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- EMDB-11027: Structure of the Mrp antiporter complex -

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Basic information

Entry
Database: EMDB / ID: EMD-11027
TitleStructure of the Mrp antiporter complex
Map dataComposite map of the MRP dimer
Sample
  • Complex: Mrp dimer
    • Protein or peptide: Multisubunit Na+/H+ antiporter, A subunit
    • Protein or peptide: Multisubunit Na+/H+ antiporter, B subunit
    • Protein or peptide: Multisubunit Na+/H+ antiporter, C subunit
    • Protein or peptide: Multisubunit Na+/H+ antiporter, D subunit
    • Protein or peptide: Multisubunit Na+/H+ antiporter, E subunit
    • Protein or peptide: Multisubunit Na+/H+ antiporter, F subunit
    • Protein or peptide: Multisubunit Na+/H+ antiporter, G subunit
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: POTASSIUM ION
KeywordsMrp antiporter / sodium/proton exchanger / bioenergetics / complex / MEMBRANE PROTEIN
Function / homology
Function and homology information


sodium:proton antiporter activity / monoatomic cation transmembrane transporter activity / antiporter activity / sodium ion transport / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / monoatomic ion transport / proton transmembrane transport / membrane / plasma membrane
Similarity search - Function
Monovalent cation proton antiporter subunit A / : / : / MrpA C-terminal/MbhE / : / MBH, subunit E / Na+/H+ antiporter subunit E / Na+/H+ antiporter subunit G / Na+/H+ antiporter MnhB subunit-related protein / Na(+)/H(+) antiporter subunit F-like ...Monovalent cation proton antiporter subunit A / : / : / MrpA C-terminal/MbhE / : / MBH, subunit E / 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
Multisubunit Na+/H+ antiporter, G subunit / Multisubunit Na+/H+ antiporter, C subunit / Multisubunit Na+/H+ antiporter, B subunit / Multisubunit Na+/H+ antiporter, A subunit / Multisubunit Na+/H+ antiporter, F subunit / Multisubunit Na+/H+ antiporter, E subunit / Multisubunit Na+/H+ antiporter, D subunit
Similarity search - Component
Biological speciesAnoxybacillus flavithermus WK1 (bacteria) / Anoxybacillus flavithermus (strain DSM 21510 / WK1) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsSteiner J / Sazanov LA
CitationJournal: Elife / Year: 2020
Title: Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter.
Authors: Julia Steiner / Leonid Sazanov /
Abstract: Multiple resistance and pH adaptation (Mrp) antiporters are multi-subunit Na (or K)/H exchangers representing an ancestor of many essential redox-driven proton pumps, such as respiratory complex I. ...Multiple resistance and pH adaptation (Mrp) antiporters are multi-subunit Na (or K)/H exchangers representing an ancestor of many essential redox-driven proton pumps, such as respiratory complex I. The mechanism of coupling between ion or electron transfer and proton translocation in this large protein family is unknown. Here, we present the structure of the Mrp complex from solved by cryo-EM at 3.0 Å resolution. It is a dimer of seven-subunit protomers with 50 trans-membrane helices each. Surface charge distribution within each monomer is remarkably asymmetric, revealing probable proton and sodium translocation pathways. On the basis of the structure we propose a mechanism where the coupling between sodium and proton translocation is facilitated by a series of electrostatic interactions between a cation and key charged residues. This mechanism is likely to be applicable to the entire family of redox proton pumps, where electron transfer to substrates replaces cation movements.
History
DepositionMay 12, 2020-
Header (metadata) releaseAug 12, 2020-
Map releaseAug 12, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6z16
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11027.png

Downloads & links

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Map

FileDownload / File: emd_11027.map.gz / Format: CCP4 / Size: 28 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of the MRP dimer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.84 Å/pix.
x 254 pix.
= 213.36 Å		0.84 Å/pix.
x 265 pix.
= 222.6 Å		0.84 Å/pix.
x 109 pix.
= 91.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.05012599 - 0.09747261
Average (Standard dev.)0.0010237437 (±0.006049292)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions265109254
Spacing254265109
CellA: 213.36 Å / B: 222.59999 Å / C: 91.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.840.840.84
M x/y/z254265109
origin x/y/z0.0000.0000.000
length x/y/z213.360222.60091.560
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ254265109
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS109265254
D min/max/mean-0.0500.0970.001

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Supplemental data

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Sample components

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Entire : Mrp dimer

EntireName: Mrp dimer
Components
  • Complex: Mrp dimer
    • Protein or peptide: Multisubunit Na+/H+ antiporter, A subunit
    • Protein or peptide: Multisubunit Na+/H+ antiporter, B subunit
    • Protein or peptide: Multisubunit Na+/H+ antiporter, C subunit
    • Protein or peptide: Multisubunit Na+/H+ antiporter, D subunit
    • Protein or peptide: Multisubunit Na+/H+ antiporter, E subunit
    • Protein or peptide: Multisubunit Na+/H+ antiporter, F subunit
    • Protein or peptide: Multisubunit Na+/H+ antiporter, G subunit
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: POTASSIUM ION

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Supramolecule #1: Mrp dimer

SupramoleculeName: Mrp dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Anoxybacillus flavithermus WK1 (bacteria)
Molecular weightTheoretical: 440 KDa

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Macromolecule #1: Multisubunit Na+/H+ antiporter, A subunit

MacromoleculeName: Multisubunit Na+/H+ antiporter, A subunit / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Anoxybacillus flavithermus (strain DSM 21510 / WK1) (bacteria)
Molecular weightTheoretical: 92.059953 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLKKNETFYT YCSYKKEDGY VRRGLIVLPT LHIAMFAPFL LALLVPFFYK CIRSLHVGWF VFPLPIALFV YFLSYIDDVR NDEVIRATM PWIPSLRISF DAYVDGLSLL FALLITGIGS LVVLYSIYYL QKGKEPLGNF YVYLLLFMGA MLGVVLSDHL I ALYMFWEL ...String:
MLKKNETFYT YCSYKKEDGY VRRGLIVLPT LHIAMFAPFL LALLVPFFYK CIRSLHVGWF VFPLPIALFV YFLSYIDDVR NDEVIRATM PWIPSLRISF DAYVDGLSLL FALLITGIGS LVVLYSIYYL QKGKEPLGNF YVYLLLFMGA MLGVVLSDHL I ALYMFWEL TSISSFLLIA YWFKRDRSRY GAQKSMLITM FGGLLMLGGF VALAIAGGTY NIRELVHTPL TEHPLFIPAL VL ILFGAFT KSAQFPFYIW LPDAMEAPTP VSAYLHSATM VKAGIYVIAR LTPIFAVSSV WVWTVALVGL VTLCWASFLA SKQ TDLKAI LAYSTVSQLG LITSLLGIGG LSFHYDGMGE NVFMVAVLAA IFHLFNHATF KGSLFMVVGI VDHETGTRDI RRLG GLMTI MPITFTIALI GSLSMAGLPP FNGFLSKEMF FTAMLRAKDV AGWAVILPVV AWVASIFTFL YSALLVSRTF FGTYK PHVL KKEAHEAPFG MLIAPIVLAS LVVFIGFVPN VLSDSVLAPA VYAVLYGLFA PNEALDVHIS HWHGFTPELF MTIGVL LFG LVLYRTFPKW KKIYYRLSER MSLNFFYDQS FVWMERGARS FISRVMNGSM RTYLMYIFTS LVALLLFTIG WHEQWHI DL SRLAHVRVYE VVLAIGILAA TVTTVIAKSR LTAIVSLGAV GYAVALFFVL FRAPDLALTQ LVIETISVAL FLLCFYHL P KFTQKQESVR FHLGNALVSL AVGMTMSIIA FLAYAGKHFD SISQYYVDNT YEKAAGKNMV NVILVDFRGF DTLFEICVL AIAALGIYAM VKLRLAKEEE R

UniProtKB: Multisubunit Na+/H+ antiporter, A subunit

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Macromolecule #2: Multisubunit Na+/H+ antiporter, B subunit

MacromoleculeName: Multisubunit Na+/H+ antiporter, B subunit / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Anoxybacillus flavithermus (strain DSM 21510 / WK1) (bacteria)
Molecular weightTheoretical: 15.421317 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKRNDVILRT TTAVVTPIIV LFSVQLFFAG HYYPGGGFIG GLMTAGAIVL LLLAFDIETV RKMVPINYKW LVAIGLLFAV GTGMSSMFL DRPFLTHAYK YVHLPLLDHT SLHTAVLFDL GVYFVVVGVT MIIIETIGES D

UniProtKB: Multisubunit Na+/H+ antiporter, B subunit

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Macromolecule #3: Multisubunit Na+/H+ antiporter, C subunit

MacromoleculeName: Multisubunit Na+/H+ antiporter, C subunit / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Anoxybacillus flavithermus (strain DSM 21510 / WK1) (bacteria)
Molecular weightTheoretical: 11.625945 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MELLMIVVIG CLFAAATYLL LSKSLLRIII GTGLLSHGAH LLLLTMGGLK AGAPPLLGEK ASRYVDPLPQ ALILTAIVIS FGVTAFFLV LAYRSYQEIG TDHMEGMKGD

UniProtKB: Multisubunit Na+/H+ antiporter, C subunit

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Macromolecule #4: Multisubunit Na+/H+ antiporter, D subunit

MacromoleculeName: Multisubunit Na+/H+ antiporter, D subunit / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Anoxybacillus flavithermus (strain DSM 21510 / WK1) (bacteria)
Molecular weightTheoretical: 53.767875 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSNLLLLPIV IPLVTAIVLI FFPKHVFWQR VVSLAATVGL VVASGALLHR VHTDGIQTLN VGNWPAPFGI TLVSDSLSAL LVLTTSIIA LACLVYSFYA IGHKRETFYY YSFFQFLIVG VNGAFTTGDL FNLFVFFEVM LMSSYVLLVL GGTKIQLRET I KYTLVNVI ...String:
MSNLLLLPIV IPLVTAIVLI FFPKHVFWQR VVSLAATVGL VVASGALLHR VHTDGIQTLN VGNWPAPFGI TLVSDSLSAL LVLTTSIIA LACLVYSFYA IGHKRETFYY YSFFQFLIVG VNGAFTTGDL FNLFVFFEVM LMSSYVLLVL GGTKIQLRET I KYTLVNVI SSALFVVAVA YLYAVTGTLN MAHLADRINA LGSSPILTVI AVLFIIVFGL KGAIFPLYFW LPGAYYAPPT PV LALFGGL LTKVGVYSIL RTFTLLFTHD AAYTHTLLAW LALGTIIIGV IGAVAYNDMR YIVIYNIIAA VGVMIFGISI MTP ESVEGT IFYLLQDMVM KAMLFLFVGI IFSITRSNDI RSFSGLITSY PLLGWAFFIA ALSLAGIPPL SGFIGKLLIV KASF DAQLI FEAIVILLSS LLVLYSVMKI FMNGFWGEKK GFEQKQVDGR LFPVLFLLVL SVAYGIGIEF VRPFVLDAVN VLVDP SMYI EAVLKE

UniProtKB: Multisubunit Na+/H+ antiporter, D subunit

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

MacromoleculeName: Multisubunit Na+/H+ antiporter, E subunit / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Anoxybacillus flavithermus (strain DSM 21510 / WK1) (bacteria)
Molecular weightTheoretical: 18.037582 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAFQILLNVI LAFVWMFLTV SFDGASFLVG YMIGLFILFI LRRFFHSRFY LVPVFVIIKL LFIFFKELIL SNIAVAKVVM QRSLTIQPA IFALPTELKK EWEITVLAML ITLTPGTLVL DVSDDGSTLY IHALNSPDVH EAIESIKQSF EKTIMEVSK

UniProtKB: Multisubunit Na+/H+ antiporter, E subunit

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Macromolecule #6: Multisubunit Na+/H+ antiporter, F subunit

MacromoleculeName: Multisubunit Na+/H+ antiporter, F subunit / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Anoxybacillus flavithermus (strain DSM 21510 / WK1) (bacteria)
Molecular weightTheoretical: 9.657734 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MMLNIALVIL SLAMVGFLYR VVKGPSTADR IIALDAMGIT LAGIVAIVSM LLNTSAFLDV ILLIGILAFV GTVAFAKFLE KGVVIERGN DR

UniProtKB: Multisubunit Na+/H+ antiporter, F subunit

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Macromolecule #7: Multisubunit Na+/H+ antiporter, G subunit

MacromoleculeName: Multisubunit Na+/H+ antiporter, G subunit / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Anoxybacillus flavithermus (strain DSM 21510 / WK1) (bacteria)
Molecular weightTheoretical: 12.900172 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSSNVGTIAN ALVVVLILLG AVLTLLSAVG AIRLPDVYTR SHAISKSTTL GIMCILLGAF LHFFIENNHF NSRLLLGIVF IFMTSPVAA HLISRAAYYA NVERWEGTVR DDLKQKAGGK

UniProtKB: Multisubunit Na+/H+ antiporter, G subunit

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Macromolecule #8: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 8 / Number of copies: 26 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

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Macromolecule #9: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 9 / Number of copies: 4 / Formula: K
Molecular weightTheoretical: 39.098 Da

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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

Concentration0.16 mg/mL
BufferpH: 6
GridModel: Quantifoil R0.6/1 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 1.2 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 88.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 892069
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 285688
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 4 / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

4hea

source_name: PDB, initial_model_type: experimental model

6cfw

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6z16:
Structure of the Mrp antiporter complex

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