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- EMDB-3487: PabMCM single octameric ring -

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Basic information

Entry
Database: EMDB / ID: EMD-3487
TitlePabMCM single octameric ring
Map dataPabMCM octamer
Sample
  • Complex: Octameric ring composed of 8 identical subunits of PabMCM helicase
Biological speciesPyrococcus abyssi GE5 (archaea)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 22.0 Å
AuthorsSpagnolo L / Cannone G
CitationJournal: Sci Rep / Year: 2017
Title: Structure of an octameric form of the minichromosome maintenance protein from the archaeon Pyrococcus abyssi.
Authors: Giuseppe Cannone / Silvia Visentin / Adeline Palud / Ghislaine Henneke / Laura Spagnolo /
Abstract: Cell division is a complex process that requires precise duplication of genetic material. Duplication is concerted by replisomes. The Minichromosome Maintenance (MCM) replicative helicase is a ...Cell division is a complex process that requires precise duplication of genetic material. Duplication is concerted by replisomes. The Minichromosome Maintenance (MCM) replicative helicase is a crucial component of replisomes. Eukaryotic and archaeal MCM proteins are highly conserved. In fact, archaeal MCMs are powerful tools for elucidating essential features of MCM function. However, while eukaryotic MCM2-7 is a heterocomplex made of different polypeptide chains, the MCM complexes of many Archaea form homohexamers from a single gene product. Moreover, some archaeal MCMs are polymorphic, and both hexameric and heptameric architectures have been reported for the same polypeptide. Here, we present the structure of the archaeal MCM helicase from Pyrococcus abyssi in its single octameric ring assembly. To our knowledge, this is the first report of a full-length octameric MCM helicase.
History
DepositionNov 13, 2016-
Header (metadata) releaseDec 7, 2016-
Map releaseFeb 22, 2017-
UpdateAug 2, 2017-
Current statusAug 2, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.628
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.628
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3487.png

Downloads & links

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Map

FileDownload / File: emd_3487.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPabMCM octamer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.04 Å/pix.
x 80 pix.
= 483.2 Å		6.04 Å/pix.
x 80 pix.
= 483.2 Å		6.04 Å/pix.
x 80 pix.
= 483.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.628 / Movie #1: 0.628
Minimum - Maximum-1.2021604 - 2.8240795
Average (Standard dev.)0.004520832 (±0.13483387)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 483.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.046.046.04
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z483.200483.200483.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
D min/max/mean-1.2022.8240.005

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Supplemental data

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Sample components

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Entire : Octameric ring composed of 8 identical subunits of PabMCM helicase

EntireName: Octameric ring composed of 8 identical subunits of PabMCM helicase
Components
  • Complex: Octameric ring composed of 8 identical subunits of PabMCM helicase

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Supramolecule #1: Octameric ring composed of 8 identical subunits of PabMCM helicase

SupramoleculeName: Octameric ring composed of 8 identical subunits of PabMCM helicase
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: Modified pET28
Molecular weightTheoretical: 1.26 MDa

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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

BufferpH: 7.4
StainingType: NEGATIVE / Material: Uranyl acetate
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI 20
Image recordingFilm or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 10000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: PROJECTION MATCHING

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