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- EMDB-5004: Structure of the Copper Transporting ATPase of A. fulgidus by Cry... -

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Basic information

Entry
Database: EMDB / ID: EMD-5004
TitleStructure of the Copper Transporting ATPase of A. fulgidus by Cryo-electron microscopy.
Map dataThis is one unit cell masked from CopA DeltaC tubular crystals imaged by cryo-EM
Sample
  • Sample: DeltaC construct of CopA, the copper transporting ATPase of A. fulgidus
  • Protein or peptide: P-type ATPase
KeywordsP-type ATPase / copper / metal binding domain / helical reconstruction
Function / homology
Function and homology information


P-type divalent copper transporter activity => GO:0043682 / P-type divalent copper transporter activity / positive regulation of cardiac muscle cell contraction / positive regulation of calcium ion import into sarcoplasmic reticulum / positive regulation of ATPase-coupled calcium transmembrane transporter activity / positive regulation of fast-twitch skeletal muscle fiber contraction / H zone / P-type Cu+ transporter / P-type monovalent copper transporter activity / calcium ion import into sarcoplasmic reticulum ...P-type divalent copper transporter activity => GO:0043682 / P-type divalent copper transporter activity / positive regulation of cardiac muscle cell contraction / positive regulation of calcium ion import into sarcoplasmic reticulum / positive regulation of ATPase-coupled calcium transmembrane transporter activity / positive regulation of fast-twitch skeletal muscle fiber contraction / H zone / P-type Cu+ transporter / P-type monovalent copper transporter activity / calcium ion import into sarcoplasmic reticulum / negative regulation of striated muscle contraction / regulation of striated muscle contraction / copper ion homeostasis / P-type Ca2+ transporter / P-type calcium transporter activity / I band / endoplasmic reticulum-Golgi intermediate compartment / sarcoplasmic reticulum membrane / sarcoplasmic reticulum / intracellular calcium ion homeostasis / calcium ion transport / copper ion binding / calcium ion binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
: / Heavy metal-associated domain, copper ion-binding / P-type ATPase, subfamily IIA, SERCA-type / P-type ATPase, subfamily IB / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA ...: / Heavy metal-associated domain, copper ion-binding / P-type ATPase, subfamily IIA, SERCA-type / P-type ATPase, subfamily IB / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / Cation transport ATPase (P-type) / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Probable copper-exporting P-type ATPase / Copper-exporting P-type ATPase / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Similarity search - Component
Methodhelical reconstruction / cryo EM / Resolution: 17.5 Å
AuthorsWu C / Rice WJ / Stokes DL
CitationJournal: Structure / Year: 2008
Title: Structure of a copper pump suggests a regulatory role for its metal-binding domain.
Authors: Chen-Chou Wu / William J Rice / David L Stokes /
Abstract: P-type ATPases play an important role in Cu homeostasis, which provides sufficient Cu for metalloenzyme biosynthesis but prevents oxidative damage of free Cu to the cell. The P(IB) group of P-type ...P-type ATPases play an important role in Cu homeostasis, which provides sufficient Cu for metalloenzyme biosynthesis but prevents oxidative damage of free Cu to the cell. The P(IB) group of P-type ATPases includes ATP-dependent pumps of Cu and other transition metal ions, and it is distinguished from other family members by the presence of N-terminal metal-binding domains (MBD). We have determined structures of two constructs of a Cu pump from Archaeoglobus fulgidus (CopA) by cryoelectron microscopy of tubular crystals, which reveal the overall architecture and domain organization of the molecule. By comparing these structures, we localized its N-terminal MBD within the cytoplasmic domains that use ATP hydrolysis to drive the transport cycle. We have built a pseudoatomic model by fitting existing crystallographic structures into the cryoelectron microscopy maps for CopA, which suggest a Cu-dependent regulatory role for the MBD.
History
DepositionFeb 14, 2008-
Header (metadata) releaseFeb 26, 2008-
Map releaseApr 22, 2009-
UpdateApr 23, 2009-
Current statusApr 23, 2009Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 13
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 13
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3j09
  • Surface level: 13
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-2voy
  • Surface level: 13
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5004_1.gif

Downloads & links

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Map

FileDownload / File: emd_5004.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is one unit cell masked from CopA DeltaC tubular crystals imaged by cryo-EM
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2 Å/pix.
x 101 pix.
= 202. Å		2 Å/pix.
x 101 pix.
= 202. Å		2 Å/pix.
x 101 pix.
= 202. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 10.0 / Movie #1: 13
Minimum - Maximum-48.613700000000001 - 75.387500000000003
Average (Standard dev.)0.528807 (±4.943)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions101101101
Spacing101101101
CellA=B=C: 202 Å
α=β=γ: 90 °

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-48.61475.3870.529

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Supplemental data

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Sample components

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Entire : DeltaC construct of CopA, the copper transporting ATPase of A. fu...

EntireName: DeltaC construct of CopA, the copper transporting ATPase of A. fulgidus
Components
  • Sample: DeltaC construct of CopA, the copper transporting ATPase of A. fulgidus
  • Protein or peptide: P-type ATPase

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Supramolecule #1000: DeltaC construct of CopA, the copper transporting ATPase of A. fu...

SupramoleculeName: DeltaC construct of CopA, the copper transporting ATPase of A. fulgidus
type: sample / ID: 1000 / Oligomeric state: homodimer / Number unique components: 1
Molecular weightTheoretical: 80 KDa / Method: SDS-PAGE

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Macromolecule #1: P-type ATPase

MacromoleculeName: P-type ATPase / type: protein_or_peptide / ID: 1 / Name.synonym: Cu pump / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: Yes
Source (natural)Strain: Archaeoglobus fulgidus / Location in cell: plasma membrane
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pBAD
SequenceGO: P-type divalent copper transporter activity => GO:0043682
InterPro: INTERPRO: IPR001756

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 6.1
Details: 50 mM MES, 25 mM Na2SO4, 25 mM K2SO4, 10 mM MgSO4, 2 mM 2-mercaptoethanol, 200 uM BCDS,
GridDetails: 300 mesh holey carbon
VitrificationCryogen name: ETHANE / Chamber humidity: 75 % / Chamber temperature: 100 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: home made plunger
Method: Blot for 2-5 seconds before plunging. Plunge in cold room.
Detailscrystals grown at 45 to 55 C

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG/UT
TemperatureAverage: 100 K
Alignment procedureLegacy - Astigmatism: objective astigmatism corrected at 200,000X mag
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 24 / Average electron dose: 10 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 51300 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Oxford / Specimen holder model: OTHER

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.5 Å / Resolution method: FSC 0.5 CUT-OFF
CTF correctionDetails: each tube

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Atomic model buiding 1

Initial modelPDB ID:

2b8e

DetailsDomains separately fitted by manual docking using O and Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-2voy:
CryoEM model of CopA, the copper transporting ATPase from Archaeoglobus fulgidus

PDB-3j09:
High resolution helical reconstruction of the bacterial p-type ATPase copper transporter CopA

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