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Polymorphism and double hexamer structure in the archaeal minichromosome maintenance (MCM) helicase from Methanobacterium thermoautotrophicum.

by single particle reconstruction, at 25 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.008, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.008, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1134
TitlePolymorphism and double hexamer structure in the archaeal minichromosome maintenance (MCM) helicase from Methanobacterium thermoautotrophicum.
Maptest map
SampleArchaeal helicase MCM from Methanobacterium thermoautotrophicum
AuthorsGomez-Llorente Y, Fletcher RJ, Chen XS, Carazo JM, San Martin C
DateDeposition: 2005-03-16, Header release: 2005-07-01, Map release: 2006-07-01, Last update: 2011-05-26
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.008, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.008, Image by UCSF CHIMERA

Supplemental images
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Article
Citation - Primary
ArticleJ. Biol. Chem., Vol. 280, Issue 49, Page 40909-15, Year 2005
TitlePolymorphism and double hexamer structure in the archaeal minichromosome maintenance (MCM) helicase from Methanobacterium thermoautotrophicum.
AuthorsYacob Gómez-Llorente, Ryan J Fletcher, Xiaojiang S Chen, José M Carazo, Carmen San Martín
Biocomputing Unit, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Darwin 3, 28049 Madrid, Spain.
KeywordsChromosomes, Archaeal (chemistry), DNA Helicases (chemistry, 3.6.4.-), DNA, Bacterial (metabolism), Escherichia coli (genetics), Methanobacterium (enzymology), Microscopy, Electron, Models, Molecular, Polymorphism, Genetic, Protein Folding, Recombinant Proteins (chemistry)
LinksDOI: 10.1074/jbc.M509760200, PubMed: 16221680
Map
Fileemd_1134.map.gz ( map file in CCP4 format, 3457 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
96 pix
3.5 A/pix
= 336. A
96 pix
3.5 A/pix
= 336. A
96 pix
3.5 A/pix
= 336. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.00163, 0.008 (movie #1):
Minimum - Maximum: -0.092504 - 0.0759447
Average (Standard dev.): -0.000648781 (0.00679169)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions969696
Origin-48-48-48
Limit474747
Spacing969696
Unit CellA= B= C: 336 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 3.5 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z3.53.53.5
M x/y/z969696
origin x/y/z0.0000.0000.000
length x/y/z336.000336.000336.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-90-90-190
NX/NY/NZ180180380
MAP C/R/S123
start NC/NR/NS-48-48-48
NC/NR/NS969696
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.0930.076-0.001
Annotation Detailstest map
Supplement
Images
Images
Sample
NameArchaeal helicase MCM from Methanobacterium thermoautotrophicum
Oligomeric Statehomododecamer
Number of Components1
Experimental Mass0.9MDa
Theoretical Mass0.9MDa
Mass-estimation Methodgel filtration
Component #1: protein - MCM
Scientific nameminichromosome maintenance protein
Common NameMCM
Theoretical Mass75.6 MDa
Experimental Mass75.6 MDa
Oligomeric Detailsdodecamer
Number of Copies12
Scientific Name of SpeciesMethanothermobacter thermautotrophicus
Common Name of SpeciesMethanobacterium thermoautotrophicum
NCBI taxonomy145262
StrainDelta H
Recombinant expressionYes
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
LinksInter Pro: IPR:001208, Gene Ontology: GO:0006270
Experiment
Sample Preparation
Specimen Conc0.1 mg/ml
Staining2% uranyl acetate
Specimen Support Detailsglow discharged, collodion/carbon coated copper grids
Specimen Stateparticle
BufferDetails: 50 mM Tris.HCl pH 8.0, 1 mM DTT, 50 mM to 1M NaCl
pH: 8
Vitrification
Cryogen NameETHANE
Imaging
MicroscopeJEOL 1200EXII
Detailshe make and model of the microscope. Jeol 1200 EX-II. Standard Jeol 1200 holder
Electron Gun
Electron SourceTUNGSTEN HAIRPIN
Accelerating Voltage80 kV
Electron Dose10 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 60000
Astigmatismvisually corrected at 100,000x
Nominal Cs5.6 mm
Imaging ModeBRIGHT FIELD
Specimen Holder
Holderside entry
ModelOTHER
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
#1
Sampling Size7
Quant Bit Number8
ScannerZEISS SCAI
Processing
Methodsingle particle reconstruction
3D reconstruction
Algorithmprojection matching
SoftwareSPIDER, XMIPP
Resolution By Author25 A
Resolution Method3D SSNR = 1
Euler Angles Detailstheta between 75 and 90, phi between 0 and 360
Detailsreconstructed with ART
Single Particle
Number of Projections1200
Applied SymmetryC6 (6 fold cyclic)
Atomic Model Fitting
Model #0
SoftwareAmira
Download
Data from EMDB
Header (meta data in XML format)emd-1134.xml (7.4 KB)
Map dataemd_1134.map.gz (2.6 MB)
Images1134.gif (10.3 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1134
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.5 MB
Session file for UCSF-Chimera, 26.7 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5.1 MB
Session file for UCSF-Chimera, 26.7 KB