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- EMDB-5005: Structure of the Copper Transporting ATPase of A. fulgidus by Cry... -

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Basic information

Entry
Database: EMDB / ID: 5005
TitleStructure of the Copper Transporting ATPase of A. fulgidus by Cryo-electron microscopy.
KeywordsP-type ATPase / copper / metal binding domain / helical reconstruction
SampleDelta-N DeltaC construct of CopA, the copper transporting ATPase of A. fulgidus
Map dataThis is one unit cell masked from CopA DeltaN DeltaC tubular crystals imaged by cryo-EM
Methodhelical reconstruction, at 17.5 Å resolution
AuthorsWu C / Rice WJ / Stokes DL
CitationStructure, 2008, 16, 976-985

Structure, 2008, 16, 976-985 StrPapers
Structure of a copper pump suggests a regulatory role for its metal-binding domain.
Chen-Chou Wu / William J Rice / David L Stokes

Validation ReportPDB-ID: 2voy

SummaryFull reportAbout validation report
DateDeposition: Feb 21, 2008 / Header (metadata) release: Feb 26, 2008 / Map release: Apr 22, 2009 / Last update: Apr 23, 2009

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 14
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 14
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

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Map

Fileemd_5005.map.gz (map file in CCP4 format, 4026 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
101 pix
2 Å/pix.
= 202. Å
101 pix
2 Å/pix.
= 202. Å
101 pix
2 Å/pix.
= 202. Å

Surface

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Images are generated by Spider package.

Voxel sizeX=Y=Z: 2 Å
Density
Contour Level:20, 14 (movie #1):
Minimum - Maximum-54.9078 - 56.0148
Average (Standard dev.)0.334285 (4.17111)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions101101101
Origin000
Limit100100100
Spacing101101101
CellA=B=C: 202 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z222
M x/y/z101101101
origin x/y/z0.0000.0000.000
length x/y/z202.000202.000202.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-40-32-96
NX/NY/NZ8165193
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS101101101
D min/max/mean-54.90856.0150.334

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Supplemental data

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Sample components

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Entire Delta-N DeltaC construct of CopA, the copper transporting ATPase ...

EntireName: Delta-N DeltaC construct of CopA, the copper transporting ATPase of A. fulgidus
Number of components: 1 / Oligomeric State: homodimer
MassTheoretical: 80 kDa / Measured by: SDS-PAGE

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Component #1: protein, P-type ATPase

ProteinName: P-type ATPase / a.k.a: Cu pump / Oligomeric Details: dimer / Recombinant expression: Yes / Number of Copies: 2
SourceStrain: Archaeoglobus fulgidus
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pBAD
Source (natural)Location in cell: plasma membrane
External referencesInterPro: InterPro: 001756 / Gene Ontology: GO: 0004008

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Experimental details

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Sample preparation

Specimen statehelical array
Helical parametersHand: RIGHT HANDED
Crystal grow detailscrystals grown at 45 to 55 C
Sample solutionSpecimen conc.: 0.5 mg/ml
Buffer solution: 50 mM MES, 25 mM Na2SO4, 25 mM K2SO4, 10 mM MgSO4, 2 mM 2-mercaptoethanol, 200 uM BCDS,
pH: 6.1
Support film300 mesh holey carbon
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 100 K / Humidity: 75 %
Method: Blot for 2-5 seconds before plunging. Plunge in cold room.
Details: Vitrification instrument: home made plunger

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Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM200FEG/UT
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 10 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal), 51300 X (calibrated)
Astigmatism: objective astigmatism corrected at 200,000X mag
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 900 - 2500 nm
Specimen HolderHolder: Oxford / Model: OTHER / Temperature: 100 K
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 24 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 8

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionAlgorithm: Helical / CTF correction: each tube / Resolution: 17.5 Å / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Details: Domains separately fitted by manual docking using O and Chimera
Input PDB model: 2B8E
Output model

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