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Atomic model of the DNA-bound methylase complex from the Type I restriction-modification enzyme EcoKI (M2S1). Based on fitting into EM map 1534.

by single particle reconstruction, at 18 A resolution

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#1: Depositted structure unit, Image by Jmol

#2: Superimposing with EM 3D map: EMDB-1534, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 2y7h
TitleAtomic model of the DNA-bound methylase complex from the Type I restriction-modification enzyme EcoKI (M2S1). Based on fitting into EM map 1534.
DescriptorTYPE-1 RESTRICTION ENZYME ECOKI SPECIFICITY PROTEIN (E.C.3.1.21.3)
TYPE I RESTRICTION ENZYME ECOKI M PROTEIN (E.C.3.1.21.3
2.1.1.72)
KeywordsTRANSFERASE/DNA, TRANSFERASE-DNA COMPLEX
AuthorsKennaway, C.K., Obarska-Kosinska, A., White, J.H., Tuszynska, I., Cooper, L.P., Bujnicki, J.M., Trinick, J., Dryden, D.T.F.
DateDeposition: 2011-01-31, Release: 2011-02-09
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Structure Visualization
MoviesMovie Page

#1: Depositted structure unit, Image by Jmol

#2: Superimposing with EM 3D map: EMDB-1534, Image by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
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EMDB-1534

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Article
Citation - primary
ArticleNucleic Acids Res., Vol. 37, Issue 3, Page 762-70, Year 2009
TitleThe structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein.
AuthorsChristopher K Kennaway, Agnieszka Obarska-Kosinska, John H White, Irina Tuszynska, Laurie P Cooper, Janusz M Bujnicki, John Trinick, David T F Dryden
Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, UK.
KeywordsDNA (chemistry, 9007-49-2), DNA modification methylase EcoKI (2.1.1.-), Escherichia coli (enzymology), Models, Molecular, Molecular Mimicry, Ocr protein, bacteriophage T7, Site-Specific DNA-Methyltransferase (Adenine-Specific) (chemistry, 2.1.1.72), Viral Proteins (chemistry)
LinksDOI: 10.1093/nar/gkn988, PubMed: 19074193, PMC: PMC2647291
Components
ID 1 : HSDS TYPE I DNA RESTRICTION SPECIFICITY SUBUNIT, S.ECOKI, TYPE I RESTRICTION ENZYME ECOKI SPECIFICITY PROTEIN, S PROTEIN
Image
DescriptionTYPE-1 RESTRICTION ENZYME ECOKI SPECIFICITY PROTEIN
Typepolypeptide(L)
Formula weight51468.723 Da
Number of molecules1
ID1
Ec3.1.21.3
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI


Strain: K
LinksUniProt: P05719, Sequence view
ID 2 : HSDM TYPE I DNA RESTRICTION METHYLTRANSFERASE SUBUNIT, M.ECOKI
Image
DescriptionTYPE I RESTRICTION ENZYME ECOKI M PROTEIN
Typepolypeptide(L)
Formula weight59378.996 Da
Number of molecules2
ID2
Ec3.1.21.3, 2.1.1.72
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
Strain: K
LinksUniProt: P08957, Sequence view
ID 3 : 5'-D(*GP*TP*TP*CP*AP*AP*CP*GP*TP*CP*GP*AP*CP*GP *TP*GP*CP*AP*AP*C)-3'
Image
Description5'-D(*GP*TP*TP*CP*AP*AP*CP*GP*TP*CP*GP*AP*CP*GP *TP*GP*CP*AP*AP*C)-3'
Typepolydeoxyribonucleotide
Formula weight6119.017 Da
Number of molecules1
ID3
DetailsFLIPPED OUT ADENINE
SourceMethod: Obtained synthetically
LinksSequence view
ID 4 : 5'-D(*GP*TP*TP*GP*CP*AP*CP*GP*TP*CP*GP*AP*CP*GP *TP*TP*GP*AP*AP*C)-3'
Image
Description5'-D(*GP*TP*TP*GP*CP*AP*CP*GP*TP*CP*GP*AP*CP*GP *TP*TP*GP*AP*AP*C)-3'
Typepolydeoxyribonucleotide
Formula weight6150.028 Da
Number of molecules1
ID4
DetailsFLIPPED OUT ADENINE BASE
SourceMethod: Obtained synthetically
LinksSequence view
ID 5 : S-ADENOSYLMETHIONINE
Image
DescriptionS-ADENOSYLMETHIONINE
Typenon-polymer
Formula weight398.436 Da
Number of molecules2
ID5
SourceMethod: Obtained synthetically
Sample
Assembly
Aggregation statePARTICLE
NameM.ECOKI WITH DNA
Buffer
Name20MM TRIS-CL, 100 MM NACL
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeNEGATIVE STAIN
Sample preparation
pH4.7
Sample concentration0.05 mg/ml
Sample support
DetailsCARBON
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: OTHER
Date2008-02-01
Electron gun
Electron sourceTUNGSTEN HAIRPIN
Accelerating voltage80 kV
Electron dose25 e/A**2
Illumination modeMEDIUM DOSE
Lens
ModeBRIGHT FIELD
MagnificationCalibrated: 39500 X, Nominal: 40000 X
CsNominal: 2 mm
Nominal defocusMax: 870 nm, Min: 275 nm
Specimen holder
Temperature294 Kelvin
Detector
TypeKODAK SO163 FILM
Processing
2D projection selection
Number of particles17807
Software nameIMAGIC, EMAN, MRC,UROX,CHIMERA
3D reconstruction
Actual pixel size3.12 A/pix
CTF correction methodFILTERED AT FIRST ZERO
DetailsHSDM N-TERMINAL DOMAIN RETRACED FROM PDB ENTRY 2AR0. DISORDERED C-TERMINUS OF HSDM MODELLED INTO DENSITY.
Magnification calibrationTMV
MethodRANDOM SPHERES STARTING MODEL
Nominal pixel size3.12 A/pix
Resolution18 A
3D fitting
MethodUROX
Refinement ProtocolRIGID BODY
Refinement SpaceREAL
3D fitting list
3D Fitting ID1
PDB entry ID1S7Z, 1YF2, 2AR0
Refine
Refine idELECTRON MICROSCOPY
Ls d res high18.00 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high18.00
Total atoms12846
Ligand atoms54
Nucleic acid atoms820
Protein atoms11972
Download
PDB format
Allpdb2y7h.ent.gz
pdb2y7h.ent (uncompressed file)
Header onlypdb2y7h.ent.gz
mmCIF format
mmCIF2y7h.cif.gz
XML format
All2y7h.xml.gz
No-atom2y7h-noatom.xml.gz
Ext-atom2y7h-extatom.xml.gz
Movie files
movie #1
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.webm (WebM/VP8 format), 3.5 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 4.7 MB