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- PDB-7e7s: WT transporter state1 -

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Basic information

Entry
Database: PDB / ID: 7e7s
TitleWT transporter state1
ComponentsSarcoplasmic/endoplasmic reticulum calcium ATPase 2
KeywordsMETAL TRANSPORT / calcium
Function / homology
Function and homology information


longitudinal sarcoplasmic reticulum / ER-nucleus signaling pathway / P-type calcium transporter activity involved in regulation of cardiac muscle cell membrane potential / regulation of calcium ion-dependent exocytosis of neurotransmitter / calcium ion transport from cytosol to endoplasmic reticulum / positive regulation of endoplasmic reticulum calcium ion concentration / calcium ion-transporting ATPase complex / regulation of cardiac muscle cell action potential involved in regulation of contraction / regulation of cardiac muscle cell membrane potential / T-tubule organization ...longitudinal sarcoplasmic reticulum / ER-nucleus signaling pathway / P-type calcium transporter activity involved in regulation of cardiac muscle cell membrane potential / regulation of calcium ion-dependent exocytosis of neurotransmitter / calcium ion transport from cytosol to endoplasmic reticulum / positive regulation of endoplasmic reticulum calcium ion concentration / calcium ion-transporting ATPase complex / regulation of cardiac muscle cell action potential involved in regulation of contraction / regulation of cardiac muscle cell membrane potential / T-tubule organization / 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 / cardiac muscle hypertrophy in response to stress / endoplasmic reticulum calcium ion homeostasis / regulation of cardiac muscle contraction by calcium ion signaling / lncRNA binding / S100 protein binding / relaxation of cardiac muscle / Reduction of cytosolic Ca++ levels / 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 / monoatomic ion transmembrane transport / 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 / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZhang, Y. / Watanabe, S. / Tsutsumi, A. / Inaba, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan) 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
DepositionFeb 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

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Assembly

Deposited unit
A: Sarcoplasmic/endoplasmic reticulum calcium ATPase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,9503
Polymers114,8701
Non-polymers802
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 / SERCA2 / SR Ca(2+)-ATPase 2 / Calcium pump 2 / Calcium-transporting ATPase sarcoplasmic reticulum ...SERCA2 / SR Ca(2+)-ATPase 2 / Calcium pump 2 / Calcium-transporting ATPase sarcoplasmic reticulum type / slow twitch skeletal muscle isoform / Endoplasmic reticulum class 1/2 Ca(2+) ATPase


Mass: 114869.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATP2A2, ATP2B / Production host: Homo sapiens (human) / References: UniProt: P16615, P-type Ca2+ transporter
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: SERCA2b with Ca / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 110 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7
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: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.1_4122: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 96416 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038031
ELECTRON MICROSCOPYf_angle_d0.46310899
ELECTRON MICROSCOPYf_dihedral_angle_d3.6811078
ELECTRON MICROSCOPYf_chiral_restr0.041279
ELECTRON MICROSCOPYf_plane_restr0.0041389

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