[English] 日本語
![](img/lk-miru.gif)
- EMDB-5004: Structure of the Copper Transporting ATPase of A. fulgidus by Cry... -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-5004 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the Copper Transporting ATPase of A. fulgidus by Cryo-electron microscopy. | |||||||||
![]() | This is one unit cell masked from CopA DeltaC tubular crystals imaged by cryo-EM | |||||||||
![]() |
| |||||||||
![]() | P-type ATPase / copper / metal binding domain / helical reconstruction | |||||||||
Function / homology | ![]() P-type divalent copper transporter activity => GO:0043682 / P-type divalent copper transporter activity / positive regulation of cardiac muscle cell contraction / positive regulation of calcium ion import into sarcoplasmic reticulum / H zone / positive regulation of fast-twitch skeletal muscle fiber contraction / positive regulation of ATPase-coupled calcium transmembrane transporter activity / P-type monovalent copper transporter activity / P-type Cu+ transporter / copper ion export ...P-type divalent copper transporter activity => GO:0043682 / P-type divalent copper transporter activity / positive regulation of cardiac muscle cell contraction / positive regulation of calcium ion import into sarcoplasmic reticulum / H zone / positive regulation of fast-twitch skeletal muscle fiber contraction / positive regulation of ATPase-coupled calcium transmembrane transporter activity / P-type monovalent copper transporter activity / P-type Cu+ transporter / copper ion export / copper ion import / calcium ion import into sarcoplasmic reticulum / negative regulation of striated muscle contraction / regulation of striated muscle contraction / copper ion homeostasis / P-type Ca2+ transporter / P-type calcium transporter activity / I band / endoplasmic reticulum-Golgi intermediate compartment / intracellular copper ion homeostasis / sarcoplasmic reticulum membrane / sarcoplasmic reticulum / intracellular calcium ion homeostasis / calcium ion transport / copper ion binding / calcium ion binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 17.5 Å | |||||||||
![]() | Wu C / Rice WJ / Stokes DL | |||||||||
![]() | ![]() Title: Structure of a copper pump suggests a regulatory role for its metal-binding domain. Authors: Chen-Chou Wu / William J Rice / David L Stokes / ![]() Abstract: P-type ATPases play an important role in Cu homeostasis, which provides sufficient Cu for metalloenzyme biosynthesis but prevents oxidative damage of free Cu to the cell. The P(IB) group of P-type ...P-type ATPases play an important role in Cu homeostasis, which provides sufficient Cu for metalloenzyme biosynthesis but prevents oxidative damage of free Cu to the cell. The P(IB) group of P-type ATPases includes ATP-dependent pumps of Cu and other transition metal ions, and it is distinguished from other family members by the presence of N-terminal metal-binding domains (MBD). We have determined structures of two constructs of a Cu pump from Archaeoglobus fulgidus (CopA) by cryoelectron microscopy of tubular crystals, which reveal the overall architecture and domain organization of the molecule. By comparing these structures, we localized its N-terminal MBD within the cytoplasmic domains that use ATP hydrolysis to drive the transport cycle. We have built a pseudoatomic model by fitting existing crystallographic structures into the cryoelectron microscopy maps for CopA, which suggest a Cu-dependent regulatory role for the MBD. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 3.7 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 10.2 KB 10.2 KB | Display Display | ![]() |
Images | ![]() | 31.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2voyMC ![]() 3j09M ![]() 5005C M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | This is one unit cell masked from CopA DeltaC tubular crystals imaged by cryo-EM | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : DeltaC construct of CopA, the copper transporting ATPase of A. fu...
Entire | Name: DeltaC construct of CopA, the copper transporting ATPase of A. fulgidus |
---|---|
Components |
|
-Supramolecule #1000: DeltaC construct of CopA, the copper transporting ATPase of A. fu...
Supramolecule | Name: DeltaC construct of CopA, the copper transporting ATPase of A. fulgidus type: sample / ID: 1000 / Oligomeric state: homodimer / Number unique components: 1 |
---|---|
Molecular weight | Theoretical: 80 KDa / Method: SDS-PAGE |
-Macromolecule #1: P-type ATPase
Macromolecule | Name: P-type ATPase / type: protein_or_peptide / ID: 1 / Name.synonym: Cu pump / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: Yes |
---|---|
Source (natural) | Strain: Archaeoglobus fulgidus / Location in cell: plasma membrane |
Recombinant expression | Organism: ![]() ![]() |
Sequence | GO: P-type divalent copper transporter activity => GO:0043682 InterPro: INTERPRO: IPR001756 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | helical reconstruction |
Aggregation state | helical array |
-
Sample preparation
Concentration | 0.5 mg/mL |
---|---|
Buffer | pH: 6.1 Details: 50 mM MES, 25 mM Na2SO4, 25 mM K2SO4, 10 mM MgSO4, 2 mM 2-mercaptoethanol, 200 uM BCDS, |
Grid | Details: 300 mesh holey carbon |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 75 % / Chamber temperature: 100 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: home made plunger Method: Blot for 2-5 seconds before plunging. Plunge in cold room. |
Details | crystals grown at 45 to 55 C |
-
Electron microscopy
Microscope | FEI/PHILIPS CM200FEG/UT |
---|---|
Temperature | Average: 100 K |
Alignment procedure | Legacy - Astigmatism: objective astigmatism corrected at 200,000X mag |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 24 / Average electron dose: 10 e/Å2 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 51300 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Oxford / Specimen holder model: OTHER |
-
Image processing
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.5 Å / Resolution method: FSC 0.5 CUT-OFF |
---|---|
CTF correction | Details: each tube |
-Atomic model buiding 1
Initial model | PDB ID: |
---|---|
Details | Domains separately fitted by manual docking using O and Chimera |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | ![]() PDB-2voy: ![]() PDB-3j09: |