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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
TitleCryoEM model of CopA, the copper transporting ATPase from Archaeoglobus fulgidus
Components
  • (CATION-TRANSPORTING ...) x 3
  • (SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE ...) x 8
  • POTENTIAL COPPER-TRANSPORTING ATPASE
KeywordsHYDROLASE / HYDROLASEP-TYPE ATPASE / CRYO-EM / HELICAL RECONSTRUCTION / MEMBRANE PROTEIN / COPPER TRANSPORTER / METAL BINDING DOMAIN
Function / homology
Function and homology information


P-type divalent copper transporter activity / positive regulation of cardiac muscle cell contraction / positive regulation of calcium ion import into sarcoplasmic reticulum / positive regulation of ATPase-coupled calcium transmembrane transporter activity / positive regulation of fast-twitch skeletal muscle fiber contraction / H zone / P-type Cu+ transporter / P-type monovalent copper transporter activity / calcium ion import into sarcoplasmic reticulum / negative regulation of striated muscle contraction ...P-type divalent copper transporter activity / positive regulation of cardiac muscle cell contraction / positive regulation of calcium ion import into sarcoplasmic reticulum / positive regulation of ATPase-coupled calcium transmembrane transporter activity / positive regulation of fast-twitch skeletal muscle fiber contraction / H zone / P-type Cu+ transporter / P-type monovalent copper transporter activity / 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 / 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
Heavy metal-associated domain, copper ion-binding / P-type ATPase, subfamily IIA, SERCA-type / P-type ATPase, subfamily IB / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Cation-transporting P-type ATPase, C-terminal ...Heavy metal-associated domain, copper ion-binding / P-type ATPase, subfamily IIA, SERCA-type / P-type ATPase, subfamily IB / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / Cation transport ATPase (P-type) / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Probable copper-exporting P-type ATPase / Copper-exporting P-type ATPase / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
ARCHAEOGLOBUS FULGIDUS (archaea)
ORYCTOLAGUS CUNICULUS (rabbit)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 18 Å
AuthorsWu, C.-C. / Rice, W.J. / Stokes, D.L.
CitationJournal: Structure / Year: 2008
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
DepositionFeb 25, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Derived calculations / Other ...Derived calculations / Other / Source and taxonomy / Version format compliance
Revision 1.2Apr 19, 2017Group: Other
Revision 1.3Oct 3, 2018Group: Author supporting evidence / Data collection / Category: em_single_particle_entity / em_software / Item: _em_software.image_processing_id
Revision 1.4May 4, 2022Group: Database references / Derived calculations / Category: database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Oct 23, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
A: POTENTIAL COPPER-TRANSPORTING ATPASE
B: SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1
C: SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1
D: SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1
E: SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1
F: CATION-TRANSPORTING ATPASE, P-TYPE
G: SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1
H: SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1
I: CATION-TRANSPORTING ATPASE
J: CATION-TRANSPORTING ATPASE
K: SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1
L: SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1


Theoretical massNumber of molelcules
Total (without water)75,30112
Polymers75,30112
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 1 types, 1 molecules A

#1: Protein POTENTIAL COPPER-TRANSPORTING ATPASE / COPA DELTA C


Mass: 8799.966 Da / Num. of mol.: 1 / Fragment: RESIDUES 72-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: O32220, Cu2+-exporting ATPase

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SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE ... , 8 types, 8 molecules BCDEGHKL

#2: Protein/peptide SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1 / CA2+-ATPASE / SERCA1 / COPA DELTA C


Mass: 4832.592 Da / Num. of mol.: 1 / Fragment: RESIDUES 36-77 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Tissue: SKELETAL MUSCLE (WHITE) / References: UniProt: P04191, EC: 3.6.3.8
#3: Protein/peptide SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1 / CA2+-ATPASE / SERCA1 / COPA DELTA C


Mass: 2514.160 Da / Num. of mol.: 1 / Fragment: RESIDUES 967-988 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Tissue: SKELETAL MUSCLE (WHITE) / References: UniProt: P04191, EC: 3.6.3.8
#4: Protein/peptide SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1 / CA2+-ATPASE / SERCA1 / COPA DELTA C


Mass: 2479.875 Da / Num. of mol.: 1 / Fragment: RESIDUES 832-854 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Tissue: SKELETAL MUSCLE (WHITE) / References: UniProt: P04191, EC: 3.6.3.8
#5: Protein/peptide SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1 / CA2+-ATPASE / SERCA1 / COPA DELTA C


Mass: 3312.832 Da / Num. of mol.: 1 / Fragment: RESIDUES 86-115 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Tissue: SKELETAL MUSCLE (WHITE) / References: UniProt: P04191, EC: 3.6.3.8
#7: Protein/peptide SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1 / CA2+-ATPASE / SERCA1 / COPA DELTA C


Mass: 4097.731 Da / Num. of mol.: 1 / Fragment: RESIDUES 243-278 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Tissue: SKELETAL MUSCLE (WHITE) / References: UniProt: P04191, EC: 3.6.3.8
#8: Protein/peptide SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1 / CA2+-ATPASE / SERCA1 / COPA DELTA C


Mass: 5093.216 Da / Num. of mol.: 1 / Fragment: RESIDUES 289-336 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Tissue: SKELETAL MUSCLE (WHITE) / References: UniProt: P04191, EC: 3.6.3.8
#11: Protein/peptide SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1 / CA2+-ATPASE / SERCA1 / COPA DELTA C


Mass: 3624.217 Da / Num. of mol.: 1 / Fragment: RESIDUES 749-780 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Tissue: SKELETAL MUSCLE (WHITE) / References: UniProt: P04191, EC: 3.6.3.8
#12: Protein/peptide SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1 / CA2+-ATPASE / SERCA1 / COPA DELTA C


Mass: 2224.596 Da / Num. of mol.: 1 / Fragment: RESIDUES 789-809 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Tissue: SKELETAL MUSCLE (WHITE) / References: UniProt: P04191, EC: 3.6.3.8

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CATION-TRANSPORTING ... , 3 types, 3 molecules FIJ

#6: Protein CATION-TRANSPORTING ATPASE, P-TYPE / PACS / COPA DELTA C


Mass: 11832.712 Da / Num. of mol.: 1 / Fragment: RESIDUES 214-326
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Plasmid: PPR-IBA1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O29777, Cu2+-exporting ATPase
#9: Protein CATION-TRANSPORTING ATPASE / COPA / COPA DELTA C


Mass: 13783.532 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Plasmid: PPR-IBA1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: O29777*PLUS, Cu2+-exporting ATPase
#10: Protein CATION-TRANSPORTING ATPASE / COPA / COPA DELTA C


Mass: 12705.334 Da / Num. of mol.: 1 / Fragment: RESIDUES 432-549
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Plasmid: PPR-IBA1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: O29777, Cu2+-exporting ATPase

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Details

Has protein modificationY
Sequence detailsEM 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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: COPA DELTA C, DELTA N DELTA C / Type: COMPLEX
Details: MICROGRAPHS SCANNED AT 14 MICRON INTERVAL USING ZEISS- SCAI SCANNER
Buffer solutionName: 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
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: LIQUID ETHANE. SAMPLES FROZEN IN COLD ROOM

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM200FEG/ST / Details: FIELD EMISSION GUN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 51300 X / Nominal defocus max: 2500 nm / Nominal defocus min: 900 nm / Cs: 2 mm
Specimen holderTemperature: 100 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 10 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 24
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: Custom / Category: 3D reconstruction / Details: HELICAL SOFTWARE FROM NIGEL UNWIN
CTF correctionDetails: INDIVIDUAL TUBES
3D reconstructionMethod: 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 buildingProtocol: OTHER / Space: REAL / Details: METHOD--MANUAL REFINEMENT PROTOCOL--X-RAY
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
12B8E

2b8e

12B8E1PDBexperimental model
22HC8

2hc8

12HC82PDBexperimental model
32EAR

2ear

12EAR3PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms5270 0 0 0 5270

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