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- EMDB-1254: Hexameric ring structure of human MCM10 DNA replication factor. -

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Basic information

Entry
Database: EMDB / ID: EMD-1254
TitleHexameric ring structure of human MCM10 DNA replication factor.
Map dataSurface views of human Mcm10 top side bottom stereo
Sample
  • Sample: recombinant human Mcm10
  • Protein or peptide: Mcm10
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 16.0 Å
AuthorsOkorokov AL / Orlova EV
CitationJournal: EMBO Rep / Year: 2007
Title: Hexameric ring structure of human MCM10 DNA replication factor.
Authors: Andrei L Okorokov / Alastair Waugh / Julie Hodgkinson / Andal Murthy / Hye Kyung Hong / Elisabetta Leo / Michael B Sherman / Kai Stoeber / Elena V Orlova / Gareth H Williams /
Abstract: The DNA replication factor minichromosome maintenance 10 (MCM10) is a conserved, abundant nuclear protein crucial for origin firing. During the transition from pre-replicative complexes to pre- ...The DNA replication factor minichromosome maintenance 10 (MCM10) is a conserved, abundant nuclear protein crucial for origin firing. During the transition from pre-replicative complexes to pre-initiation complexes, MCM10 recruitment to replication origins is required to provide a physical link between the MCM2-7 complex DNA helicase and DNA polymerases. Here, we report the molecular structure of human MCM10 as determined by electron microscopy and single-particle analysis. The MCM10 molecule is a ring-shaped hexamer with large central and smaller lateral channels and a system of inner chambers. This structure, together with biochemical data, suggests that this important protein uses its architecture to provide a docking module for assembly of the molecular machinery required for eukaryotic DNA replication.
History
DepositionAug 9, 2006-
Header (metadata) releaseAug 9, 2006-
Map releaseAug 22, 2007-
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: 0.0116
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0116
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1254.gif

Downloads & links

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Map

FileDownload / File: emd_1254.map.gz / Format: CCP4 / Size: 6.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSurface views of human Mcm10 top side bottom stereo
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.59 Å/pix.
x 120 pix.
= 190.8 Å		1.59 Å/pix.
x 120 pix.
= 190.8 Å		1.59 Å/pix.
x 120 pix.
= 190.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.59 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.0255 / Movie #1: 0.0116
Minimum - Maximum-0.0206095 - 0.0700683
Average (Standard dev.)0.00312238 (±0.0090834)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-60-60-60
Dimensions120120120
Spacing120120120
CellA=B=C: 190.8 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.591.591.59
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z190.800190.800190.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-60-60-60
NX/NY/NZ120120120
MAP C/R/S213
start NC/NR/NS-60-60-60
NC/NR/NS120120120
D min/max/mean-0.0210.0700.003

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Supplemental data

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Sample components

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Entire : recombinant human Mcm10

EntireName: recombinant human Mcm10
Components
  • Sample: recombinant human Mcm10
  • Protein or peptide: Mcm10

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Supramolecule #1000: recombinant human Mcm10

SupramoleculeName: recombinant human Mcm10 / type: sample / ID: 1000 / Details: monodisperse / Oligomeric state: homohexamer / Number unique components: 1
Molecular weightExperimental: 650 KDa / Theoretical: 590 KDa / Method: size-exclusion FPLC

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Macromolecule #1: Mcm10

MacromoleculeName: Mcm10 / type: protein_or_peptide / ID: 1 / Name.synonym: DNA replication factor / Details: UniProtKB/TrEMBL entry Q3MIR3 / Number of copies: 6 / Oligomeric state: hexamer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Location in cell: nuclear
Molecular weightExperimental: 590 KDa / Theoretical: 650 KDa
Recombinant expressionOrganism: Escherichia coli, Rosetta / Recombinant plasmid: pProEX-HT-B

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.01 mg/mL
BufferpH: 6.8
Details: 25 mM Tris-HCl pH 9.0, 150 mM NaCl, 10 mM MgCl2, 50 mM KCl
StainingType: NEGATIVE
Details: Grids were stained with 2% w/v methylamine tungstate, (Nano-W, Nanoprobes Inc.) for 1 min.
GridDetails: 400 mesh, freshly glow-discharged in air
VitrificationCryogen name: NONE

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Electron microscopy

MicroscopeFEI TECNAI 12
Detailsimages were taken on FEI Technai T10 microscope in low dose mode.
DateJan 1, 2005
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 15 / Average electron dose: 15 e/Å2 / Camera length: 500 / Od range: 1.4 / Bits/pixel: 8
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 44000
Sample stageSpecimen holder: eucentric / Specimen holder model: OTHER

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Image processing

DetailsThe particles were selected interactively at the computer terminal. close
CTF correctionDetails: each particle
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Imagic / Details: Final map was calculated from 197 best classes / Number images used: 5000
Final two d classificationNumber classes: 197

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Atomic model buiding 1

Initial modelPDB ID:

1n25


Chain - Chain ID - 0: 1 / Chain - Chain ID - 1: L / Chain - Chain ID - 2: T / Chain - Chain ID - 3: L
SoftwareName: URO
DetailsProtocol: rigid body. The domains were fitted automatically using URO
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT / Target criteria: correlation coeficient

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