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- EMDB-1410: The EM structure of human DNA polymerase gamma reveals a localize... -

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Basic information

Entry
Database: EMDB / ID: EMD-1410
TitleThe EM structure of human DNA polymerase gamma reveals a localized contact between the catalytic and accessory subunits.
Map dataThis is a map of human mitochondrial DNA polymerase gamma
Sample
  • Sample: Human mitochondrial DNA polymerase gamma polymerase gamma
  • Protein or peptide: human mitochondrial DNA polymerase gamma, catalytic subunit
  • Protein or peptide: human mitochondrial DNA polymerase gamma, dimeric accessory subunit
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 17.0 Å
AuthorsYakubovskaya E / Lukin M / Chen Z / Berriman J / Wall JS / Kobayashi R / Kisker C / Bogenhagen DF
CitationJournal: EMBO J / Year: 2007
Title: The EM structure of human DNA polymerase gamma reveals a localized contact between the catalytic and accessory subunits.
Authors: Elena Yakubovskaya / Mark Lukin / Zhixin Chen / John Berriman / Joseph S Wall / Ryuji Kobayashi / Caroline Kisker / Daniel F Bogenhagen /
Abstract: We used electron microscopy to examine the structure of human DNA pol gamma, the heterotrimeric mtDNA replicase implicated in certain mitochondrial diseases and aging models. Separate analysis of ...We used electron microscopy to examine the structure of human DNA pol gamma, the heterotrimeric mtDNA replicase implicated in certain mitochondrial diseases and aging models. Separate analysis of negatively stained preparations of the catalytic subunit, pol gammaA, and of the holoenzyme including a dimeric accessory factor, pol gammaB(2), permitted unambiguous identification of the position of the accessory factor within the holoenzyme. The model explains protection of a partial chymotryptic cleavage site after residue L(549) of pol gammaA upon binding of the accessory subunit. This interaction region is near residue 467 of pol gammaA, where a disease-related mutation has been reported to impair binding of the B subunit. One pol gammaB subunit dominates contacts with the catalytic subunit, while the second B subunit is largely exposed to solvent. A model for pol gamma is discussed that considers the effects of known mutations in the accessory subunit and the interaction of the enzyme with DNA.
History
DepositionAug 7, 2007-
Header (metadata) releaseAug 7, 2007-
Map releaseJan 7, 2008-
UpdateMar 26, 2014-
Current statusMar 26, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.942036905
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.942036905
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2g4c
  • Surface level: 0.942036905
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1410.gif

Downloads & links

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Map

FileDownload / File: emd_1410.map.gz / Format: CCP4 / Size: 825.2 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a map of human mitochondrial DNA polymerase gamma
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.49 Å/pix.
x 60 pix.
= 209.28 Å		3.49 Å/pix.
x 60 pix.
= 209.28 Å		3.49 Å/pix.
x 60 pix.
= 209.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.488 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.569 / Movie #1: 0.9420369
Minimum - Maximum-1.51567 - 3.63237
Average (Standard dev.)-0.00289475 (±0.373184)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-30-30-30
Dimensions606060
Spacing606060
CellA=B=C: 209.28 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.4883.4883.488
M x/y/z606060
origin x/y/z0.0000.0000.000
length x/y/z209.280209.280209.280
α/β/γ90.00090.00090.000
start NX/NY/NZ-50-50-50
NX/NY/NZ100100100
MAP C/R/S123
start NC/NR/NS-30-30-30
NC/NR/NS606060
D min/max/mean-1.5163.632-0.003

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Supplemental data

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Sample components

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Entire : Human mitochondrial DNA polymerase gamma polymerase gamma

EntireName: Human mitochondrial DNA polymerase gamma polymerase gamma
Components
  • Sample: Human mitochondrial DNA polymerase gamma polymerase gamma
  • Protein or peptide: human mitochondrial DNA polymerase gamma, catalytic subunit
  • Protein or peptide: human mitochondrial DNA polymerase gamma, dimeric accessory subunit

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Supramolecule #1000: Human mitochondrial DNA polymerase gamma polymerase gamma

SupramoleculeName: Human mitochondrial DNA polymerase gamma polymerase gamma
type: sample / ID: 1000 / Oligomeric state: heterotrimer / Number unique components: 2
Molecular weightExperimental: 250 KDa / Theoretical: 250 KDa

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Macromolecule #1: human mitochondrial DNA polymerase gamma, catalytic subunit

MacromoleculeName: human mitochondrial DNA polymerase gamma, catalytic subunit
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Location in cell: mitochondria
Molecular weightExperimental: 145 KDa / Theoretical: 145 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant strain: SF9

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Macromolecule #2: human mitochondrial DNA polymerase gamma, dimeric accessory subunit

MacromoleculeName: human mitochondrial DNA polymerase gamma, dimeric accessory subunit
type: protein_or_peptide / ID: 2 / Details: dimer / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Location in cell: mitochondria
Molecular weightExperimental: 110 KDa / Theoretical: 110 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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

Concentration0.025 mg/mL
BufferpH: 8
Details: 20 mM Hepes, 150 mM KCl, 1 mM EDTA, 5 mM DTT buffer.
StainingType: NEGATIVE
Details: Grids with adsorbed protein were stained with 2% uranyl acetate for 60 seconds.
GridDetails: 300-mesh copper grids (Ted Pella) coated with carbon film that were glow-discharged for 10 s.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI/PHILIPS CM200T
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 76000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.6 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.85 µm
Specialist opticsEnergy filter - Name: FEI
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN HELIUM / Tilt angle min: 60
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Number real images: 48 / Average electron dose: 10 e/Å2
Tilt angle max0

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Image processing

CTF correctionDetails: Each particle
Final two d classificationNumber classes: 48
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 8652

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