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- EMDB-35779: hSPCA1 in the early E2P state -

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Basic information

Entry
Database: EMDB / ID: EMD-35779
TitlehSPCA1 in the early E2P state
Map data
Sample
  • Complex: Secretory pathway Ca(2+)-transporting ATPase type 1
    • Protein or peptide: Calcium-transporting ATPase type 2C member 1
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM 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: 3.25 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_35779.png

Downloads & links

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Map

FileDownload / File: emd_35779.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: 0.194
Minimum - Maximum-0.86542875 - 1.5062413
Average (Standard dev.)0.00030686575 (±0.024739925)
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_35779_half_map_1.map
Projections & Slices
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Slices (1/2)
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Histogram

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Half map: #1

Fileemd_35779_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: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM 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: 100.679 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKVARFQKIP NGENETMIPV LTSKKASELP VSEVASILQA DLQNGLNKCE VSHRRAFHGW NEFDISEDEP LWKKYISQFK NPLIMLLLA SAVISVLMHQ FDDAVSITVA ILIVVTVAFV QEYRSEKSLE ELSKLVPPEC HCVREGKLEH TLARDLVPGD T VCLSVGDR ...String:
MKVARFQKIP NGENETMIPV LTSKKASELP VSEVASILQA DLQNGLNKCE VSHRRAFHGW NEFDISEDEP LWKKYISQFK NPLIMLLLA SAVISVLMHQ FDDAVSITVA ILIVVTVAFV QEYRSEKSLE ELSKLVPPEC HCVREGKLEH TLARDLVPGD T VCLSVGDR VPADLRLFEA VDLSIDESSL TGETTPCSKV TAPQPAATNG DLASRSNIAF MGTLVRCGKA KGVVIGTGEN SE FGEVFKM MQAEEAPKTP LQKSMDLLGK QLSFYSFGII GIIMLVGWLL GKDILEMFTI SVSLAVAAIP EGLPIVVTVT LAL GVMRMV KKRAIVKKLP IVETLGCCNV ICSDKTGTLT KNEMTVTHIF TSDGLHAEVT GVGYNQFGEV IVDGDVVHGF YNPA VSRIV EAGCVCNDAV IRNNTLMGKP TEGALIALAM KMGLDGLQQD YIRKAEYPFS SEQKWMAVKC VHRTQQDRPE ICFMK GAYE QVIKYCTTYQ SKGQTLTLTQ QQRDVYQQEK ARMGSAGLRV LALASGPELG QLTFLGLVGI IDPPRTGVKE AVTTLI ASG VSIKMITGDS QETAVAIASR LGLYSKTSQS VSGEEIDAMD VQQLSQIVPK VAVFYRASPR HKMKIIKSLQ KNGSVVA MT GDGVNDAVAL KAADIGVAMG QTGTDVCKEA ADMILVDDDF QTIMSAIEEG KGIYNNIKNF VRFQLSTSIA ALTLISLA T LMNFPNPLNA MQILWINIIM DGPPAQSLGV EPVDKDVIRK PPRNWKDSIL TKNLILKILV SSIIIVCGTL FVFWRELRD NVITPRDTTM TFTCFVFFDM FNALSSRSQT KSVFEIGLCS NRMFCYAVLG SIMGQLLVIY FPPLQKVFQT ESLSILDLLF LLGLTSSVC IVAEIIKKVE RSREKIQKHV SSTSSSFLEV

UniProtKB: Calcium-transporting ATPase type 2C member 1

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Macromolecule #2: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 166506
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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