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- EMDB-5271: High resolution helical reconstruction of the bacterial p-type AT... -

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Basic information

Entry
Database: EMDB / ID: EMD-5271
TitleHigh resolution helical reconstruction of the bacterial p-type ATPase copper transporter CopA.
Map dataThis is a cubic section encompassing the unit cell of a Fourier-Bessel reconstructed map of tubular vesicles - crystals of deltaC-CopA from Archaeoglobus fulgidus.
Sample
  • Sample: deltaC-CopA in DMPC-DOPE lipids
  • Protein or peptide: membrane protein
Keywordsp-type ATPase / copper transporter / CopA / Adenosine Triphosphatases / Archaeal Proteins / Archaeoglobus fulgidus / Cation Transport Proteins / Cryoelectron Microscopy
Function / homology
Function and homology information


P-type Cu+ transporter / P-type monovalent copper transporter activity / copper ion transport / copper ion binding / ATP hydrolysis activity / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
: / Heavy metal-associated domain, copper ion-binding / 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 / E1-E2 ATPase ...: / Heavy metal-associated domain, copper ion-binding / 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 / 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
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 10.0 Å
AuthorsWu C / Allen GS / Cardozo T / Stokes DL
CitationJournal: Structure / Year: 2011
Title: The architecture of CopA from Archeaoglobus fulgidus studied by cryo-electron microscopy and computational docking.
Authors: Gregory S Allen / Chen-Chou Wu / Tim Cardozo / David L Stokes /
Abstract: CopA uses ATP to pump Cu(+) across cell membranes. X-ray crystallography has defined atomic structures of several related P-type ATPases. We have determined a structure of CopA at 10 Å resolution ...CopA uses ATP to pump Cu(+) across cell membranes. X-ray crystallography has defined atomic structures of several related P-type ATPases. We have determined a structure of CopA at 10 Å resolution by cryo-electron microscopy of a new crystal form and used computational molecular docking to study the interactions between the N-terminal metal-binding domain (NMBD) and other elements of the molecule. We found that the shorter-chain lipids used to produce these crystals are associated with movements of the cytoplasmic domains, with a novel dimer interface and with disordering of the NMBD, thus offering evidence for the transience of its interaction with the other cytoplasmic domains. Docking identified a binding site that matched the location of the NMBD in our previous structure by cryo-electron microscopy, allowing a more detailed view of its binding configuration and further support for its role in autoinhibition.
History
DepositionApr 4, 2011-
Header (metadata) releaseJun 23, 2011-
Map releaseAug 16, 2011-
UpdateNov 16, 2011-
Current statusNov 16, 2011Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 130
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 130
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j08
  • Surface level: 130
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5271_1.png

Downloads & links

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Map

FileDownload / File: emd_5271.map.gz / Format: CCP4 / Size: 789.1 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a cubic section encompassing the unit cell of a Fourier-Bessel reconstructed map of tubular vesicles - crystals of deltaC-CopA from Archaeoglobus fulgidus.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2 Å/pix.
x 81 pix.
= 162. Å		2 Å/pix.
x 51 pix.
= 102. Å		2 Å/pix.
x 50 pix.
= 100. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 130.0 / Movie #1: 130
Minimum - Maximum-30.964200000000002 - 199.592999999999989
Average (Standard dev.)104.631 (±38.0715)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions515081
Spacing515081
CellA: 100 Å / B: 102 Å / C: 162 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z222
M x/y/z505181
origin x/y/z0.0000.0000.000
length x/y/z100.000102.000162.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS505181
D min/max/mean-30.964199.593104.631

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Supplemental data

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Sample components

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Entire : deltaC-CopA in DMPC-DOPE lipids

EntireName: deltaC-CopA in DMPC-DOPE lipids
Components
  • Sample: deltaC-CopA in DMPC-DOPE lipids
  • Protein or peptide: membrane protein

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Supramolecule #1000: deltaC-CopA in DMPC-DOPE lipids

SupramoleculeName: deltaC-CopA in DMPC-DOPE lipids / type: sample / ID: 1000
Details: deltaC-CopA tubular crystals were grown with a 4-to-1 mixture of DMPC-DOPE at a protein concentration of 1 mg per mL and at a lipid-to-protein weight ratio of 0.4. Dialysis was carried out ...Details: deltaC-CopA tubular crystals were grown with a 4-to-1 mixture of DMPC-DOPE at a protein concentration of 1 mg per mL and at a lipid-to-protein weight ratio of 0.4. Dialysis was carried out for 5 days in 50 ul dialysis buttons at 30 degrees C against 500 mL of 50 mM MES, pH 6.1, 25 mM Na2SO4, 25 mM K2SO4, 200 uM BCDS, 10 mM MgSO4, and 2 mM beta-mercaptoethanol. Stock solutions of lipid were made in dodecyl octaethylene glycol ether (C12E8) at 1 mg lipid per 2 mg detergent.
Number unique components: 1
Molecular weightTheoretical: 77 KDa

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Macromolecule #1: membrane protein

MacromoleculeName: membrane protein / type: protein_or_peptide / ID: 1 / Name.synonym: membrane protein / Number of copies: 2 / Oligomeric state: dimer / Recombinant expression: Yes
Source (natural)Organism: Archaeoglobus fulgidus (archaea) / Cell: E. coli / Location in cell: plasma membrane
Molecular weightTheoretical: 77 KDa
Recombinant expressionOrganism: Escherichia coli strain LMG 1940 / Recombinant plasmid: pBAD
SequenceGO: copper ion transport / InterPro: INTERPRO: IPR006403

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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

Concentration1 mg/mL
BufferpH: 6.1
Details: 50 mM MES, pH 6.1, 25 mM Na2SO4, 25 mM K2SO4, 200 uM BCDS, 10 mM MgSO4, and 2 mM beta-mercaptoethanol.
GridDetails: holey carbon grid
VitrificationCryogen name: ETHANE / Chamber temperature: 77 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: plunger / Method: blot for 5 seconds before plunging
Detailsdialysis buttons

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
TemperatureAverage: 100 K
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 12
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder: CT3500 / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: OTHER / Software - Name: EMIP
CTF correctionDetails: each tube-crystal

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