystal (Si 111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 26714 / Num. obs: 26332 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.67 % / Biso Wilson estimate: 79.966 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.068 / Net I/σ(I): 9.31
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.633 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
MxCuBEdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8001→43.378 Å / SU ML: 0.46 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 32.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1271 5.1 %RANDOM
Rwork0.2186 ---
all0.2217 24929 --
obs0.2217 24929 93.35 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.45 Å2 / ksol: 0.326 e/Å3
Displacement parametersBiso mean: 74.49 Å2
Refinement stepCycle: LAST / Resolution: 2.8001→43.378 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4602 0 0 4 4606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014674
X-RAY DIFFRACTIONf_angle_d1.2736309
X-RAY DIFFRACTIONf_dihedral_angle_d17.5761700
X-RAY DIFFRACTIONf_chiral_restr0.085740
X-RAY DIFFRACTIONf_plane_restr0.004802
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.8001-2.91220.45271220.36522307230783
2.9122-3.04470.40041180.31562436243687
3.0447-3.20510.4041360.29782552255291
3.2051-3.40590.35171280.26522649264994
3.4059-3.66870.30751510.23932685268597
3.6687-4.03770.23351400.19812755275598
4.0377-4.62140.25671570.17792764276498
4.6214-5.82020.23921670.19772753275397
5.8202-43.38290.24781520.20242757275794

+
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://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