+Open data
-Basic information
Entry | Database: PDB / ID: 8iwr | ||||||
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Title | hSPCA1 in the CaE1-ATP state | ||||||
Components | Calcium-transporting ATPase type 2C member 1 | ||||||
Keywords | METAL TRANSPORT / hSPCA1 / MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information Golgi calcium ion homeostasis / Golgi calcium ion transport / P-type manganese transporter activity / trans-Golgi network membrane organization / manganese ion transport / intracellular manganese ion homeostasis / cis-Golgi network membrane / P-type Ca2+ transporter / P-type calcium transporter activity / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules ...Golgi calcium ion homeostasis / Golgi calcium ion transport / P-type manganese transporter activity / trans-Golgi network membrane organization / manganese ion transport / intracellular manganese ion homeostasis / cis-Golgi network membrane / P-type Ca2+ transporter / P-type calcium transporter activity / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / positive regulation of Golgi to plasma membrane protein transport / Golgi cisterna membrane / Ion transport by P-type ATPases / epidermis development / calcium ion transmembrane transport / trans-Golgi network / intracellular calcium ion homeostasis / calcium ion transport / manganese ion binding / actin cytoskeleton organization / positive regulation of canonical NF-kappaB signal transduction / Golgi membrane / calcium ion binding / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.52 Å | ||||||
Authors | Liu, Z.M. / Wu, M.Q. / Wu, C. | ||||||
Funding support | China, 1items
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Citation | Journal: Cell Res / Year: 2023 Title: Structure and transport mechanism of the human calcium pump SPCA1. Authors: Mengqi Wu / Cang Wu / Tiefeng Song / Kewu Pan / Yong Wang / Zhongmin Liu / Abstract: Secretory-pathway Ca-ATPases (SPCAs) play critical roles in maintaining Ca homeostasis, but the exact mechanism of SPCAs-mediated Ca transport remains unclear. Here, we determined six cryo-electron ...Secretory-pathway Ca-ATPases (SPCAs) play critical roles in maintaining Ca homeostasis, but the exact mechanism of SPCAs-mediated Ca transport remains unclear. Here, we determined six cryo-electron microscopy (cryo-EM) structures of human SPCA1 (hSPCA1) in a series of intermediate states, revealing a near-complete conformational cycle. With the aid of molecular dynamics simulations, these structures offer a clear structural basis for Ca entry and release in hSPCA1. We found that hSPCA1 undergoes unique conformational changes during ATP binding and phosphorylation compared to other well-studied P-type II ATPases. In addition, we observed a conformational distortion of the Ca-binding site induced by the separation of transmembrane helices 4L and 6, unveiling a distinct Ca release mechanism. Particularly, we determined a structure of the long-sought CaE2P state of P-type IIA ATPases, providing valuable insights into the Ca transport cycle. Together, these findings enhance our understanding of Ca transport by hSPCA1 and broaden our knowledge of P-type ATPases. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8iwr.cif.gz | 164 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8iwr.ent.gz | 126.9 KB | Display | PDB format |
PDBx/mmJSON format | 8iwr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/8iwr ftp://data.pdbj.org/pub/pdb/validation_reports/iw/8iwr | HTTPS FTP |
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-Related structure data
Related structure data | 35777MC 8iwpC 8iwsC 8iwtC 8iwuC 8iwwC 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: 100679.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ATP2C1, KIAA1347, PMR1L, HUSSY-28 / Production host: Homo sapiens (human) / References: UniProt: P98194, P-type Ca2+ transporter |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-ACP / |
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: Secretory pathway Ca(2+)-transporting ATPase type 1 / Type: COMPLEX / Entity ID: #1 / Source: MULTIPLE SOURCES |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8 |
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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 195840 / Symmetry type: POINT | ||||||||||||||||||||||||
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