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- PDB-8iwu: hSPCA1 in the E2~P state -

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Basic information

Entry
Database: PDB / ID: 8iwu
TitlehSPCA1 in the E2~P state
ComponentsCalcium-transporting ATPase type 2C member 1
KeywordsMETAL 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 ...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 / positive regulation of Golgi to plasma membrane protein transport / Golgi cisterna membrane / Ion transport by P-type ATPases / epidermis development / trans-Golgi network / calcium ion transmembrane transport / 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 / endoplasmic reticulum / Golgi apparatus / ATP hydrolysis activity / ATP binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
P-type ATPase, subfamily IIA, PMR1-type / 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 / P-type ATPase, cytoplasmic domain N / P-type ATPase actuator domain / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site ...P-type ATPase, subfamily IIA, PMR1-type / 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 / P-type ATPase, cytoplasmic domain N / P-type ATPase actuator domain / 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 / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
TETRAFLUOROALUMINATE ION / Calcium-transporting ATPase type 2C member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.31 Å
AuthorsLiu, Z.M. / Wu, M.Q. / Wu, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32000850 China
CitationJournal: 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
DepositionMar 31, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.0Dec 27, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 27, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 27, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 27, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 27, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calcium-transporting ATPase type 2C member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,8063
Polymers100,6791
Non-polymers1272
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Calcium-transporting ATPase type 2C member 1 / ATPase 2C1 / ATP-dependent Ca(2+) pump PMR1 / Ca(2+)/Mn(2+)-ATPase 2C1 / Secretory pathway Ca(2+)- ...ATPase 2C1 / ATP-dependent Ca(2+) pump PMR1 / Ca(2+)/Mn(2+)-ATPase 2C1 / Secretory pathway Ca(2+)-transporting ATPase type 1 / SPCA1


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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Secretory pathway Ca(2+)-transporting ATPase type 1 / Type: COMPLEX / Entity ID: #1 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58486 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036950
ELECTRON MICROSCOPYf_angle_d0.5269411
ELECTRON MICROSCOPYf_dihedral_angle_d3.53941
ELECTRON MICROSCOPYf_chiral_restr0.0391131
ELECTRON MICROSCOPYf_plane_restr0.0051189

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