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- PDB-6ln5: CryoEM structure of SERCA2b T1032stop in E1-2Ca2+-AMPPCP (class1) -

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Basic information

Entry
Database: PDB / ID: 6ln5
TitleCryoEM structure of SERCA2b T1032stop in E1-2Ca2+-AMPPCP (class1)
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 / regulation of cardiac muscle cell action potential involved in regulation of contraction / T-tubule organization / 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 / regulation of cardiac muscle cell action potential involved in regulation of contraction / T-tubule organization / regulation of cardiac muscle cell membrane potential / ribbon synapse / sarcoplasmic reticulum calcium ion transport / platelet dense tubular network membrane / calcium ion import into sarcoplasmic reticulum / 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 / lncRNA binding / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / Ion transport by P-type ATPases / autophagosome assembly / regulation of cardiac conduction / epidermis development / positive regulation of heart rate / Ion homeostasis / positive regulation of cardiac muscle cell apoptotic process / sarcoplasmic reticulum membrane / response to endoplasmic reticulum stress / sarcoplasmic reticulum / negative regulation of receptor binding / 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 / haloacid dehalogenase-like hydrolase / 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, subfamily IIA, SERCA-type / haloacid dehalogenase-like hydrolase / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Sarcoplasmic/endoplasmic reticulum calcium ATPase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsZhang, Y. / Tsutsumi, A. / Watanabe, S. / Inaba, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: Sci Adv / Year: 2020
Title: Cryo-EM structures of SERCA2b reveal the mechanism of regulation by the luminal extension tail.
Authors: Yuxia Zhang / Michio Inoue / Akihisa Tsutsumi / Satoshi Watanabe / Tomohiro Nishizawa / Kazuhiro Nagata / Masahide Kikkawa / Kenji Inaba /
Abstract: Sarco/endoplasmic reticulum Ca ATPase (SERCA) pumps Ca from the cytosol into the ER and maintains the cellular calcium homeostasis. Herein, we present cryo-electron microscopy (cryo-EM) structures of ...Sarco/endoplasmic reticulum Ca ATPase (SERCA) pumps Ca from the cytosol into the ER and maintains the cellular calcium homeostasis. Herein, we present cryo-electron microscopy (cryo-EM) structures of human SERCA2b in E1∙2Ca-adenylyl methylenediphosphonate (AMPPCP) and E2-BeF states at 2.9- and 2.8-Å resolutions, respectively. The structures revealed that the luminal extension tail (LE) characteristic of SERCA2b runs parallel to the lipid-water boundary near the luminal ends of transmembrane (TM) helices TM10 and TM7 and approaches the luminal loop flanked by TM7 and TM8. While the LE served to stabilize the cytosolic and TM domain arrangement of SERCA2b, deletion of the LE rendered the overall conformation resemble that of SERCA1a and SERCA2a and allowed multiple conformations. Thus, the LE appears to play a critical role in conformational regulation in SERCA2b, which likely explains the different kinetic properties of SERCA2b from those of other isoforms lacking the LE.
History
DepositionDec 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed
Revision 1.2Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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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)117,0425
Polymers116,4321
Non-polymers6104
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1100 Å2
ΔGint-25 kcal/mol
Surface area42770 Å2

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Components

#1: Protein Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 / SR Ca(2+)-ATPase 2 / Calcium pump 2 / Calcium-transporting ATPase sarcoplasmic reticulum type / ...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: 116432.453 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-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN
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 MUTATION with AMPPCP -1 / 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: 1.16_3549: / Classification: refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 172314 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037985
ELECTRON MICROSCOPYf_angle_d0.43410844
ELECTRON MICROSCOPYf_dihedral_angle_d2.7654830
ELECTRON MICROSCOPYf_chiral_restr0.041273
ELECTRON MICROSCOPYf_plane_restr0.0041377

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