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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 | |||||||||
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Title | High resolution helical reconstruction of the bacterial p-type ATPase copper transporter CopA. | |||||||||
![]() | This is a cubic section encompassing the unit cell of a Fourier-Bessel reconstructed map of tubular vesicles - crystals of deltaC-CopA from Archaeoglobus fulgidus. | |||||||||
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![]() | p-type ATPase / copper transporter / CopA / Adenosine Triphosphatases / Archaeal Proteins / Archaeoglobus fulgidus / Cation Transport Proteins / Cryoelectron Microscopy | |||||||||
Function / homology | ![]() P-type divalent copper transporter activity / P-type monovalent copper transporter activity / P-type Cu+ transporter / copper ion export / copper ion import / copper ion transport / intracellular copper ion homeostasis / copper ion binding / ATP hydrolysis activity / ATP binding ...P-type divalent copper transporter activity / P-type monovalent copper transporter activity / P-type Cu+ transporter / copper ion export / copper ion import / copper ion transport / intracellular copper ion homeostasis / copper ion binding / ATP hydrolysis activity / ATP binding / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 10.0 Å | |||||||||
![]() | Wu C / Allen GS / Cardozo T / Stokes DL | |||||||||
![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 677.1 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.2 KB 10.2 KB | Display Display | ![]() |
Images | ![]() | 220.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 306.9 KB | Display | ![]() |
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Full document | ![]() | 306.5 KB | Display | |
Data in XML | ![]() | 4.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3j08MC ![]() 3j09C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | This is a cubic section encompassing the unit cell of a Fourier-Bessel reconstructed map of tubular vesicles - crystals of deltaC-CopA from Archaeoglobus fulgidus. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : deltaC-CopA in DMPC-DOPE lipids
Entire | Name: deltaC-CopA in DMPC-DOPE lipids |
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Components |
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-Supramolecule #1000: deltaC-CopA in DMPC-DOPE lipids
Supramolecule | Name: 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 |
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Molecular weight | Theoretical: 77 KDa |
-Macromolecule #1: membrane protein
Macromolecule | Name: membrane protein / type: protein_or_peptide / ID: 1 / Name.synonym: membrane protein / Number of copies: 2 / Oligomeric state: dimer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 77 KDa |
Recombinant expression | Organism: Escherichia coli strain LMG 1940 / Recombinant plasmid: pBAD |
Sequence | GO: copper ion transport / InterPro: INTERPRO: IPR006403 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | helical array |
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Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 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. |
Grid | Details: holey carbon grid |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 77 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: plunger / Method: blot for 5 seconds before plunging |
Details | dialysis buttons |
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Electron microscopy
Microscope | FEI/PHILIPS CM200FEG |
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Temperature | Average: 100 K |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 12 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination 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 stage | Specimen holder: CT3500 / Specimen holder model: GATAN LIQUID NITROGEN |
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Image processing
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: OTHER / Software - Name: EMIP |
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CTF correction | Details: each tube-crystal |