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- EMDB-32348: The 'Ca2+-unbound' BeF3- of SERCA2b -

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Basic information

Entry
Database: EMDB / ID: EMD-32348
TitleThe 'Ca2+-unbound' BeF3- of SERCA2b
Map datamap_masked
Sample
  • Complex: SERCA2b with Ca
    • Protein or peptide: Sarcoplasmic/endoplasmic reticulum calcium ATPase 2
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION
Keywordscalcium / METAL TRANSPORT
Function / homology
Function and homology information


ER-nucleus signaling pathway / longitudinal sarcoplasmic reticulum / positive regulation of endoplasmic reticulum calcium ion concentration / regulation of calcium ion-dependent exocytosis of neurotransmitter / calcium ion transport from cytosol to endoplasmic reticulum / P-type calcium transporter activity involved in regulation of cardiac muscle cell membrane potential / calcium ion-transporting ATPase complex / T-tubule organization / regulation of cardiac muscle cell action potential involved in regulation of contraction / regulation of cardiac muscle cell membrane potential ...ER-nucleus signaling pathway / longitudinal sarcoplasmic reticulum / positive regulation of endoplasmic reticulum calcium ion concentration / regulation of calcium ion-dependent exocytosis of neurotransmitter / calcium ion transport from cytosol to endoplasmic reticulum / P-type calcium transporter activity involved in regulation of cardiac muscle cell membrane potential / calcium ion-transporting ATPase complex / T-tubule organization / regulation of cardiac muscle cell action potential involved in regulation of contraction / regulation of cardiac muscle cell membrane potential / ribbon synapse / platelet dense tubular network membrane / calcium ion import into sarcoplasmic reticulum / Pre-NOTCH Processing in Golgi / P-type Ca2+ transporter / sarcoplasmic reticulum calcium ion transport / negative regulation of heart contraction / transition between fast and slow fiber / P-type calcium transporter activity / regulation of the force of heart contraction / endoplasmic reticulum calcium ion homeostasis / cardiac muscle hypertrophy in response to stress / regulation of cardiac muscle contraction by calcium ion signaling / S100 protein binding / relaxation of cardiac muscle / Reduction of cytosolic Ca++ levels / lncRNA binding / organelle localization by membrane tethering / autophagosome membrane docking / mitochondrion-endoplasmic reticulum membrane tethering / positive regulation of heart rate / positive regulation of cardiac muscle cell apoptotic process / Ion transport by P-type ATPases / autophagosome assembly / regulation of cardiac conduction / epidermis development / Ion homeostasis / sarcoplasmic reticulum membrane / response to endoplasmic reticulum stress / negative regulation of receptor binding / sarcoplasmic reticulum / calcium ion transmembrane transport / intracellular calcium ion homeostasis / neuron cellular homeostasis / cellular response to oxidative stress / monoatomic ion transmembrane transport / transmembrane transporter binding / cell adhesion / calcium ion binding / endoplasmic reticulum membrane / enzyme binding / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
P-type ATPase, subfamily IIA, SERCA-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, SERCA-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 / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Sarcoplasmic/endoplasmic reticulum calcium ATPase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsZhang Y / Watanabe S
Funding support Japan, 4 items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)18H03978 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)21H04758 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)21H05247 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)21K15036 Japan
CitationJournal: EMBO J / Year: 2021
Title: Cryo-EM analysis provides new mechanistic insight into ATP binding to Ca -ATPase SERCA2b.
Authors: Yuxia Zhang / Satoshi Watanabe / Akihisa Tsutsumi / Hiroshi Kadokura / Masahide Kikkawa / Kenji Inaba /
Abstract: Sarco/endoplasmic reticulum Ca -ATPase (SERCA) 2b is a ubiquitous SERCA family member that conducts Ca uptake from the cytosol to the ER. Herein, we present a 3.3 Å resolution cryo-electron ...Sarco/endoplasmic reticulum Ca -ATPase (SERCA) 2b is a ubiquitous SERCA family member that conducts Ca uptake from the cytosol to the ER. Herein, we present a 3.3 Å resolution cryo-electron microscopy (cryo-EM) structure of human SERCA2b in the E1·2Ca state, revealing a new conformation for Ca -bound SERCA2b with a much closer arrangement of cytosolic domains than in the previously reported crystal structure of Ca -bound SERCA1a. Multiple conformations generated by 3D classification of cryo-EM maps reflect the intrinsically dynamic nature of the cytosolic domains in this state. Notably, ATP binding residues of SERCA2b in the E1·2Ca state are located at similar positions to those in the E1·2Ca -ATP state; hence, the cryo-EM structure likely represents a preformed state immediately prior to ATP binding. Consistently, a SERCA2b mutant with an interdomain disulfide bridge that locks the closed cytosolic domain arrangement displayed significant autophosphorylation activity in the presence of Ca . We propose a novel mechanism of ATP binding to SERCA2b.
History
DepositionDec 6, 2021-
Header (metadata) releaseDec 14, 2022-
Map releaseDec 14, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32348.png

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Map

FileDownload / File: emd_32348.map.gz / Format: CCP4 / Size: 18.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap_masked
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AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 170 pix.
= 211.65 Å		1.25 Å/pix.
x 170 pix.
= 211.65 Å		1.25 Å/pix.
x 170 pix.
= 211.65 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.245 Å
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Contour LevelBy AUTHOR: 0.055
Minimum - Maximum-0.27997664 - 0.45351067
Average (Standard dev.)-0.00003179078 (±0.013595393)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions170170170
Spacing170170170
CellA=B=C: 211.65 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_32348_msk_1.map
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Additional map: map

Fileemd_32348_additional_1.map
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Half map: half1

Fileemd_32348_half_map_1.map
Annotationhalf1
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Half map: half2

Fileemd_32348_half_map_2.map
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Sample components

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Entire : SERCA2b with Ca

EntireName: SERCA2b with Ca
Components
  • Complex: SERCA2b with Ca
    • Protein or peptide: Sarcoplasmic/endoplasmic reticulum calcium ATPase 2
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: SERCA2b with Ca

SupramoleculeName: SERCA2b with Ca / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 110 kDa/nm

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Macromolecule #1: Sarcoplasmic/endoplasmic reticulum calcium ATPase 2

MacromoleculeName: Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 / 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: 114.869664 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MENAHTKTVE EVLGHFGVNE STGLSLEQVK KLKERWGSNE LPAEEGKTLL ELVIEQFEDL LVRILLLAAC ISFVLAWFEE GEETITAFV EPFVILLILV ANAIVGVWQE RNAENAIEAL KEYEPEMGKV YRQDRKSVQR IKAKDIVPGD IVEIAVGDKV P ADIRLTSI ...String:
MENAHTKTVE EVLGHFGVNE STGLSLEQVK KLKERWGSNE LPAEEGKTLL ELVIEQFEDL LVRILLLAAC ISFVLAWFEE GEETITAFV EPFVILLILV ANAIVGVWQE RNAENAIEAL KEYEPEMGKV YRQDRKSVQR IKAKDIVPGD IVEIAVGDKV P ADIRLTSI KSTTLRVDQS ILTGESVSVI KHTDPVPDPR AVNQDKKNML FSGTNIAAGK AMGVVVATGV NTEIGKIRDE MV ATEQERT PLQQKLDEFG EQLSKVISLI CIAVWIINIG HFNDPVHGGS WIRGAIYYFK IAVALAVAAI PEGLPAVITT CLA LGTRRM AKKNAIVRSL PSVETLGCTS VICSDKTGTL TTNQMSVCRM FILDRVEGDT CSLNEFTITG STYAPIGEVH KDDK PVNCH QYDGLVELAT ICALCNDSAL DYNEAKGVYE KVGEATETAL TCLVEKMNVF DTELKGLSKI ERANACNSVI KQLMK KEFT LEFSRDRKSM SVYCTPNKPS RTSMSKMFVK GAPEGVIDRC THIRVGSTKV PMTSGVKQKI MSVIREWGSG SDTLRC LAL ATHDNPLRRE EMHLEDSANF IKYETNLTFV GCVGMLDPPR IEVASSVKLC RQAGIRVIMI TGDNKGTAVA ICRRIGI FG QDEDVTSKAF TGREFDELNP SAQRDACLNA RCFARVEPSH KSKIVEFLQS FDEITAMTGD GVNDAPALKK AEIGIAMG S GTAVAKTASE MVLADDNFST IVAAVEEGRA IYNNMKQFIR YLISSNVGEV VCIFLTAALG FPEALIPVQL LWVNLVTDG LPATALGFNP PDLDIMNKPP RNPKEPLISG WLFFRYLAIG CYVGAATVGA AAWWFIAADG GPRVSFYQLS HFLQCKEDNP DFEGVDCAI FESPYPMTMA LSVLVTIEMC NALNSLSENQ SLLRMPPWEN IWLVGSICLS MSLHFLILYV EPLPLIFQIT P LNVTQWLM VLKISLPVIL MDETLKFVAR NYLEPGKECV QPATKSCSFS ACTDGISWPF VLLIMPLVIW VYSTDTNFSD MF WS

UniProtKB: Sarcoplasmic/endoplasmic reticulum calcium ATPase 2

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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: 7
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: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 217584
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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