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- EMDB-1134: Polymorphism and double hexamer structure in the archaeal minichr... -

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Basic information

Entry
Database: EMDB / ID: EMD-1134
TitlePolymorphism and double hexamer structure in the archaeal minichromosome maintenance (MCM) helicase from Methanobacterium thermoautotrophicum.
Map datatest map
Sample
  • Sample: Archaeal helicase MCM from Methanobacterium thermoautotrophicum
  • Protein or peptide: minichromosome maintenance protein
Function / homologyMCM domain / DNA replication initiation
Function and homology information
Biological speciesMethanothermobacter thermautotrophicus (archaea)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 25.0 Å
AuthorsGomez-Llorente Y / Fletcher RJ / Chen XS / Carazo JM / San Martin C
CitationJournal: J Biol Chem / Year: 2005
Title: Polymorphism and double hexamer structure in the archaeal minichromosome maintenance (MCM) helicase from Methanobacterium thermoautotrophicum.
Authors: Yacob Gómez-Llorente / Ryan J Fletcher / Xiaojiang S Chen / José M Carazo / Carmen San Martín /
Abstract: Methanobacterium thermoautotrophicum minichromosome maintenance complex (mtMCM), a cellular replicative helicase, is a useful model for the more complex eukaryotic MCMs. Biochemical and ...Methanobacterium thermoautotrophicum minichromosome maintenance complex (mtMCM), a cellular replicative helicase, is a useful model for the more complex eukaryotic MCMs. Biochemical and crystallographic evidence indicates that mtMCM assembles as a double hexamer (dHex), but previous electron microscopy studies reported only the presence of single heptamers or single hexamers (Pape, T., Meka, H., Chen, S., Vicentini, G., Van Heel, M., and Onesti, S. (2003) EMBO Rep. 4, 1079-1083; Yu, X., VanLoock, M. S., Poplawski, A., Kelman, Z., Xiang, T., Tye, B. K., and Egelman, E. H. (2002) EMBO Rep. 3, 792-797). Here we present the first three-dimensional electron microscopy reconstruction of the full-length mtMCM dHex in which two hexamers contact each other via the structurally well defined N-terminal domains. The dHex has obvious side openings that resemble the side channels of LTag (large T antigen). 6-fold and 7-fold rings were observed in the same mtMCM preparation, but we determined that assembly as a double ring favors 6-fold structures. Additionally, open rings were also detected, which suggests a direct mtMCM loading mechanism onto DNA.
History
DepositionMar 16, 2005-
Header (metadata) releaseJul 1, 2005-
Map releaseJul 1, 2006-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.008
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1134.gif

Downloads & links

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Map

FileDownload / File: emd_1134.map.gz / Format: CCP4 / Size: 3.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationtest map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.5 Å/pix.
x 96 pix.
= 336. Å		3.5 Å/pix.
x 96 pix.
= 336. Å		3.5 Å/pix.
x 96 pix.
= 336. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.5 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.00163 / Movie #1: 0.008
Minimum - Maximum-0.092504 - 0.0759447
Average (Standard dev.)-0.000648781 (±0.00679169)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-48-48-48
Dimensions969696
Spacing969696
CellA=B=C: 336 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/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
α/β/γ90.00090.00090.000
start NX/NY/NZ-90-90-190
NX/NY/NZ180180380
MAP C/R/S123
start NC/NR/NS-48-48-48
NC/NR/NS969696
D min/max/mean-0.0930.076-0.001

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Supplemental data

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Sample components

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Entire : Archaeal helicase MCM from Methanobacterium thermoautotrophicum

EntireName: Archaeal helicase MCM from Methanobacterium thermoautotrophicum
Components
  • Sample: Archaeal helicase MCM from Methanobacterium thermoautotrophicum
  • Protein or peptide: minichromosome maintenance protein

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Supramolecule #1000: Archaeal helicase MCM from Methanobacterium thermoautotrophicum

SupramoleculeName: Archaeal helicase MCM from Methanobacterium thermoautotrophicum
type: sample / ID: 1000 / Oligomeric state: homododecamer / Number unique components: 1
Molecular weightExperimental: 900 KDa / Theoretical: 900 KDa / Method: gel filtration

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Macromolecule #1: minichromosome maintenance protein

MacromoleculeName: minichromosome maintenance protein / type: protein_or_peptide / ID: 1 / Name.synonym: MCM / Number of copies: 12 / Oligomeric state: dodecamer / Recombinant expression: Yes
Source (natural)Organism: Methanothermobacter thermautotrophicus (archaea) / Strain: Delta H / synonym: Methanobacterium thermoautotrophicum
Molecular weightExperimental: 75.6 MDa / Theoretical: 75.6 MDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceGO: DNA replication initiation / InterPro: MCM domain

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 8 / Details: 50 mM Tris.HCl pH 8.0, 1 mM DTT, 50 mM to 1M NaCl
StainingType: NEGATIVE / Details: 2% uranyl acetate
GridDetails: glow discharged, collodion/carbon coated copper grids
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL 1200EXII
Alignment procedureLegacy - Astigmatism: visually corrected at 100,000x
Detailshe make and model of the microscope. Jeol 1200 EX-II. Standard Jeol 1200 holder
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Average electron dose: 10 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 80 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 5.6 mm / Nominal magnification: 60000
Sample stageSpecimen holder: side entry / Specimen holder model: OTHER

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Image processing

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: OTHER / Software - Name: SPIDER, XMIPP / Details: reconstructed with ART / Number images used: 1200
Final angle assignmentDetails: theta between 75 and 90, phi between 0 and 360

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Atomic model buiding 1

SoftwareName: Amira

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