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- EMDB-1355: Molecular architecture of the human GINS complex. -

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Basic information

Entry
Database: EMDB / ID: EMD-1355
TitleMolecular architecture of the human GINS complex.
Map dataThis is an image of a surface of the human GINS complex
Sample
  • Sample: Human GINS complex
  • Protein or peptide: hPsf1p
  • Protein or peptide: hPsf2
  • Protein or peptide: hPsf3
  • Protein or peptide: hSld5
Function / homologyDNA replication complex GINS protein Psf2 / GINS complex, subunit Psf3 / GINS complex subunit Sld5 / GINS complex, subunit Psf1
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 33.0 Å
AuthorsBoskovic J / Coloma J / Aparicio T / Zhou M / Robinson CV / Mendez J / Montoya G
CitationJournal: EMBO Rep / Year: 2007
Title: Molecular architecture of the human GINS complex.
Authors: Jasminka Boskovic / Javier Coloma / Tomás Aparicio / Min Zhou / Carol V Robinson / Juan Méndez / Guillermo Montoya /
Abstract: Chromosomal DNA replication is strictly regulated through a sequence of steps that involve many macromolecular protein complexes. One of these is the GINS complex, which is required for initiation ...Chromosomal DNA replication is strictly regulated through a sequence of steps that involve many macromolecular protein complexes. One of these is the GINS complex, which is required for initiation and elongation phases in eukaryotic DNA replication. The GINS complex consists of four paralogous subunits. At the G1/S transition, GINS is recruited to the origins of replication where it assembles with cell-division cycle protein (Cdc)45 and the minichromosome maintenance mutant (MCM)2-7 to form the Cdc45/Mcm2-7/GINS (CMG) complex, the presumed replicative helicase. We isolated the human GINS complex and have shown that it can bind to DNA. By using single-particle electron microscopy and three-dimensional reconstruction, we obtained a medium-resolution volume of the human GINS complex, which shows a horseshoe shape. Analysis of the protein interactions using mass spectrometry and monoclonal antibody mapping shows the subunit organization within the GINS complex. The structure and DNA-binding data suggest how GINS could interact with DNA and also its possible role in the CMG helicase complex.
History
DepositionApr 26, 2007-
Header (metadata) releaseApr 27, 2007-
Map releaseApr 27, 2008-
UpdateDec 5, 2012-
Current statusDec 5, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6.996754617
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 6.996754617
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1355.gif

Downloads & links

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Map

FileDownload / File: emd_1355.map.gz / Format: CCP4 / Size: 5.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is an image of a surface of the human GINS complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.56 Å/pix.
x 112 pix.
= 398.72 Å		3.56 Å/pix.
x 112 pix.
= 398.72 Å		3.56 Å/pix.
x 112 pix.
= 398.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.56 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 7.0 / Movie #1: 6.9967546
Minimum - Maximum-6.29377747 - 12.94470596
Average (Standard dev.)0.0 (±0.76636928)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-56-56-56
Dimensions112112112
Spacing112112112
CellA=B=C: 398.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.563.563.56
M x/y/z112112112
origin x/y/z0.0000.0000.000
length x/y/z398.720398.720398.720
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-56-56-56
NC/NR/NS112112112
D min/max/mean-6.29412.945-0.000

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Supplemental data

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Sample components

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Entire : Human GINS complex

EntireName: Human GINS complex
Components
  • Sample: Human GINS complex
  • Protein or peptide: hPsf1p
  • Protein or peptide: hPsf2
  • Protein or peptide: hPsf3
  • Protein or peptide: hSld5

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Supramolecule #1000: Human GINS complex

SupramoleculeName: Human GINS complex / type: sample / ID: 1000 / Details: The sample was monodisperse / Oligomeric state: Monomer / Number unique components: 4
Molecular weightExperimental: 983.73 KDa / Theoretical: 981.22 KDa / Method: Nano-flow MS of the intact complex

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Macromolecule #1: hPsf1p

MacromoleculeName: hPsf1p / type: protein_or_peptide / ID: 1 / Name.synonym: GINS1 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Organelle: Nucleus
Molecular weightExperimental: 229.88 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET_MCN
SequenceInterPro: GINS complex, subunit Psf1

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Macromolecule #2: hPsf2

MacromoleculeName: hPsf2 / type: protein_or_peptide / ID: 2 / Name.synonym: GINS2 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Organelle: Nucleus
Molecular weightExperimental: 214.28 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET_MCN
SequenceInterPro: DNA replication complex GINS protein Psf2

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Macromolecule #3: hPsf3

MacromoleculeName: hPsf3 / type: protein_or_peptide / ID: 3 / Name.synonym: GINS3 / Details: Hexa His-tag on its N-terminal / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Organelle: Nucleus
Molecular weightExperimental: 240 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET_MCN
SequenceInterPro: GINS complex, subunit Psf3

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Macromolecule #4: hSld5

MacromoleculeName: hSld5 / type: protein_or_peptide / ID: 4 / Name.synonym: GINS4 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Organelle: Nucleus
Molecular weightExperimental: 260.47 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET_MCN
SequenceInterPro: GINS complex subunit Sld5

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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

Concentration0.1 mg/mL
BufferpH: 8
Details: 10 mM Tris-HCl pH 8.0, 100 mM NaCl, 0.5 mM EDTA, 10% glycerol, 1 mM DTT
StainingType: NEGATIVE
Details: Grids with adsorbed protein were stained with 0.2 % uranyl acetate for 1 min
GridDetails: 400 mesh copper-rhodium grid
VitrificationCryogen name: NONE

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Electron microscopy

MicroscopeJEOL 1230
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
DetailsElectron microscope was JEOL JEM-120, 120kV. Specimen holder, JEOL type M: 207EM-11020. Images were colected in low-dose conditions
DateNov 18, 2007
Image recordingCategory: FILM / Film or detector model: KODAK 4489 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 3.56 µm / Number real images: 40 / Details: Minolta Dimage Scan Multi Pro. Scan at 2400 dpi / Bits/pixel: 16
Tilt angle min0
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DIFFRACTION / Cs: 2.9 mm / Nominal magnification: 60000
Sample stageSpecimen holder: Eucentric / Specimen holder model: OTHER / Tilt angle max: 20

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Image processing

CTF correctionDetails: Each micrograph
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 33.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 5290

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