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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 | ||||||
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Title | High resolution helical reconstruction of the bacterial p-type ATPase copper transporter CopA | ||||||
![]() | copper-exporting P-type ATPase A | ||||||
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Function / homology | ![]() P-type divalent copper transporter activity / P-type monovalent copper transporter activity / P-type Cu+ transporter / copper ion export / copper ion import / intracellular copper ion homeostasis / copper ion binding / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Wu, C. / Allen, G.S. / Cardozo, T. / Stokes, D.L. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 216 KB | Display | ![]() |
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PDB format | ![]() | 168.6 KB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5271MC ![]() 3j09C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | 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.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: O29777, ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
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Sample preparation
Component | Name: 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. |
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Molecular weight | Value: 0.077 MDa / Experimental value: NO |
Buffer solution | pH: 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 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() Details: 50 mM MES, pH 6.1, 25 mM Na2SO4, 25 mM K2SO4, 200 uM BCDS, 10 mM MgSO4, 2 mM beta-mercaptoethanol |
Vitrification![]() | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temp: 77 K / Method: blot for 5 seconds before plunging |
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Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS CM200FEG / Date: Jan 1, 2009 |
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Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() ![]() |
Specimen holder | Specimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: CT3500 / Temperature: 100 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Film or detector model: KODAK SO-163 FILM |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
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Processing
EM software | Name: EMIP / Category: 3D reconstruction![]() | ||||||||||||
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CTF correction![]() | Details: each tube-crystal | ||||||||||||
3D reconstruction![]() | Method: Fourier-Bessel / Resolution: 10 Å / Resolution method: OTHER / Symmetry type: HELICAL | ||||||||||||
Refinement step | Cycle: LAST
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