6ZHH | pdb_00006zhh

Ca2+-ATPase from Listeria Monocytogenes with G4 insertion.

PDB DOI: https://doi.org/10.2210/pdb6ZHH/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Listeria monocytogenes
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD

Deposited: 2020-06-23 Released: 2021-05-19
Deposition Author(s): Basse Hansen, S., Dyla, M., Neumann, C., Quistgaard, E.M.H., Lauwring Andersen, J., Kjaergaard, M., Nissen, P.
Funding Organization(s): Lundbeckfonden, Danish Council for Independent Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.285 (Depositor), 0.287 (DCC)
R-Value Work:
0.255 (Depositor), 0.255 (DCC)
R-Value Observed:
0.255 (Depositor)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 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 Biology 433: 167015-167015

PubMed: 33933469 Search on PubMed
DOI: https://doi.org/10.1016/j.jmb.2021.167015
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 810.99 kDa
Atom Count: 54,572
Modeled Residue Count: 7,035
Deposited Residue Count: 7,288
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium-transporting ATPase	A, B, C, D, E A, B, C, D, E, F, G, H	911	Listeria monocytogenes	Mutation(s): 0 Gene Names: A3R04_02860 EC: 7.2.2.10 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8Y8Q5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PCW Query on PCW Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain CA [auth C] SDF format, chain FA [auth D] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain T [auth B] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain U [auth B] SDF format, chain S [auth B] SDF format, chain K [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain T [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain U [auth B] MOL2 format, chain S [auth B] MOL2 format, chain K [auth A] mmCIF format, chain AA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain T [auth B] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain U [auth B] mmCIF format, chain S [auth B] mmCIF format, chain K [auth A]	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		Interactions Focus chain AA [auth C] Focus chain CA [auth C] Focus chain FA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain CA [auth C] Focus chain FA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
CE1 Query on CE1 Download:Ideal Coordinates CCD File SDF format, chain IA [auth D] SDF format, chain KA [auth D] SDF format, chain LA [auth D] SDF format, chain JA [auth D] SDF format, chain HA [auth D] SDF format, chain GA [auth D] SDF format, chain BA [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain BA [auth C] mmCIF format, chain IA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain LA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain BA [auth C]	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		Interactions Focus chain BA [auth C] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth D] Interactions & Density Focus chain BA [auth C] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth D]
BEF (Subject of Investigation/LOI) Query on BEF Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain MA [auth E] SDF format, chain OA [auth F] SDF format, chain SA [auth H] SDF format, chain V [auth C] SDF format, chain QA [auth G] MOL2 format, chain DA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain MA [auth E] MOL2 format, chain OA [auth F] MOL2 format, chain SA [auth H] MOL2 format, chain V [auth C] MOL2 format, chain QA [auth G] mmCIF format, chain DA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain MA [auth E] mmCIF format, chain OA [auth F] mmCIF format, chain SA [auth H] mmCIF format, chain V [auth C] mmCIF format, chain QA [auth G]	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		Interactions Focus chain DA [auth D] Focus chain I [auth A] Focus chain M [auth B] Focus chain MA [auth E] Focus chain OA [auth F] Focus chain QA [auth G] Focus chain SA [auth H] Focus chain V [auth C] Interactions & Density Focus chain DA [auth D] Focus chain I [auth A] Focus chain M [auth B] Focus chain MA [auth E] Focus chain OA [auth F] Focus chain QA [auth G] Focus chain SA [auth H] Focus chain V [auth C]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain N [auth B] SDF format, chain PA [auth F] SDF format, chain RA [auth G] SDF format, chain TA [auth H] SDF format, chain W [auth C] SDF format, chain NA [auth E] SDF format, chain J [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain N [auth B] MOL2 format, chain PA [auth F] MOL2 format, chain RA [auth G] MOL2 format, chain TA [auth H] MOL2 format, chain W [auth C] MOL2 format, chain NA [auth E] MOL2 format, chain J [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain N [auth B] mmCIF format, chain PA [auth F] mmCIF format, chain RA [auth G] mmCIF format, chain TA [auth H] mmCIF format, chain W [auth C] mmCIF format, chain NA [auth E] mmCIF format, chain J [auth A]	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		Interactions Focus chain EA [auth D] Focus chain J [auth A] Focus chain N [auth B] Focus chain NA [auth E] Focus chain PA [auth F] Focus chain RA [auth G] Focus chain TA [auth H] Focus chain W [auth C] Interactions & Density Focus chain EA [auth D] Focus chain J [auth A] Focus chain N [auth B] Focus chain NA [auth E] Focus chain PA [auth F] Focus chain RA [auth G] Focus chain TA [auth H] Focus chain W [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.285 (Depositor), 0.287 (DCC)
R-Value Work: 0.255 (Depositor), 0.255 (DCC)
R-Value Observed: 0.255 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.062	α = 90
b = 188.499	β = 91.94
c = 350.007	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-05-19

Deposition Author(s):

Lauwring Andersen, J.

Kjaergaard, M.

Nissen, P.

Funding Organization	Location	Grant Number
Lundbeckfonden	Denmark	R248-2016-2518
Danish Council for Independent Research	Denmark	7014-00328B

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
Version 1.3: 2025-10-01
Changes: Advisory, Derived calculations, Structure summary