6ZHG

Ca2+-ATPase from Listeria Monocytogenes in complex with AlF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.327 
  • R-Value Work: 0.308 
  • R-Value Observed: 0.309 

Starting Model: experimental
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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 ATPase894Listeria monocytogenesMutation(s): 0 
Gene Names: 
A3R04_02860A7B93_02035A7E37_07960A7T84_03145A8N46_03115A9303_08250AA141_02585AA38_03115AA57_04345AA58_04340AAT23_05730AAT89_01270AAV13_08720AC638_15100ACX75_14550AD67_04590ADT87_13595AE163_09080AE275_03115AF000_06545AF016_12590AF040_14630AF045_14565AF209_04695AF234_14885AFS24_04345AFT50_03135AFU02_10535AFU61_04345AFW07_04365AFW50_00270AFW67_02600AFW77_02595AFW96_04345AFY00_02970AFY08_04620AFY14_04625AK14_13510AL416_02600ALZ22_03115AO083_04340AOA99_03360AOX92_14460AOX97_03115APD69_03345APD94_04680APE52_04350APE55_04330APE78_08730APE79_10640APS82_08405APY22_11485APY32_10565AR034_01900AR095_04345ARG48_02025ARG59_04340ARG63_02035ARG65_02035ARG77_04695ARG88_04330ARH36_03115ARH47_03115ARH65_03115ARK03_06875ARQ26_09135ARS01_02200ARS03_11205ARS22_01415ARS28_14570ARS93_04670ART37_07935ARX30_08235ARX42_11895ARX92_07785ARY16_02855ARZ28_06760ARZ35_04215AX342_04340B1O05_03115B1O10_11590B1O28_10515B4X86_08480B6N70_00210BG061_14125BG923_10000BGC67_07100BHE45_01350BHY47_13215D1B71_01000D3132_13730D3B94_03440D8W60_04330DC65_04595DRA50_03655E0I17_04300E0I30_11095E0U16_02120E1003_07560E1013_04820E1027_03585E1029_14335E1043_09385E1052_08335E1312_04595E1520_02235E1984_14165E1P51_04330E1P72_02110E1S82_14615E1S83_04140E1S89_01415E1S94_10525E1T01_09845E1T18_01060E1T34_01085E1T48_04575E1T74_10380E1U30_14270E1U44_07385E1U67_11485E1U91_11060E1V18_11470E1V41_12830E1V44_01000E1V46_01695E1V59_10805E1V65_07835E1V69_04540E1W03_01325E1W46_07930E1W58_07000E1W61_04670E1W84_05640E1X50_00065E1X55_00065E1X60_00065E1X63_00065E1X65_10050E1X77_00065E1Y04_07980E1Y22_07260E1Y36_10040E1Y39_06885E1Y54_04665E1Y60_14085E1Y76_10360E1Y85_07210E1Y87_04560E1Z07_06265E1Z13_07150E1Z38_04405E1Z70_06110E1Z81_11410E1Z94_06145E2B22_10915E2B94_09335E2G00_14170E3362_01060E3W12_04070E3W83_06115E3Y59_01330EFC17_14975EFC32_14240EHH67_01225EID73_03115EID74_03115EL440_01100ELF21_11070ELL77_14930EON24_08110EVB16_07950EVC89_14095EX531_05960EYJ23_03110EYJ25_09250EZ544_07110EZ549_04550EZ567_04430EZ579_10250EZ585_00065EZJ50_04320F2B64_09785F9O35_02210FDO43_01425FDP94_12205FJL09_07065FJL15_09360FJL32_05590FJL36_07055FJU16_09110FL790_12360FMU94_04385FMZ78_07455FORC68_0870FPD59_04610FR205_09240FR217_09360GCV90_03275GT55_11320GU61_02025GU73_02025GX56_09050GX92_03115GY66_03115GY90_03605HL26_09525HL28_10595HN15_02035IA39_04370ID69_03115IU04_04610IX93_03955JJ01_03115JL21_03115JU65_09035LJ99_03115MY31_04390NB32_00070NB83_10590NI81_01900OJ48_06380Q842_09175Q988_10290R014_10950R016_03115RI86_13235SH19_04830TS11_06645TS76_03180TS78_02750TX39_14805TX56_02090TX65_02090UA79_03115UL23_02205UL40_07420UL41_04355WN76_13220X855_03115XN56_04310XN57_03335XN85_12310XN87_03395Y170_01010Y243_04300Y473_03115Y519_03115Y529_03115Z603_10025Z676_02255Z689_01060

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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8Y8Q5
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.327 
  • R-Value Work: 0.308 
  • R-Value Observed: 0.309 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.272α = 90
b = 69.213β = 90
c = 124.258γ = 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