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- EMDB-15693: Structure of Bacillus pseudofirmus Mrp antiporter complex, monome... -

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Basic information

Entry
Database: EMDB / ID: EMD-15693
TitleStructure of Bacillus pseudofirmus Mrp antiporter complex, monomer, processed at original pixel size (0.837 A/pix)
Map data
Sample
  • Complex: MrpABCDEFG complex
Biological speciesAlkalihalobacillus pseudofirmus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.25 Å
AuthorsLee Y
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)ZI 552/5-1 Germany
CitationJournal: Nat Commun / Year: 2022
Title: Ion transfer mechanisms in Mrp-type antiporters from high resolution cryoEM and molecular dynamics simulations.
Authors: Yongchan Lee / Outi Haapanen / Anton Altmeyer / Werner Kühlbrandt / Vivek Sharma / Volker Zickermann /
Abstract: Multiple resistance and pH adaptation (Mrp) cation/proton antiporters are essential for growth of a variety of halophilic and alkaliphilic bacteria under stress conditions. Mrp-type antiporters are ...Multiple resistance and pH adaptation (Mrp) cation/proton antiporters are essential for growth of a variety of halophilic and alkaliphilic bacteria under stress conditions. Mrp-type antiporters are closely related to the membrane domain of respiratory complex I. We determined the structure of the Mrp antiporter from Bacillus pseudofirmus by electron cryo-microscopy at 2.2 Å resolution. The structure resolves more than 99% of the sidechains of the seven membrane subunits MrpA to MrpG plus 360 water molecules, including ~70 in putative ion translocation pathways. Molecular dynamics simulations based on the high-resolution structure revealed details of the antiport mechanism. We find that switching the position of a histidine residue between three hydrated pathways in the MrpA subunit is critical for proton transfer that drives gated trans-membrane sodium translocation. Several lines of evidence indicate that the same histidine-switch mechanism operates in respiratory complex I.
History
DepositionAug 30, 2022-
Header (metadata) releaseNov 9, 2022-
Map releaseNov 9, 2022-
UpdateNov 9, 2022-
Current statusNov 9, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15693.png

Downloads & links

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Map

FileDownload / File: emd_15693.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 512 pix.
= 428.544 Å		0.84 Å/pix.
x 512 pix.
= 428.544 Å		0.84 Å/pix.
x 512 pix.
= 428.544 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.837 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018
Minimum - Maximum-0.07321835 - 0.14081211
Average (Standard dev.)3.310528e-05 (±0.0016952495)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 428.544 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15693_msk_1.map
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Half map: #1

Fileemd_15693_half_map_1.map
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Half map: #2

Fileemd_15693_half_map_2.map
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Sample components

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Entire : MrpABCDEFG complex

EntireName: MrpABCDEFG complex
Components
  • Complex: MrpABCDEFG complex

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Supramolecule #1: MrpABCDEFG complex

SupramoleculeName: MrpABCDEFG complex / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Alkalihalobacillus pseudofirmus (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6z16

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 451946
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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