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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, Made by UCSF CHIMERA

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

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

Supplemental images

1134.gif
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Similar strucutres (beta)

Diagram

EMDB-1090

PDB-1s1h

PDB-3j0z
List of similar structure data about Omokage system
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, 3.6.1.-), 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 ( map file in CCP4 format, 3539 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)
Contour Level:0.00163, 0.008 (movie #1):
Minimum - Maximum: -0.092504 - 0.0759447
Average (Standard dev.): -0.000648781 (0.00679169)
Data Typefloat (32-bit)
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 96 96 96
Origin : -48 -48 -48
Limit : 47 47 47
Spacing : 96 96 96
Unit CellA = 336 A , B = 336 A , C = 336 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees
Pixel SpacingX = 3.5 A , Y = 3.5 A , 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-48-48-48
NC,NX/NR,NY/NS,NZ969696
D min/max/mean-0.0930.076-0.001
Annotation Detailstest map
Supplement
Images
Images

1134.gif
Sample
NameArchaeal helicase MCM from Methanobacterium thermoautotrophicum
Oligomeric Statehomododecamer
Number of Components1
Experimental Mass0.9 MDa
Theoretical Mass0.9 MDa
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 (NCBI Taxonomy: 145262)
Common Name of SpeciesMethanobacterium thermoautotrophicum
StrainDelta H
Recombinant expressionYes
Engineered SourceExp System: Escherichia coli (NCBI Taxonomy: 562)
LinksInterPro: 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: 8.0
Vitrification
Cryogen NameETHANE
Imaging
MicroscopeOTHER
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 X,
Astigmatismvisually corrected at 100,000x
Nominal Cs5.6 mm
Imaging ModeBRIGHT FIELD
Specimen Holder
Holderside entry ( OTHER )
Camera
DetectorKodak SO163 film
Image Acquisition
Sampling Size7 microns
Quant Bit Number8
ScannerZEISS SCAI
Processing
Methodsingle particle reconstruction
3 D reconstruction
Algorithmprojection matching
SoftwareSPIDER, XMIPP
Resolution By Author25
Resolution Method3D SSNR = 1
Euler Angles Detailstheta between 75 and 90, phi between 0 and 360
Detailsreconstructed with ART
Single Particle
Number of Projections1200
Atomic Model Fitting
Model #0
SoftwareAmira
Download
Data from EMDB
Header (meta data in XML format)emd-1134.xml (7.3 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