+Open data
-Basic information
Entry | Database: PDB / ID: 7xun | |||||||||||||||
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Title | Structure of ATP7B C983S/C985S/D1027A mutant | |||||||||||||||
Components | Copper-transporting ATPase 2 | |||||||||||||||
Keywords | TRANSLOCATE / METAT TRANSPORT / P-type Cu(+) transporter / Translocase / METAL TRANSPORT | |||||||||||||||
Function / homology | Function and homology information protein maturation by copper ion transfer / copper ion transmembrane transporter activity / P-type divalent copper transporter activity / P-type monovalent copper transporter activity / P-type Cu+ transporter / sequestering of calcium ion / copper ion export / copper ion import / copper ion transport / xenobiotic detoxification by transmembrane export across the plasma membrane ...protein maturation by copper ion transfer / copper ion transmembrane transporter activity / P-type divalent copper transporter activity / P-type monovalent copper transporter activity / P-type Cu+ transporter / sequestering of calcium ion / copper ion export / copper ion import / copper ion transport / xenobiotic detoxification by transmembrane export across the plasma membrane / intracellular zinc ion homeostasis / response to copper ion / Ion transport by P-type ATPases / intracellular copper ion homeostasis / monoatomic ion transmembrane transport / lactation / trans-Golgi network membrane / establishment of localization in cell / late endosome / copper ion binding / Golgi membrane / Golgi apparatus / ATP hydrolysis activity / mitochondrion / ATP binding / membrane / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||||||||
Authors | Yang, G. / Xu, L. / Guo, J. / Wu, Z. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: Cell Rep / Year: 2023 Title: Structures of the human Wilson disease copper transporter ATP7B. Authors: Guo-Min Yang / Lingyi Xu / Rou-Min Wang / Xin Tao / Zi-Wei Zheng / Shenghai Chang / Demin Ma / Cheng Zhao / Yi Dong / Shan Wu / Jiangtao Guo / Zhi-Ying Wu / Abstract: The P-type ATPase ATP7B exports cytosolic copper and plays an essential role in the regulation of cellular copper homeostasis. Mutants of ATP7B cause Wilson disease (WD), an autosomal recessive ...The P-type ATPase ATP7B exports cytosolic copper and plays an essential role in the regulation of cellular copper homeostasis. Mutants of ATP7B cause Wilson disease (WD), an autosomal recessive disorder of copper metabolism. Here, we present cryoelectron microscopy (cryo-EM) structures of human ATP7B in the E1 state in the apo, the putative copper-bound, and the putative cisplatin-bound forms. In ATP7B, the N-terminal sixth metal-binding domain (MBD6) binds at the cytosolic copper entry site of the transmembrane domain (TMD), facilitating the delivery of copper from the MBD6 to the TMD. The sulfur-containing residues in the TMD of ATP7B mark the copper transport pathway. By comparing structures of the E1 state human ATP7B and E2-P state frog ATP7B, we propose the ATP-driving copper transport model of ATP7B. These structures not only advance our understanding of the mechanisms of ATP7B-mediated copper export but can also guide the development of therapeutics for the treatment of WD. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xun.cif.gz | 151.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xun.ent.gz | 107.5 KB | Display | PDB format |
PDBx/mmJSON format | 7xun.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xun_validation.pdf.gz | 962.9 KB | Display | wwPDB validaton report |
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Full document | 7xun_full_validation.pdf.gz | 972.4 KB | Display | |
Data in XML | 7xun_validation.xml.gz | 31.9 KB | Display | |
Data in CIF | 7xun_validation.cif.gz | 45.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xu/7xun ftp://data.pdbj.org/pub/pdb/validation_reports/xu/7xun | HTTPS FTP |
-Related structure data
Related structure data | 33475MC 7xukC 7xumC 7xuoC 8ioyC 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: 162033.516 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ATP7B / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P35670, P-type Cu+ transporter |
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-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: ATP7B / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293 |
Buffer solution | pH: 7.4 |
Specimen | 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: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1300 nm / Nominal defocus min: 1100 nm |
Image recording | Electron dose: 62 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 338254 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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