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- PDB-7w7u: The 'Ca2+-unbound' BeF3- of SERCA2b -

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Basic information

Entry
Database: PDB / ID: 7w7u
TitleThe 'Ca2+-unbound' BeF3- of SERCA2b
ComponentsSarcoplasmic/endoplasmic reticulum calcium ATPase 2
KeywordsMETAL TRANSPORT / calcium
Function / homology
Function and homology information


longitudinal sarcoplasmic reticulum / ER-nucleus signaling pathway / positive regulation of endoplasmic reticulum calcium ion concentration / P-type calcium transporter activity involved in regulation of cardiac muscle cell membrane potential / calcium ion transport from cytosol to endoplasmic reticulum / regulation of calcium ion-dependent exocytosis of neurotransmitter / 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 ...longitudinal sarcoplasmic reticulum / ER-nucleus signaling pathway / positive regulation of endoplasmic reticulum calcium ion concentration / P-type calcium transporter activity involved in regulation of cardiac muscle cell membrane potential / calcium ion transport from cytosol to endoplasmic reticulum / regulation of calcium ion-dependent exocytosis of neurotransmitter / 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 / sarcoplasmic reticulum calcium ion transport / platelet dense tubular network membrane / calcium ion import into sarcoplasmic reticulum / ribbon synapse / Pre-NOTCH Processing in Golgi / P-type Ca2+ transporter / negative regulation of heart contraction / P-type calcium transporter activity / regulation of the force of heart contraction / transition between fast and slow fiber / endoplasmic reticulum calcium ion homeostasis / cardiac muscle hypertrophy in response to stress / S100 protein binding / regulation of cardiac muscle contraction by calcium ion signaling / Reduction of cytosolic Ca++ levels / relaxation of cardiac muscle / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / lncRNA binding / Ion transport by P-type ATPases / autophagosome assembly / regulation of cardiac conduction / epidermis development / positive regulation of heart rate / positive regulation of cardiac muscle cell apoptotic process / Ion homeostasis / sarcoplasmic reticulum membrane / response to endoplasmic reticulum stress / sarcoplasmic reticulum / negative regulation of receptor binding / calcium ion transmembrane transport / neuron cellular homeostasis / intracellular calcium ion 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 / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting 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, subfamily IIA, SERCA-type / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / Sarcoplasmic/endoplasmic reticulum calcium ATPase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsZhang, Y. / Watanabe, S. / Tsutsumi, A. / Inaba, K.
Funding support Japan, 4items
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
Citation
Journal: Cell Rep / Year: 2022
Title: Multiple sub-state structures of SERCA2b reveal conformational overlap at transition steps during the catalytic cycle.
Authors: Yuxia Zhang / Chigusa Kobayashi / Xiaohan Cai / Satoshi Watanabe / Akihisa Tsutsumi / Masahide Kikkawa / Yuji Sugita / Kenji Inaba /
Abstract: Sarco/endoplasmic reticulum Ca ATPase (SERCA) pumps Ca into the endoplasmic reticulum (ER). Herein, we present cryo-electron microscopy (EM) structures of three intermediates of SERCA2b: Ca-bound ...Sarco/endoplasmic reticulum Ca ATPase (SERCA) pumps Ca into the endoplasmic reticulum (ER). Herein, we present cryo-electron microscopy (EM) structures of three intermediates of SERCA2b: Ca-bound phosphorylated (E1P·2Ca) and Ca-unbound dephosphorylated (E2·Pi) intermediates and another between the E2P and E2·Pi states. Our cryo-EM analysis demonstrates that the E1P·2Ca state exists in low abundance and preferentially transitions to an E2P-like structure by releasing Ca and that the Ca release gate subsequently undergoes stepwise closure during the dephosphorylation processes. Importantly, each intermediate adopts multiple sub-state structures including those like the next one in the catalytic series, indicating conformational overlap at transition steps, as further substantiated by atomistic molecular dynamic simulations of SERCA2b in a lipid bilayer. The present findings provide insight into how enzymes accelerate catalytic cycles.
#1: Journal: 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, 2021Deposition site: PDBJ / Processing site: PDBJ
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)114,9603
Polymers114,8701
Non-polymers902
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
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-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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 / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
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
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 217584 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0027980
ELECTRON MICROSCOPYf_angle_d0.510831
ELECTRON MICROSCOPYf_dihedral_angle_d3.881072
ELECTRON MICROSCOPYf_chiral_restr0.0411272
ELECTRON MICROSCOPYf_plane_restr0.0051379

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