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- EMDB-51510: Structure of a Ca2+ bound phosphoenzyme intermediate in the inwar... -

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Basic information

Entry
Database: EMDB / ID: EMD-51510
TitleStructure of a Ca2+ bound phosphoenzyme intermediate in the inward-to-outward transition of Ca2+-ATPase 1 from Listeria monocytogenes
Map data
Sample
  • Complex: Ca2+-ATPase 1 from Listeria monocytogenes (LMCA1) with Ca2+, PO4- and Mg2+.
    • Protein or peptide: Calcium-transporting ATPase lmo0841
  • Ligand: CALCIUM ION
  • Ligand: MAGNESIUM ION
KeywordsMembrane Protein / Intermediate / P-type ATPase / Calcium Transport
Function / homology
Function and homology information


P-type ion transporter activity / P-type Ca2+ transporter / P-type calcium transporter activity / monoatomic ion transmembrane transport / ATP hydrolysis activity / ATP binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
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 ...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 / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Calcium-transporting ATPase lmo0841
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsHansen SB / Flygaard RF / Kjaergaard M / Nissen P
Funding support Germany, Denmark, 4 items
OrganizationGrant numberCountry
Boehringer Ingelheim Fonds (BIF) Germany
Danish Council for Independent Research7014-00328B Denmark
LundbeckfondenR310-2018-3713 Denmark
Novo Nordisk FoundationNNF20OC0060483 Denmark
CitationJournal: EMBO Rep / Year: 2025
Title: Structure of the [Ca]E2P intermediate of Ca-ATPase 1 from Listeria monocytogenes.
Authors: Sara Basse Hansen / Rasmus Kock Flygaard / Magnus Kjaergaard / Poul Nissen /
Abstract: Active transport by P-type Ca-ATPases maintain internal calcium stores and a low cytosolic calcium concentration. Structural studies of mammalian sarco/endoplasmic reticulum Ca-ATPases (SERCA) have ...Active transport by P-type Ca-ATPases maintain internal calcium stores and a low cytosolic calcium concentration. Structural studies of mammalian sarco/endoplasmic reticulum Ca-ATPases (SERCA) have revealed several steps of the transport cycle, but a calcium-releasing intermediate has remained elusive. Single-molecule FRET studies of the bacterial Ca-ATPase LMCA1 revealed an intermediate of the transition between so-called [Ca]E1P and E2P states and suggested that calcium release from this intermediate was the essentially irreversible step of transport. Here, we present a 3.5 Å resolution cryo-EM structure for a four-glycine insertion mutant of LMCA1 in a lipid nanodisc obtained under conditions with calcium and ATP and adopting such an intermediate state, denoted [Ca]E2P. The cytosolic domains are positioned in the E2P-like conformation, while the calcium-binding transmembrane (TM) domain adopts a calcium-bound E1P-ADP-like conformation. Missing density for the E292 residue at the calcium site (the equivalent of SERCA1a E309) suggests flexibility and a site poised for calcium release and proton uptake. The structure suggests a mechanism where ADP release and re-organization of the cytoplasmic domains precede calcium release.
History
DepositionSep 9, 2024-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51510.png

Downloads & links

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Map

FileDownload / File: emd_51510.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.29 Å/pix.
x 240 pix.
= 310.56 Å		1.29 Å/pix.
x 240 pix.
= 310.56 Å		1.29 Å/pix.
x 240 pix.
= 310.56 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.294 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.225
Minimum - Maximum-0.1149608 - 0.78842133
Average (Standard dev.)0.0003421209 (±0.019822842)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 310.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_51510_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_51510_half_map_2.map
Projections & Slices
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Sample components

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Entire : Ca2+-ATPase 1 from Listeria monocytogenes (LMCA1) with Ca2+, PO4-...

EntireName: Ca2+-ATPase 1 from Listeria monocytogenes (LMCA1) with Ca2+, PO4- and Mg2+.
Components
  • Complex: Ca2+-ATPase 1 from Listeria monocytogenes (LMCA1) with Ca2+, PO4- and Mg2+.
    • Protein or peptide: Calcium-transporting ATPase lmo0841
  • Ligand: CALCIUM ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Ca2+-ATPase 1 from Listeria monocytogenes (LMCA1) with Ca2+, PO4-...

SupramoleculeName: Ca2+-ATPase 1 from Listeria monocytogenes (LMCA1) with Ca2+, PO4- and Mg2+.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Listeria monocytogenes (bacteria)

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Macromolecule #1: Calcium-transporting ATPase lmo0841

MacromoleculeName: Calcium-transporting ATPase lmo0841 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: P-type Ca2+ transporter
Source (natural)Organism: Listeria monocytogenes (bacteria)
Molecular weightTheoretical: 99.416422 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAEIYRKSAA ETFTQLEATE KGLTTSEVTK RQEKYGFNEL KNKKKGGGGD PLWKLFLETF KDPMVIVLVI AALVQLVLGE VVESLIIFL VLIVNSIISV VQTRKAESSL DALREMSAPV AKVIRDGSKQ SIHARELVPG DVVILDAGDF VPADGRLFES G SLKIDEGM ...String:
MAEIYRKSAA ETFTQLEATE KGLTTSEVTK RQEKYGFNEL KNKKKGGGGD PLWKLFLETF KDPMVIVLVI AALVQLVLGE VVESLIIFL VLIVNSIISV VQTRKAESSL DALREMSAPV AKVIRDGSKQ SIHARELVPG DVVILDAGDF VPADGRLFES G SLKIDEGM LTGESEAVEK YIDTIPDEVG LGDRVNMVFS GSLVVYGRGM FVVTGTASET EIGKIAGLLE TAEAKQTPLQ RK LESFSKK LGLGILALCV LIFAVEAGRV LLGDNSADMA TAILNAFMFA VAVAVAAIPE ALSSIVTIVL AVGTNKMAKQ HAI IRKLPA VETLGSTSVI CT(PHD)KTGTLTQ NKMTVVDYYL PDGTKENFPE SPENWSEGER RLIHIAVLCN DSNINSEGKE LGDPTEVAL IAFSNKNNQD YNEIREKFIR EGEIPFDSDR KLMSTLHTFN ENKAMLTKGG PDVMFARCSY VFLDGEEKPM T EEILAKLK ETNEEFSNQA LRVLAYGYKR MPADTTELKL EDEQDIVLVG LTAMIDPPRE AVYASIEESK KAGIRTVMIT GD HKTTAQA IGRDIGLMDA DDIALTGQEL DAMPEEELDK KLEHIAVYAR VSPENKIRIV KAWQKKGKIT AMTGDGVNDA PAL KQADIG VAMGSGTDVA KDSAAMILTD DNFVSIVDAV GVGRTVFDNI KKSIAYLFAG NLGAIIAILF ALVLDWINPF TALQ LLFIN LVNDSLPAIA LGMEKAEPDV MKRKPRDINE GIFAGGTMRA VISRGVLIGI AVIISQYIGM QISPEMSVAM AFTTL ILAR TLQTFAARSN VQTAFGAGFF SNKYVIGAVL LCFVLYGITV LPGAREIFSI PASFGLHEWS IAAGLALAAV VMMEII KVV QNKFFKDYDI PTTENLYFQG LEHHHHHHHH HH

UniProtKB: Calcium-transporting ATPase lmo0841

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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: 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

Concentration0.7 mg/mL
BufferpH: 7.6
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 58.75 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6zhh

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 101034
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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