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- EMDB-1190: Molecular structure of human geminin. -

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Basic information

Entry
Database: EMDB / ID: EMD-1190
TitleMolecular structure of human geminin.
Map data3D map of human Geminin, asymmetrical reconstruction of the tetramer
Sample
  • Sample: Human replication licensing factor Geminin
  • Protein or peptide: Geminin
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 18.0 Å
AuthorsOkorokov AL / Orlova EV / Kingsbury SR / Bagneris C / Gohlke U / Williams GH / Stoeber K
CitationJournal: Nat Struct Mol Biol / Year: 2004
Title: Molecular structure of human geminin.
Authors: Andrei L Okorokov / Elena V Orlova / Sarah R Kingsbury / Claire Bagneris / Ulrich Gohlke / Gareth H Williams / Kai Stoeber /
Abstract: The origin licensing repressor geminin is a unique bifunctional protein providing a molecular link between cellular proliferation, differentiation and genomic stability. Here we report the first ...The origin licensing repressor geminin is a unique bifunctional protein providing a molecular link between cellular proliferation, differentiation and genomic stability. Here we report the first molecular structure of human geminin, determined by EM and image processing at a resolution of 17.5 A. The geminin molecule is a tetramer formed by two dimers with monomers interacting via coiled-coil domains. The unusual structural organization of geminin provides molecular insight into its bifunctional nature.
History
DepositionAug 17, 2004-
Header (metadata) releaseFeb 17, 2006-
Map releaseFeb 17, 2006-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.005912297
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.005912297
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1190.gif

Downloads & links

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Map

FileDownload / File: emd_1190.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D map of human Geminin, asymmetrical reconstruction of the tetramer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 200 pix.
= 212. Å		1.06 Å/pix.
x 200 pix.
= 212. Å		1.06 Å/pix.
x 200 pix.
= 212. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.00323 / Movie #1: 0.0059123
Minimum - Maximum-0.0288309 - 0.064641
Average (Standard dev.)0.000280778 (±0.00294759)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 212 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z212.000212.000212.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-96-96-96
NX/NY/NZ192192192
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0290.0650.000

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Supplemental data

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Sample components

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Entire : Human replication licensing factor Geminin

EntireName: Human replication licensing factor Geminin
Components
  • Sample: Human replication licensing factor Geminin
  • Protein or peptide: Geminin

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Supramolecule #1000: Human replication licensing factor Geminin

SupramoleculeName: Human replication licensing factor Geminin / type: sample / ID: 1000
Details: sample was produced in E. coli and purified by affinity chromatography followed by the ion-exchange and size exclusion chromatography steps. The resulting sample was homogeneous.
Oligomeric state: tetrameric / Number unique components: 1
Molecular weightExperimental: 103 KDa

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Macromolecule #1: Geminin

MacromoleculeName: Geminin / type: protein_or_peptide / ID: 1 / Name.synonym: Geminin / Details: tetramer / Number of copies: 4 / Oligomeric state: tetramer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Lung and Urinary bladder / Organelle: nucleus
Molecular weightExperimental: 90 KDa / Theoretical: 103 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET14b

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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

Concentration0.05 mg/mL
BufferpH: 7 / Details: 10 mM Tris HCl pH 8.0 100 mM NaCl
StainingType: NEGATIVE
Details: negative staining with 2% methylamine vanadate, pH 8.0 or with 2% methylamine tungstate, pH 6.8
GridDetails: 400 mesh carbon-coated copper grid
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, 2003
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 4 / Average electron dose: 20 e/Å2 / Camera length: 500 / Od range: 1.5 / Bits/pixel: 8
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsCalibrated magnification: 44000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.1 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 44000
Sample stageSpecimen holder: standard specimen holder / Specimen holder model: OTHER

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Image processing

Detailsselection was done manualy
CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Imagic-5 / Details: Asymmetrical reconstruction / Number images used: 3300
Final two d classificationNumber classes: 300

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Atomic model buiding 1

SoftwareName: O
DetailsProtocol: Rigid body. The coiled-coil domains were separately fitted by manual docking using program O
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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