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- EMDB-0912: WT transporter state2 -

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Basic information

Entry
Database: EMDB / ID: EMD-0912
TitleWT transporter state2
Map data
Sample
  • Complex: SERCA2b with ACP
    • Protein or peptide: Sarcoplasmic/endoplasmic reticulum calcium ATPase 2
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: CALCIUM 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 / P-type calcium transporter activity / transition between fast and slow fiber / 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 / S100 protein binding / relaxation of cardiac muscle / Reduction of cytosolic Ca++ levels / lncRNA binding / organelle localization by membrane tethering / autophagosome membrane docking / positive regulation of heart rate / mitochondrion-endoplasmic reticulum membrane tethering / 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: 2.9 Å
AuthorsZhang Y / Tsutsumi A
Funding support Japan, 1 items
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 23, 2019-
Header (metadata) releaseAug 26, 2020-
Map releaseAug 26, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.08
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  • Surface view with fitted model
  • Atomic models: PDB-6lle
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0912.png

Downloads & links

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Map

FileDownload / File: emd_0912.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 168 pix.
= 209.16 Å		1.25 Å/pix.
x 168 pix.
= 209.16 Å		1.25 Å/pix.
x 168 pix.
= 209.16 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.245 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.08
Minimum - Maximum-0.46057254 - 0.8635808
Average (Standard dev.)-0.00007423792 (±0.020001948)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions168168168
Spacing168168168
CellA=B=C: 209.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2451.2451.245
M x/y/z168168168
origin x/y/z0.0000.0000.000
length x/y/z209.160209.160209.160
α/β/γ90.00090.00090.000
start NX/NY/NZ-31-35-52
NX/NY/NZ11798209
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS168168168
D min/max/mean-0.4610.864-0.000

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Supplemental data

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Mask #1

Fileemd_0912_msk_1.map
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Additional map: non-sharpened map

Fileemd_0912_additional.map
Annotationnon-sharpened map
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Additional map: non-sharpened map

Fileemd_0912_additional_1.map
Annotationnon-sharpened map
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Half map: unfiltered half1 map

Fileemd_0912_half_map_1.map
Annotationunfiltered half1 map
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Half map: unfiltered half2 map

Fileemd_0912_half_map_2.map
Annotationunfiltered half2 map
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Sample components

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Entire : SERCA2b with ACP

EntireName: SERCA2b with ACP
Components
  • Complex: SERCA2b with ACP
    • Protein or peptide: Sarcoplasmic/endoplasmic reticulum calcium ATPase 2
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: CALCIUM ION

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Supramolecule #1: SERCA2b with ACP

SupramoleculeName: SERCA2b with ACP / 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: 117.764875 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGGVAMPGAE DDVVRENLYF QGKDGLAAME NAHTKTVEEV LGHFGVNEST GLSLEQVKKL KERWGSNELP AEEGKTLLEL VIEQFEDLL VRILLLAACI SFVLAWFEEG EETITAFVEP FVILLILVAN AIVGVWQERN AENAIEALKE YEPEMGKVYR Q DRKSVQRI ...String:
MGGVAMPGAE DDVVRENLYF QGKDGLAAME NAHTKTVEEV LGHFGVNEST GLSLEQVKKL KERWGSNELP AEEGKTLLEL VIEQFEDLL VRILLLAACI SFVLAWFEEG EETITAFVEP FVILLILVAN AIVGVWQERN AENAIEALKE YEPEMGKVYR Q DRKSVQRI KAKDIVPGDI VEIAVGDKVP ADIRLTSIKS TTLRVDQSIL TGESVSVIKH TDPVPDPRAV NQDKKNMLFS GT NIAAGKA MGVVVATGVN TEIGKIRDEM VATEQERTPL QQKLDEFGEQ LSKVISLICI AVWIINIGHF NDPVHGGSWI RGA IYYFKI AVALAVAAIP EGLPAVITTC LALGTRRMAK KNAIVRSLPS VETLGCTSVI CSDKTGTLTT NQMSVCRMFI LDRV EGDTC SLNEFTITGS TYAPIGEVHK DDKPVNCHQY DGLVELATIC ALCNDSALDY NEAKGVYEKV GEATETALTC LVEKM NVFD TELKGLSKIE RANACNSVIK QLMKKEFTLE FSRDRKSMSV YCTPNKPSRT SMSKMFVKGA PEGVIDRCTH IRVGST KVP MTSGVKQKIM SVIREWGSGS DTLRCLALAT HDNPLRREEM HLEDSANFIK YETNLTFVGC VGMLDPPRIE VASSVKL CR QAGIRVIMIT GDNKGTAVAI CRRIGIFGQD EDVTSKAFTG REFDELNPSA QRDACLNARC FARVEPSHKS KIVEFLQS F DEITAMTGDG VNDAPALKKA EIGIAMGSGT AVAKTASEMV LADDNFSTIV AAVEEGRAIY NNMKQFIRYL ISSNVGEVV CIFLTAALGF PEALIPVQLL WVNLVTDGLP ATALGFNPPD LDIMNKPPRN PKEPLISGWL FFRYLAIGCY VGAATVGAAA WWFIAADGG PRVSFYQLSH FLQCKEDNPD FEGVDCAIFE SPYPMTMALS VLVTIEMCNA LNSLSENQSL LRMPPWENIW L VGSICLSM SLHFLILYVE PLPLIFQITP LNVTQWLMVL KISLPVILMD ETLKFVARNY LEPGKECVQP ATKSCSFSAC TD GISWPFV LLIMPLVIWV YSTDTNFSDM FWS

UniProtKB: Sarcoplasmic/endoplasmic reticulum calcium ATPase 2

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Macromolecule #2: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER

MacromoleculeName: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / type: ligand / ID: 2 / Number of copies: 1 / Formula: ACP
Molecular weightTheoretical: 505.208 Da
Chemical component information

ChemComp-ACP:
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / AMP-PCP, energy-carrying molecule analogue*YM

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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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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 455130
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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