+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18204 | |||||||||
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Title | Copper-transporting ATPase HMA4 in E2P state with AlF | |||||||||
Map data | ||||||||||
Sample |
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Keywords | P-ATPase / TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information P-type monovalent copper transporter activity / P-type Cu+ transporter / vacuolar membrane / copper ion binding / ATP hydrolysis activity / ATP binding Similarity search - Function | |||||||||
Biological species | Oryza sativa Japonica Group (Japanese rice) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Guo Z / Gourdon P / Wang K | |||||||||
Funding support | Denmark, 2 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Diverse roles of the metal binding domains and transport mechanism of copper transporting P-type ATPases. Authors: Zongxin Guo / Fredrik Orädd / Viktoria Bågenholm / Christina Grønberg / Jian Feng Ma / Peter Ott / Yong Wang / Magnus Andersson / Per Amstrup Pedersen / Kaituo Wang / Pontus Gourdon / Abstract: Copper transporting P-type (P-) ATPases are essential for cellular homeostasis. Nonetheless, the E1-E1P-E2P-E2 states mechanism of P-ATPases remains poorly understood. In particular, the role of the ...Copper transporting P-type (P-) ATPases are essential for cellular homeostasis. Nonetheless, the E1-E1P-E2P-E2 states mechanism of P-ATPases remains poorly understood. In particular, the role of the intrinsic metal binding domains (MBDs) is enigmatic. Here, four cryo-EM structures and molecular dynamics simulations of a P-ATPase are combined to reveal that in many eukaryotes the MBD immediately prior to the ATPase core, MBD, serves a structural role, remodeling the ion-uptake region. In contrast, the MBD prior to MBD, MBD, likely assists in copper delivery to the ATPase core. Invariant Tyr, Asn and Ser residues in the transmembrane domain assist in positioning sulfur-providing copper-binding amino acids, allowing for copper uptake, binding and release. As such, our findings unify previously conflicting data on the transport and regulation of P-ATPases. The results are critical for a fundamental understanding of cellular copper homeostasis and for comprehension of the molecular bases of P-disorders and ongoing clinical trials. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18204.map.gz | 62.4 MB | EMDB map data format | |
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Header (meta data) | emd-18204-v30.xml emd-18204.xml | 15.3 KB 15.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18204_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_18204.png | 28.4 KB | ||
Filedesc metadata | emd-18204.cif.gz | 5.8 KB | ||
Others | emd_18204_half_map_1.map.gz emd_18204_half_map_2.map.gz | 116.1 MB 116.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18204 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18204 | HTTPS FTP |
-Validation report
Summary document | emd_18204_validation.pdf.gz | 711.9 KB | Display | EMDB validaton report |
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Full document | emd_18204_full_validation.pdf.gz | 711.4 KB | Display | |
Data in XML | emd_18204_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | emd_18204_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18204 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18204 | HTTPS FTP |
-Related structure data
Related structure data | 8q75MC 8q73C 8q74C 8q76C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_18204.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.832 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_18204_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_18204_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Copper-transporting ATPase HMA4 from Oryza sativa subsp. japonica
Entire | Name: Copper-transporting ATPase HMA4 from Oryza sativa subsp. japonica |
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Components |
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-Supramolecule #1: Copper-transporting ATPase HMA4 from Oryza sativa subsp. japonica
Supramolecule | Name: Copper-transporting ATPase HMA4 from Oryza sativa subsp. japonica type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Oryza sativa Japonica Group (Japanese rice) |
-Macromolecule #1: Copper-transporting ATPase HMA4
Macromolecule | Name: Copper-transporting ATPase HMA4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Oryza sativa Japonica Group (Japanese rice) |
Molecular weight | Theoretical: 94.744531 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: EVDELQEQEI AVCRLQIKGM ACTSCSESVE RALQMVPGVK KAAVGLALEE AKVHFDPNIT SRDLIIEAIE DAGFGADLIS SGDDVNKVH LKLEGVSSPE DIKLIQSRLE SVEGVNNVEC DTAGQTIIVA YDPDVTGPRL LIQCIQDAAQ PPKYFNASLY S PPKQREAE ...String: EVDELQEQEI AVCRLQIKGM ACTSCSESVE RALQMVPGVK KAAVGLALEE AKVHFDPNIT SRDLIIEAIE DAGFGADLIS SGDDVNKVH LKLEGVSSPE DIKLIQSRLE SVEGVNNVEC DTAGQTIIVA YDPDVTGPRL LIQCIQDAAQ PPKYFNASLY S PPKQREAE RHHEIRNYRN QFLWSCLFSV PVFMFSMVLP MISPFGDWLF YKVCNNMTIG MLLRWLLCSP VQFIIGWRFY VG AYHALKR GYSNMDVLVA LGTNAAYFYS VYIVLKALTS ESFEGQDFFE TSAMLISFIL LGKYLEVVAK GKTSDALSKL TEL APETAC LLTLDKDGNA ISETEISTQL LQRNDVIKIV PGEKVPVDGV VIKGQSHVNE SMITGEARPI AKKPGDKVIG GTVN DNGCI IVKVTHVGSE TALSQIVQLV EAAQLARAPV QKLADRISRF FVPTVVVAAF LTWLGWFVAG QFDIYPREWI PKAMD SFEL ALQFGISVLV VACPCALGLA TPTAVMVATG KGASQGVLIK GGNALEKAHK VKAIIFDKTG TLTVGKPSVV QTKVFS KIP LLELCDLAAG AEANSEHPLS KAIVEYTKKL REQYGSHSDH IMESKDFEVH PGAGVSANVE GKLVLVGNKR LMQEFEV PI SSEVEGHMSE TEELARTCVL VAIDRTICGA LSVSDPLKPE AGRAISYLSS MGISSIMVTG DNWATAKSIA KEVGIGTV F AEIDPVGKAE KIKDLQMKGL TVAMVGDGIN DSPALAAADV GLAIGAGTDV AIEAADIVLM RSSLEDVITA IDLSRKTLS RIRLNYVWAL GYNVLGMPVA AGVLFPFTGI RLPPWLAGAC MAASSVSVVC SSLLLQLYKK PLHVEEVAAG PKNDPDLV UniProtKB: Copper-transporting ATPase HMA4 |
-Macromolecule #2: TETRAFLUOROALUMINATE ION
Macromolecule | Name: TETRAFLUOROALUMINATE ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: ALF |
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Molecular weight | Theoretical: 102.975 Da |
Chemical component information | ChemComp-ALF: |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 2.5 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |