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- PDB-3j08: High resolution helical reconstruction of the bacterial p-type AT... -

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Basic information

Entry
Database: PDB / ID: 3j08
TitleHigh resolution helical reconstruction of the bacterial p-type ATPase copper transporter CopA
Componentscopper-exporting P-type ATPase A
KeywordsHYDROLASE / METAL TRANSPORT / p-type ATPase / copper transporter / CopA / adenosine triphosphatases / archaeal proteins / cation transport proteins / cryoelectron microscopy
Function / homology
Function and homology information


P-type divalent copper transporter activity / P-type Cu+ transporter / P-type monovalent copper transporter activity / copper ion homeostasis / 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 / P-type ATPase actuator domain / P-type ATPase, haloacid dehalogenase domain ...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 / P-type ATPase actuator domain / 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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 10 Å
AuthorsWu, C. / Allen, G.S. / Cardozo, T. / Stokes, D.L.
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
DepositionMay 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Database references
Revision 1.2Jul 18, 2018Group: Author supporting evidence / Data collection
Category: em_image_scans / em_single_particle_entity / em_software
Item: _em_software.image_processing_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: copper-exporting P-type ATPase A
B: copper-exporting P-type ATPase A


Theoretical massNumber of molelcules
Total (without water)138,4282
Polymers138,4282
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein copper-exporting P-type ATPase A / CopA


Mass: 69213.789 Da / Num. of mol.: 2 / Fragment: deltaC-CopA (UNP residues 93-737)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: copA, pacS, AF_0473 / Production host: Escherichia coli (E. coli)
References: UniProt: O29777, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: deltaC-CopA in DMPC-DOPE lipids / Type: COMPLEX
Details: DeltaC-CopA tubular crystals were grown with a 4-to-1 mixture of DMPC-DOPE at a protein concentration of 1 mg/mL and at a lipid-to-protein weight ratio of 0.4. Dialysis was carried out for 5 ...Details: DeltaC-CopA tubular crystals were grown with a 4-to-1 mixture of DMPC-DOPE at a protein concentration of 1 mg/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 303K 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.
Molecular weightValue: 0.077 MDa / Experimental value: NO
Buffer solutionpH: 6.1
Details: 50 mM MES, pH 6.1, 25 mM Na2SO4, 25 mM K2SO4, 200 uM BCDS, 10 mM MgSO4, 2 mM beta-mercaptoethanol
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: 50 mM MES, pH 6.1, 25 mM Na2SO4, 25 mM K2SO4, 200 uM BCDS, 10 mM MgSO4, 2 mM beta-mercaptoethanol
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temp: 77 K / Method: blot for 5 seconds before plunging

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM200FEG / Date: Jan 1, 2009
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2 mm / Camera length: 0 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: CT3500 / Temperature: 100 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingFilm or detector model: KODAK SO-163 FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: EMIP / Category: 3D reconstruction
CTF correctionDetails: each tube-crystal
3D reconstructionMethod: Fourier-Bessel / Resolution: 10 Å / Resolution method: OTHER / Symmetry type: HELICAL
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms9734 0 0 0 9734

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