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- EMDB-14124: Structure of Bacillus pseudofirmus Mrp antiporter complex, monomer -

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Basic information

Entry
Database: EMDB / ID: EMD-14124
TitleStructure of Bacillus pseudofirmus Mrp antiporter complex, monomer
Map data
Sample
  • Complex: MrpABCDEFG complex
    • Protein or peptide: Na+/H+ antiporter subunit D
    • Protein or peptide: Na+/H+ antiporter subunit A
    • Protein or peptide: Na(+)/H(+) antiporter subunit B
    • Protein or peptide: Na(+)/H(+) antiporter subunit C
    • Protein or peptide: Na+/H+ antiporter subunit E
    • Protein or peptide: Na(+)/H(+) antiporter subunit F
    • Protein or peptide: Na+/H+ antiporter subunit G1
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: water
Function / homology
Function and homology information


: / monoatomic ion transmembrane transporter activity / antiporter activity / inorganic cation transmembrane transport / monoatomic cation transmembrane transporter activity / sodium ion transport / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / monoatomic ion transport / proton transmembrane transport ...: / monoatomic ion transmembrane transporter activity / antiporter activity / inorganic cation transmembrane transport / monoatomic cation transmembrane transporter activity / sodium ion transport / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / monoatomic ion transport / proton transmembrane transport / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Monovalent cation proton antiporter subunit A / Na+/H+ antiporter subunit E / Na+/H+ antiporter subunit G / Na+/H+ antiporter MnhB subunit-related protein / Na(+)/H(+) antiporter subunit F-like / MrpA C-terminal/MbhD / Na+/H+ ion antiporter subunit / Na+/H+ antiporter subunit / Domain related to MnhB subunit of Na+/H+ antiporter / Multiple resistance and pH regulation protein F (MrpF / PhaF) ...Monovalent cation proton antiporter subunit A / Na+/H+ antiporter subunit E / Na+/H+ antiporter subunit G / Na+/H+ antiporter MnhB subunit-related protein / Na(+)/H(+) antiporter subunit F-like / MrpA C-terminal/MbhD / Na+/H+ ion antiporter subunit / Na+/H+ antiporter subunit / Domain related to MnhB subunit of Na+/H+ antiporter / Multiple resistance and pH regulation protein F (MrpF / PhaF) / MBH, subunit D / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH:ubiquinone oxidoreductase / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter
Similarity search - Domain/homology
Na+/H+ antiporter subunit D / Na+/H+ antiporter subunit E / Na+/H+ antiporter subunit G1 / Na(+)/H(+) antiporter subunit B / Na+/H+ antiporter subunit A / Na(+)/H(+) antiporter subunit F / Na(+)/H(+) antiporter subunit C
Similarity search - Component
Biological speciesAlkalihalobacillus pseudofirmus (bacteria) / Alkalihalophilus pseudofirmus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.24 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
DepositionJan 12, 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_14124.png

Downloads & links

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Map

FileDownload / File: emd_14124.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 400 pix.
= 428.544 Å		1.07 Å/pix.
x 400 pix.
= 428.544 Å		1.07 Å/pix.
x 400 pix.
= 428.544 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07136 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.081582725 - 0.16127488
Average (Standard dev.)4.8987786e-05 (±0.0022556074)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 428.544 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14124_msk_1.map
Projections & Slices
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Half map: #2

Fileemd_14124_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_14124_half_map_2.map
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Sample components

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Entire : MrpABCDEFG complex

EntireName: MrpABCDEFG complex
Components
  • Complex: MrpABCDEFG complex
    • Protein or peptide: Na+/H+ antiporter subunit D
    • Protein or peptide: Na+/H+ antiporter subunit A
    • Protein or peptide: Na(+)/H(+) antiporter subunit B
    • Protein or peptide: Na(+)/H(+) antiporter subunit C
    • Protein or peptide: Na+/H+ antiporter subunit E
    • Protein or peptide: Na(+)/H(+) antiporter subunit F
    • Protein or peptide: Na+/H+ antiporter subunit G1
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: water

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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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Macromolecule #1: Na+/H+ antiporter subunit D

MacromoleculeName: Na+/H+ antiporter subunit D / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Alkalihalophilus pseudofirmus (bacteria)
Molecular weightTheoretical: 54.605082 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNNLVILPIL IPFIVGTILI LFAKNHSLQR VISGFTVIGM LLVAIYLAMD VYQNGISVLE LGNWQAPFGI VLVADMFATM MVILASIVG VVCLFFAFQT ISSEREKYYF YPFYFFLLAG VNGAFLTGDL FNLFVFFEVM LIASYILIVL GGTKYQLRES L KYVMINVF ...String:
MNNLVILPIL IPFIVGTILI LFAKNHSLQR VISGFTVIGM LLVAIYLAMD VYQNGISVLE LGNWQAPFGI VLVADMFATM MVILASIVG VVCLFFAFQT ISSEREKYYF YPFYFFLLAG VNGAFLTGDL FNLFVFFEVM LIASYILIVL GGTKYQLRES L KYVMINVF ASILFIVGVA YIYSVTGTLN MADLAVKVGQ LEQTGVLNVI AVIFLVVFAM KGGLFPLYFW LPRSYYGPPA AI AALFGGL LTKVGIYAIM RTFTLIFTHD PDFTHMLILI LAGLTMFFGV LGAVSQFDFK RILSYHIISQ VGYMVMGLGI YTQ LAIAGA IYYIAHHIIV KAALFLFAGA TQRITGTTDL KKMGGLLKTH PWLAWMFFIS AISLAGIPPL SGFFSKFALI LAAF LNENY IIAAVALAVG LLTLFSMMKI FIYAFWGEQK HTEQQANFKV GKLLLPIVPL VALTIILGFA AEPIFQYSLQ VADQI LDPT IYIESVLKE

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Macromolecule #2: Na+/H+ antiporter subunit A

MacromoleculeName: Na+/H+ antiporter subunit A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Alkalihalophilus pseudofirmus (bacteria)
Molecular weightTheoretical: 89.301781 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTVLHWATIS PFLLAILIPF LYKYARRIHT GWFVLALPLV LFIYFIRYLS VTSTGGVVEH TIPWVPSLGI NFTVFVDGLS LLFALLITG IGTLVILYSI FYLSKKTESL NNFYVYLLMF MGAMLGVVLS DNLIVLYVFW ELTSLASSLL ISYWFHREKS T YGAQKSML ...String:
MTVLHWATIS PFLLAILIPF LYKYARRIHT GWFVLALPLV LFIYFIRYLS VTSTGGVVEH TIPWVPSLGI NFTVFVDGLS LLFALLITG IGTLVILYSI FYLSKKTESL NNFYVYLLMF MGAMLGVVLS DNLIVLYVFW ELTSLASSLL ISYWFHREKS T YGAQKSML ITVFGGFAML GGFSLLYVMT GTFSIRGIIE NVDLVTSSEL FLPAMILVLL GAFTKSAQFP FHIWLPDAME AP TPVSAYL HSATMVKAGI YLVARLTPVF AGSAEWFWLL TGFGVVTLLW GSTSAVRQKD LKGILAFSTV SQLGLIMTLL GLG SAAIYF GDSVDPAFYS FAIMAAIFHL INHATFKGSL FMTAGIIDHE TGTRDIRKLG GLMAIMPVTF TVSLIGLASM AGLP PFNGF LSKEMFFTAL LRATEMNTFN METFGIIIVV LAWIASVFTF LYCLIMFFKT FTGKFKPENY DVKVHEAPIG MLISP VILG SLVIVFGFFP NILAYTIIEP AMQAILPTLL ADGEVFYVNI YMWHGFNAEL FMTMGVVAAG IILFLMMKNW AKTAFY MKE RDPLNWFYDN SLSGVITGSQ AVTRIQMTGL LRDYFAYMTT FMILLLGYTM FRYDAFTIDT TNVTGIAPYI WVITLVF IA ATLSIPFINK RITAVVVVGV IGFLLALLFV VFRAPDLALT QLLVETVTVL LLMLAFYHLP ELRKEEFKPR FNIVNLII S IGVGFLVTAI ALSSLALGNE AGIEPISQFF VENSKELAGG YNMVNVILVD FRGLDTLLEV LVLGIAALGV IALIKLRMT GREDV

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Macromolecule #3: Na(+)/H(+) antiporter subunit B

MacromoleculeName: Na(+)/H(+) antiporter subunit B / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Alkalihalophilus pseudofirmus (bacteria)
Molecular weightTheoretical: 15.748639 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKNLKSNDVL LHSVTRVVTF IILAFSVYLF FAGHNNPGGG FIGGLMTASA LLLMYLGFDM KSIKKAIPFD FTKMIAFGLL LAIITGFGG LLVGDPYLTQ YFEYYQIPIL GETELTTALP FDLGIYLVVV GIALTIILTI AEDDM

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Macromolecule #4: Na(+)/H(+) antiporter subunit C

MacromoleculeName: Na(+)/H(+) antiporter subunit C / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Alkalihalophilus pseudofirmus (bacteria) / Strain: ATCC BAA-2126 / JCM 17055 / OF4
Molecular weightTheoretical: 12.229499 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MEILMSITVG VLFMVGTYLI LTKSLLRVVV GLILLSHGAH LLLLTMAGLQ RGAPPLLHLE ATTYSDPLPQ ALILTAIVIS FGVTSFLLV LAYRTYKEHK TDDLDQLRGS ADE

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Macromolecule #5: Na+/H+ antiporter subunit E

MacromoleculeName: Na+/H+ antiporter subunit E / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Alkalihalophilus pseudofirmus (bacteria)
Molecular weightTheoretical: 18.357852 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAFQILLNLV IAVIWVNFQN SYTAVDFLIG YVVGIFILFV LRRFLRFDFY MRRVWAIIKL IVLFFKELIL ANIDVIKIVL SPKMNIQPG IVAVPTKLKT DWELSLLASL ISLTPGTLSM DFSDDNKYIY IHAIDVPNKE KMIRDIHDTF ERAILEVTN

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Macromolecule #6: Na(+)/H(+) antiporter subunit F

MacromoleculeName: Na(+)/H(+) antiporter subunit F / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Alkalihalophilus pseudofirmus (bacteria)
Molecular weightTheoretical: 10.024184 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MFQSILMIVL VVMSISLFVC FIRTLIGPTM SDRIVALDTF GINLIGFIGV IMMLQETLAY SEVVLVISIL AFIGSIALSK FIERGVVFD RG

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Macromolecule #7: Na+/H+ antiporter subunit G1

MacromoleculeName: Na+/H+ antiporter subunit G1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Alkalihalophilus pseudofirmus (bacteria)
Molecular weightTheoretical: 14.947675 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MTAVEIIISI FVLIGGFLSL LGSIGIIRFP DVYGRLHAAT KSATLGVISI MLATFLFFFL VHGEFVGKLL LTILFVFLTA PVAGMMMGR SAYRVGVPLW EKSTQDDLKK MYEKKMKGSN HHHHHHDYKD DDDK

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Macromolecule #8: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 8 / Number of copies: 3 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM / Phosphatidylethanolamine

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Macromolecule #9: water

MacromoleculeName: water / type: ligand / ID: 9 / Number of copies: 360 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
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

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.24 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 513743
FSC plot (resolution estimation)

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