6LLY

CryoEM structure of SERCA2b WT in E2-BeF3- state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM structures of SERCA2b reveal the mechanism of regulation by the luminal extension tail.

Zhang, Y.Inoue, M.Tsutsumi, A.Watanabe, S.Nishizawa, T.Nagata, K.Kikkawa, M.Inaba, K.

(2020) Sci Adv 6: eabb0147-eabb0147

  • DOI: 10.1126/sciadv.abb0147
  • Primary Citation of Related Structures:  
    6LLE, 6LN5, 6LN7, 6LN6, 6LLY, 6LN9, 6LN8

  • PubMed Abstract: 
  • Sarco/endoplasmic reticulum Ca 2+ ATPase (SERCA) pumps Ca 2+ 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 2+ -adenylyl methylenediphosphonate (AMPPCP) and E2-BeF 3 - states at 2 ...

    Sarco/endoplasmic reticulum Ca 2+ ATPase (SERCA) pumps Ca 2+ 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 2+ -adenylyl methylenediphosphonate (AMPPCP) and E2-BeF 3 - 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.


    Organizational Affiliation

    Core Research for Evolutional Science and Technology (CREST), Kawaguchi, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sarcoplasmic/endoplasmic reticulum calcium ATPase 2A1070Homo sapiensMutation(s): 0 
Gene Names: ATP2A2ATP2B
EC: 7.2.2.10
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P16615 (Homo sapiens)
Explore P16615 
Go to UniProtKB:  P16615
PHAROS:  P16615
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BEF
Query on BEF

Download Ideal Coordinates CCD File 
B [auth A]BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-26
    Type: Initial release
  • Version 1.1: 2020-09-09
    Changes: Database references
  • Version 1.2: 2020-09-16
    Changes: Database references