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- EMDB-35781: hSPCA1 in the CaE1P-ADP state -

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Basic information

Entry
Database: EMDB / ID: EMD-35781
TitlehSPCA1 in the CaE1P-ADP state
Map data
Sample
  • Complex: Secretory pathway Ca(2+)-transporting ATPase type 1
    • Protein or peptide: Calcium-transporting ATPase type 2C member 1
  • Ligand: CALCIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: TETRAFLUOROALUMINATE ION
KeywordshSPCA1 / MEMBRANE PROTEIN / METAL TRANSPORT
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
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 / Cation transport ATPase (P-type) / E1-E2 ATPase / 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 / Cation transport ATPase (P-type) / E1-E2 ATPase / 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
Calcium-transporting ATPase type 2C member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.71 Å
AuthorsLiu ZM / Wu MQ / Wu C
Funding support China, 1 items
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, 2023-
Header (metadata) releaseDec 27, 2023-
Map releaseDec 27, 2023-
UpdateDec 27, 2023-
Current statusDec 27, 2023Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35781.png

Downloads & links

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Map

FileDownload / File: emd_35781.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 360 pix.
= 302.4 Å		0.84 Å/pix.
x 360 pix.
= 302.4 Å		0.84 Å/pix.
x 360 pix.
= 302.4 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.118
Minimum - Maximum-0.49214652 - 0.87651664
Average (Standard dev.)0.00036126332 (±0.01497407)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 302.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35781_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35781_half_map_2.map
Projections & Slices
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Sample components

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Entire : Secretory pathway Ca(2+)-transporting ATPase type 1

EntireName: Secretory pathway Ca(2+)-transporting ATPase type 1
Components
  • Complex: Secretory pathway Ca(2+)-transporting ATPase type 1
    • Protein or peptide: Calcium-transporting ATPase type 2C member 1
  • Ligand: CALCIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: TETRAFLUOROALUMINATE ION

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Supramolecule #1: Secretory pathway Ca(2+)-transporting ATPase type 1

SupramoleculeName: Secretory pathway Ca(2+)-transporting ATPase type 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Calcium-transporting ATPase type 2C member 1

MacromoleculeName: Calcium-transporting ATPase type 2C member 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: P-type Ca2+ transporter
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 97.806797 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MIPVLTSKKA SELPVSEVAS ILQADLQNGL NKCEVSHRRA FHGWNEFDIS EDEPLWKKYI SQFKNPLIML LLASAVISVL MHQFDDAVS ITVAILIVVT VAFVQEYRSE KSLEELSKLV PPECHCVREG KLEHTLARDL VPGDTVCLSV GDRVPADLRL F EAVDLSID ...String:
MIPVLTSKKA SELPVSEVAS ILQADLQNGL NKCEVSHRRA FHGWNEFDIS EDEPLWKKYI SQFKNPLIML LLASAVISVL MHQFDDAVS ITVAILIVVT VAFVQEYRSE KSLEELSKLV PPECHCVREG KLEHTLARDL VPGDTVCLSV GDRVPADLRL F EAVDLSID ESSLTGETTP CSKVTAPQPA ATNGDLASRS NIAFMGTLVR CGKAKGVVIG TGENSEFGEV FKMMQAEEAP KT PLQKSMD LLGKQLSFYS FGIIGIIMLV GWLLGKDILE MFTISVSLAV AAIPEGLPIV VTVTLALGVM RMVKKRAIVK KLP IVETLG CCNVICSDKT GTLTKNEMTV THIFTSDGLH AEVTGVGYNQ FGEVIVDGDV VHGFYNPAVS RIVEAGCVCN DAVI RNNTL MGKPTEGALI ALAMKMGLDG LQQDYIRKAE YPFSSEQKWM AVKCVHRTQQ DRPEICFMKG AYEQVIKYCT TYQSK GQTL TLTQQQRDVY QQEKARMGSA GLRVLALASG PELGQLTFLG LVGIIDPPRT GVKEAVTTLI ASGVSIKMIT GDSQET AVA IASRLGLYSK TSQSVSGEEI DAMDVQQLSQ IVPKVAVFYR ASPRHKMKII KSLQKNGSVV AMTGDGVNDA VALKAAD IG VAMGQTGTDV CKEAADMILV DDDFQTIMSA IEEGKGIYNN IKNFVRFQLS TSIAALTLIS LATLMNFPNP LNAMQILW I NIIMDGPPAQ SLGVEPVDKD VIRKPPRNWK DSILTKNLIL KILVSSIIIV CGTLFVFWRE LRDNVITPRD TTMTFTCFV FFDMFNALSS RSQTKSVFEI GLCSNRMFCY AVLGSIMGQL LVIYFPPLQK VFQTESLSIL DLLFLLGLTS SVCIVAEIIK KVERSREKI QKHV

UniProtKB: Calcium-transporting ATPase type 2C member 1

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #4: TETRAFLUOROALUMINATE ION

MacromoleculeName: TETRAFLUOROALUMINATE ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ALF
Molecular weightTheoretical: 102.975 Da
Chemical component information

ChemComp-ALF:
TETRAFLUOROALUMINATE ION

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.71 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 88366
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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