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Yorodumi- 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 | ||||||
Components | copper-exporting P-type ATPase A | ||||||
Keywords | HYDROLASE / 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 monovalent copper transporter activity / P-type Cu+ transporter / copper ion export / copper ion import / intracellular copper ion homeostasis / copper ion binding / ATP hydrolysis activity / ATP binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 10 Å | ||||||
Authors | Wu, C. / Allen, G.S. / Cardozo, T. / Stokes, D.L. | ||||||
Citation | Journal: 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 |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
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PDBx/mmCIF format | 3j08.cif.gz | 216 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3j08.ent.gz | 168.6 KB | Display | PDB format |
PDBx/mmJSON format | 3j08.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3j08_validation.pdf.gz | 737.1 KB | Display | wwPDB validaton report |
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Full document | 3j08_full_validation.pdf.gz | 781.1 KB | Display | |
Data in XML | 3j08_validation.xml.gz | 41.4 KB | Display | |
Data in CIF | 3j08_validation.cif.gz | 60.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j0/3j08 ftp://data.pdbj.org/pub/pdb/validation_reports/j0/3j08 | HTTPS FTP |
-Related structure data
Related structure data | 5271MC 3j09C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) 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
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
-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: 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 |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temp: 77 K / Method: blot for 5 seconds before plunging |
-Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS CM200FEG / Date: Jan 1, 2009 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2 mm / Camera length: 0 mm |
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 |
-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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