6A69

Cryo-EM structure of a P-type ATPase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.11 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of the human plasma membrane Ca2+-ATPase 1 in complex with its obligatory subunit neuroplastin.

Gong, D.Chi, X.Ren, K.Huang, G.Zhou, G.Yan, N.Lei, J.Zhou, Q.

(2018) Nat Commun 9: 3623-3623

  • DOI: 10.1038/s41467-018-06075-7
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Plasma membrane Ca 2+ -ATPases (PMCAs) are key regulators of global Ca 2+ homeostasis and local intracellular Ca 2+ dynamics. Recently, Neuroplastin (NPTN) and basigin were identified as previously unrecognized obligatory subunits of PMCAs that dramatically increase the efficiency of PMCA-mediated Ca 2+ clearance ...

    Plasma membrane Ca 2+ -ATPases (PMCAs) are key regulators of global Ca 2+ homeostasis and local intracellular Ca 2+ dynamics. Recently, Neuroplastin (NPTN) and basigin were identified as previously unrecognized obligatory subunits of PMCAs that dramatically increase the efficiency of PMCA-mediated Ca 2+ clearance. Here, we report the cryo-EM structure of human PMCA1 (hPMCA1) in complex with NPTN at a resolution of 4.1 Å for the overall structure and 3.9 Å for the transmembrane domain. The single transmembrane helix of NPTN interacts with the TM 8-9 -linker and TM10 of hPMCA1. The subunits are required for the hPMCA1 functional activity. The NPTN-bound hPMCA1 closely resembles the E1-Mg 2+ structure of endo(sarco)plasmic reticulum Ca 2+ ATPase and the Ca 2+ site is exposed through a large open cytoplasmic pathway. This structure provides insight into how the subunits bind to the PMCAs and serves as an important basis for understanding the functional mechanisms of this essential calcium pump family.


    Organizational Affiliation

    Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China. zhouqiang00@tsinghua.org.cn.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Plasma membrane calcium-transporting ATPase 1A1274Homo sapiensMutation(s): 0 
Gene Names: ATP2B1PMCA1
EC: 3.6.3.8 (PDB Primary Data), 7.2.2.10 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
Plasma membrane Ca2+-ATPase 1 (PMCA1) in complex with its obligatory subunit neuroplastin (NPTP)
Find proteins for P20020 (Homo sapiens)
Explore P20020 
Go to UniProtKB:  P20020
NIH Common Fund Data Resources
PHAROS  P20020
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NeuroplastinB282Homo sapiensMutation(s): 0 
Gene Names: NPTNSDFR1SDR1
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
Plasma membrane Ca2+-ATPase 1 (PMCA1) in complex with its obligatory subunit neuroplastin (NPTP)
Find proteins for Q9Y639 (Homo sapiens)
Explore Q9Y639 
Go to UniProtKB:  Q9Y639
NIH Common Fund Data Resources
PHAROS  Q9Y639
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
B
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.11 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary