6ZHH

Ca2+-ATPase from Listeria Monocytogenes with G4 insertion.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Crystal Structure of the Ca 2+ -ATPase 1 from Listeria monocytogenes reveals a Pump Primed for Dephosphorylation.

Hansen, S.B.Dyla, M.Neumann, C.Quistgaard, E.M.H.Andersen, J.L.Kjaergaard, M.Nissen, P.

(2021) J Mol Biol 433: 167015-167015

  • DOI: https://doi.org/10.1016/j.jmb.2021.167015
  • Primary Citation of Related Structures:  
    6ZHF, 6ZHG, 6ZHH

  • PubMed Abstract: 

    Many bacteria export intracellular calcium using active transporters homologous to the sarco/endoplasmic reticulum Ca 2+ -ATPase (SERCA). Here we present three crystal structures of Ca 2+ -ATPase 1 from Listeria monocytogenes (LMCA1). Structures with BeF 3 - mimicking a phosphoenzyme state reveal a closed state, which is intermediate between the outward-open E2P and the proton-occluded E2-P* conformations known for SERCA. It suggests that LMCA1 in the E2P state is pre-organized for dephosphorylation upon Ca 2+ release, consistent with the rapid dephosphorylation observed in single-molecule studies. An arginine side-chain occupies the position equivalent to calcium binding site I in SERCA, leaving a single Ca 2+ binding site in LMCA1, corresponding to SERCA site II. Observing no putative transport pathways dedicated to protons, we infer a direct proton counter transport through the Ca 2+ exchange pathways. The LMCA1 structures provide insight into the evolutionary divergence and conserved features of this important class of ion transporters.


  • Organizational Affiliation

    Department of Molecular Biology and Genetics, Aarhus University, Denmark; The Danish Research Institute for Translational Neuroscience (DANDRITE), Nordic EMBL Partnership for Molecular Medicine, Denmark.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Calcium-transporting ATPase
A, B, C, D, E
A, B, C, D, E, F, G, H
911Listeria monocytogenesMutation(s): 0 
Gene Names: A3R04_02860
Membrane Entity: Yes 
UniProt
Find proteins for Q8Y8Q5 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
Explore Q8Y8Q5 
Go to UniProtKB:  Q8Y8Q5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8Y8Q5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PCW
Query on PCW

Download Ideal Coordinates CCD File 
AA [auth C]
CA [auth C]
FA [auth D]
K [auth A]
L [auth A]
AA [auth C],
CA [auth C],
FA [auth D],
K [auth A],
L [auth A],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
X [auth C],
Y [auth C],
Z [auth C]
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H85 N O8 P
SNKAWJBJQDLSFF-NVKMUCNASA-O
CE1
Query on CE1

Download Ideal Coordinates CCD File 
BA [auth C]
GA [auth D]
HA [auth D]
IA [auth D]
JA [auth D]
BA [auth C],
GA [auth D],
HA [auth D],
IA [auth D],
JA [auth D],
KA [auth D],
LA [auth D]
O-DODECANYL OCTAETHYLENE GLYCOL
C28 H58 O9
YYELLDKEOUKVIQ-UHFFFAOYSA-N
BEF (Subject of Investigation/LOI)
Query on BEF

Download Ideal Coordinates CCD File 
DA [auth D]
I [auth A]
M [auth B]
MA [auth E]
OA [auth F]
DA [auth D],
I [auth A],
M [auth B],
MA [auth E],
OA [auth F],
QA [auth G],
SA [auth H],
V [auth C]
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
EA [auth D]
J [auth A]
N [auth B]
NA [auth E]
PA [auth F]
EA [auth D],
J [auth A],
N [auth B],
NA [auth E],
PA [auth F],
RA [auth G],
TA [auth H],
W [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.062α = 90
b = 188.499β = 91.94
c = 350.007γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
LundbeckfondenDenmarkR248-2016-2518
Danish Council for Independent ResearchDenmark7014-00328B

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-19
    Type: Initial release
  • Version 1.1: 2021-07-28
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description