+Open data
-Basic information
Entry | Database: PDB / ID: 8q74 | |||||||||
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Title | Copper-transporting ATPase HMA4 in E1 state with Cu | |||||||||
Components | Copper-transporting ATPase HMA4 | |||||||||
Keywords | TRANSPORT PROTEIN / P-ATPase | |||||||||
Function / homology | Function and homology information P-type Cu+ transporter / P-type monovalent copper transporter activity / vacuolar membrane / copper ion binding / ATP hydrolysis activity / ATP binding Similarity search - Function | |||||||||
Biological species | Oryza sativa Japonica Group (Japanese rice) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.68 Å | |||||||||
Authors | Guo, Z. / Gourdon, P. / Wang, K. | |||||||||
Funding support | Denmark, 2items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8q74.cif.gz | 147.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8q74.ent.gz | 111.8 KB | Display | PDB format |
PDBx/mmJSON format | 8q74.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8q74_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 8q74_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8q74_validation.xml.gz | 42 KB | Display | |
Data in CIF | 8q74_validation.cif.gz | 60.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q7/8q74 ftp://data.pdbj.org/pub/pdb/validation_reports/q7/8q74 | HTTPS FTP |
-Related structure data
Related structure data | 18203MC 8q73C 8q75C 8q76C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 105236.398 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice) Gene: HMA4 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q6H7M3 |
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#2: Chemical | ChemComp-CU / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Copper-transporting ATPase HMA4 from Oryza sativa subsp. japonica Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||||||||||||
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Source (natural) | Organism: Oryza sativa Japonica Group (Japanese rice) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Saccharomyces cerevisiae (brewer's yeast) | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 / Details: 20mM tris-hcl, 150mM NaCl, o.5mM CuCl2, 1mM TCEP | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 2500 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 246045 / Symmetry type: POINT | ||||||||||||||||||||||||
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