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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0927 | |||||||||
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Title | mutation transporter state1-1 | |||||||||
![]() | sharpened map | |||||||||
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![]() | cacium / METAL TRANSPORT | |||||||||
Function / homology | ![]() 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 / 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 / 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 / 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 / cardiac muscle hypertrophy in response to stress / endoplasmic reticulum calcium ion homeostasis / regulation of cardiac muscle contraction by calcium ion signaling / S100 protein binding / lncRNA binding / relaxation of cardiac muscle / Reduction of cytosolic Ca++ levels / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / 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 / monoatomic ion transmembrane transport / 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 / 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 | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
![]() | Zhang Y / Tsutsumi A | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 2.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.2 KB 17.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 6.1 KB | Display | ![]() |
Images | ![]() | 51.2 KB | ||
Masks | ![]() | 18.1 MB | ![]() | |
Filedesc metadata | ![]() | 5.9 KB | ||
Others | ![]() ![]() ![]() | 13.7 MB 13.8 MB 13.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ln8MC ![]() 0912C ![]() 0915C ![]() 0924C ![]() 0925C ![]() 0926C ![]() 0928C ![]() 6lleC ![]() 6llyC ![]() 6ln5C ![]() 6ln6C ![]() 6ln7C ![]() 6ln9C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.245 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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-Additional map: non-sharpened map
File | emd_0927_additional.map | ||||||||||||
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Annotation | non-sharpened map | ||||||||||||
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Density Histograms |
-Half map: half1 map
File | emd_0927_half_map_1.map | ||||||||||||
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Annotation | half1 map | ||||||||||||
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-Half map: half2 map
File | emd_0927_half_map_2.map | ||||||||||||
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Annotation | half2 map | ||||||||||||
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Sample components
-Entire : SERCA2b MUTATION with BEF -1
Entire | Name: SERCA2b MUTATION with BEF -1 |
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Components |
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-Supramolecule #1: SERCA2b MUTATION with BEF -1
Supramolecule | Name: SERCA2b MUTATION with BEF -1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 110 kDa/nm |
-Macromolecule #1: Sarcoplasmic/endoplasmic reticulum calcium ATPase 2
Macromolecule | Name: Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: P-type Ca2+ transporter |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 116.432453 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 YS UniProtKB: Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 |
-Macromolecule #2: BERYLLIUM TRIFLUORIDE ION
Macromolecule | Name: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: BEF |
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Molecular weight | Theoretical: 66.007 Da |
Chemical component information | ![]() ChemComp-BEF: |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |