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- PDB-2voy: CryoEM model of CopA, the copper transporting ATPase from Archaeo... -
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Basic information
Entry | Database: PDB / ID: 2voy | ||||||
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Title | CryoEM model of CopA, the copper transporting ATPase from Archaeoglobus fulgidus | ||||||
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![]() | HYDROLASE / HYDROLASEP-TYPE ATPASE / CRYO-EM / HELICAL RECONSTRUCTION / MEMBRANE PROTEIN / COPPER TRANSPORTER / METAL BINDING DOMAIN | ||||||
Function / homology | ![]() 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 ...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 | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 18 Å | ||||||
![]() | Wu, C.-C. / Rice, W.J. / Stokes, D.L. | ||||||
![]() | ![]() 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 |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 141 KB | Display | ![]() |
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PDB format | ![]() | 110.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5004MC ![]() 5005MC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 8799.966 Da / Num. of mol.: 1 / Fragment: RESIDUES 72-147 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE ... , 8 types, 8 molecules BCDEGHKL
#2: Protein/peptide | Mass: 4832.592 Da / Num. of mol.: 1 / Fragment: RESIDUES 36-77 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#3: Protein/peptide | Mass: 2514.160 Da / Num. of mol.: 1 / Fragment: RESIDUES 967-988 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#4: Protein/peptide | Mass: 2479.875 Da / Num. of mol.: 1 / Fragment: RESIDUES 832-854 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#5: Protein/peptide | Mass: 3312.832 Da / Num. of mol.: 1 / Fragment: RESIDUES 86-115 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#7: Protein/peptide | Mass: 4097.731 Da / Num. of mol.: 1 / Fragment: RESIDUES 243-278 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#8: Protein/peptide | Mass: 5093.216 Da / Num. of mol.: 1 / Fragment: RESIDUES 289-336 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#11: Protein/peptide | Mass: 3624.217 Da / Num. of mol.: 1 / Fragment: RESIDUES 749-780 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#12: Protein/peptide | Mass: 2224.596 Da / Num. of mol.: 1 / Fragment: RESIDUES 789-809 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-CATION-TRANSPORTING ... , 3 types, 3 molecules FIJ
#6: Protein | Mass: 11832.712 Da / Num. of mol.: 1 / Fragment: RESIDUES 214-326 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#9: Protein | Mass: 13783.532 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#10: Protein | Mass: 12705.334 Da / Num. of mol.: 1 / Fragment: RESIDUES 432-549 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Details
Sequence details | EM MAP TO WHICH THIS SEQUENCE WAS MODELED PDB ENTRIES USED TO MODEL CHAIN A: 1JWW PDB ENTRIES USED ...EM MAP TO WHICH THIS SEQUENCE WAS MODELED PDB ENTRIES USED TO MODEL CHAIN A: 1JWW PDB ENTRIES USED TO MODEL CHAINS B, C, D, E, G, H, K, L: 1WPG PDB ENTRIES USED TO MODEL CHAIN F: 2HC8 PDB ENTRIES USED TO MODEL CHAINS I, J: 2B8E |
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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 |
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Sample preparation
Component | Name: COPA DELTA C, DELTA N DELTA C / Type: COMPLEX Details: MICROGRAPHS SCANNED AT 14 MICRON INTERVAL USING ZEISS- SCAI SCANNER |
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Buffer solution | Name: 50 MM MES PH 6.1 25 MM NA2SO4 25 MM K2SO4 10 MM MGSO4 2 MM 2-MERCAPTOETHANOL 0.2 MM BCDS pH: 6.1 Details: 50 MM MES PH 6.1 25 MM NA2SO4 25 MM K2SO4 10 MM MGSO4 2 MM 2-MERCAPTOETHANOL 0.2 MM BCDS |
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: LIQUID ETHANE. SAMPLES FROZEN IN COLD ROOM |
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Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS CM200FEG/ST / Details: FIELD EMISSION GUN |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 51300 X / Nominal defocus max: 2500 nm / Nominal defocus min: 900 nm / Cs: 2 mm |
Specimen holder | Temperature: 100 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 10 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 24 |
Radiation wavelength | Relative weight: 1 |
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Processing
EM software | Name: Custom / Category: 3D reconstruction / Details: HELICAL SOFTWARE FROM NIGEL UNWIN | ||||||||||||
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CTF correction | Details: INDIVIDUAL TUBES | ||||||||||||
3D reconstruction | Method: TUBES DIVIDED INTO THIRDS, QUARTERS, OR FIFTHS AND CORRECTED FOR IN-PLACE ROTATION, OUT-OF-PLANE TILT, Z-SHIFT, ROTATION ABOUT Z-AXIS Resolution: 18 Å / Nominal pixel size: 2 Å / Actual pixel size: 2 Å Details: ALL AVERAGING DONE IN FOURIER SPACE. ALL TUBES AVERAGED HAD IDENTICAL HELICAL SYMMETRY Symmetry type: HELICAL | ||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL / Details: METHOD--MANUAL REFINEMENT PROTOCOL--X-RAY | ||||||||||||
Atomic model building |
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Refinement step | Cycle: LAST
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