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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-30567 | |||||||||
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Title | Structure of Mrp complex from Dietzia sp. DQ12-45-1b | |||||||||
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![]() | Sodium/proton antiporter / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() : / monoatomic ion transmembrane transporter activity / monoatomic cation transmembrane transporter activity / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / membrane => GO:0016020 / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
![]() | Li B / Zhang KD | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the Mrp complex reveals molecular mechanism of this giant bacterial sodium proton pump. Authors: Bin Li / Kaiduan Zhang / Yong Nie / Xianping Wang / Yan Zhao / Xuejun C Zhang / Xiao-Lei Wu / ![]() Abstract: Multiple resistance and pH adaptation (Mrp) complexes are sophisticated cation/proton exchangers found in a vast variety of alkaliphilic and/or halophilic microorganisms, and are critical for their ...Multiple resistance and pH adaptation (Mrp) complexes are sophisticated cation/proton exchangers found in a vast variety of alkaliphilic and/or halophilic microorganisms, and are critical for their survival in highly challenging environments. This family of antiporters is likely to represent the ancestor of cation pumps found in many redox-driven transporter complexes, including the complex I of the respiratory chain. Here, we present the three-dimensional structure of the Mrp complex from a sp. strain solved at 3.0-Å resolution using the single-particle cryoelectron microscopy method. Our structure-based mutagenesis and functional analyses suggest that the substrate translocation pathways for the driving substance protons and the substrate sodium ions are separated in two modules and that symmetry-restrained conformational change underlies the functional cycle of the transporter. Our findings shed light on mechanisms of redox-driven primary active transporters, and explain how driving substances of different electric charges may drive similar transport processes. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 95.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.6 KB 16.6 KB | Display Display | ![]() |
Images | ![]() | 476.4 KB | ||
Filedesc metadata | ![]() | 6.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7d3uMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Mrp complex of Dietzia sp. DQ12-45-1b
Entire | Name: Mrp complex of Dietzia sp. DQ12-45-1b |
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Components |
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-Supramolecule #1: Mrp complex of Dietzia sp. DQ12-45-1b
Supramolecule | Name: Mrp complex of Dietzia sp. DQ12-45-1b / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Monovalent Na+/H+ antiporter subunit D
Macromolecule | Name: Monovalent Na+/H+ antiporter subunit D / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 59.028 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MTLESALTLF VAVPLLTAGV LVAVASRTRL ILTVLFAVLG TQLAAAVATV PWVSDGSVVV HQVALWAPGV SIPFVLDMFS ALMLTVTSL LTLTCAAFAV AAGEAYKRFY PPLVLLVTAG VNGALLTGDL FNFFVFVEVM LLPSYGLMMI TRSGRASVVG V AASRLYIS ...String: MTLESALTLF VAVPLLTAGV LVAVASRTRL ILTVLFAVLG TQLAAAVATV PWVSDGSVVV HQVALWAPGV SIPFVLDMFS ALMLTVTSL LTLTCAAFAV AAGEAYKRFY PPLVLLVTAG VNGALLTGDL FNFFVFVEVM LLPSYGLMMI TRSGRASVVG V AASRLYIS VNLLASTILL IGVALIYGVT GTVNIAQLHG AASEDTAVAV ATALVLFALA IKAAVVPVHG WLARAYPKMS PA VTAMFSG LHTKIAIYAI YRIYAVIFDG DSRYLWVGVV VFSATMLIGV LGAVGEAAPR SILAFHMVSQ IGYILLGVAL FGP IGLTAG IFYLLHHMIV KAALFLAIGA IEVRYGPRRL GQLSGLAKTE PLVAVAFFAS AMSLAGIPPF SGFVAKLSLI IAAL DAGQI AAAAVAVVVS ILTLLSMLKI WTGIFLGEPT PTDSRTLPEG LDPAHSEATG IPDGRDVDGR HRDGVEITGA AAGAT PTDT MAPASTTATA TATDTVTETA SVADTAEAGS PDPDMVPPGR RIGLALAAPA LALSVVTLAL GLGGQLLLEL SGTAAA NLY DPTTYIQAVL G UniProtKB: Monovalent Na+/H+ antiporter subunit D |
-Macromolecule #2: Monovalent Na+/H+ antiporter subunit A
Macromolecule | Name: Monovalent Na+/H+ antiporter subunit A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 100.097484 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: VTLTLALAVA FGIAAISPLL ARTMGRDAGW PLAAMLGGLA LYIWFAIPVD TVASVEWMPA LGVELRLSLD PLARVFTMIV LGIGAVVMA YSSRYLGRGS GHGGYYGLMT LFAASMLGLV LADDVVVLFV AWEFTTLCSF FLITLAGPKG TQPAVRTLLV T VAGGLCLL ...String: VTLTLALAVA FGIAAISPLL ARTMGRDAGW PLAAMLGGLA LYIWFAIPVD TVASVEWMPA LGVELRLSLD PLARVFTMIV LGIGAVVMA YSSRYLGRGS GHGGYYGLMT LFAASMLGLV LADDVVVLFV AWEFTTLCSF FLITLAGPKG TQPAVRTLLV T VAGGLCLL TAAALMVVRT GTTVLSEILV DPVWSADPAF AAVIAVLIAM AAFTKSAQFP FQAWLPDAMV AATPVSAYLH AA AMVKAGI YLLLRFSEAL HDVPVWNLLL ITCGMTTAVL GAVFAMQRDD LKELLAYSTI SQLGFLVATI GVGTPAAMVA AII HTIAHA LFKSSLFMFV GVVDHQTGTR AMSGLPRLYR IMPGTAIGVG LAAASMAGLP PLLGFVSKEW MFKSMLDAPG GAWA GPALG ALAVFAATFT FAYSARFLLG GFVTHGPPAG PGPEPVHSTP ETIEAPRASF FLPAALPAVL GLVLGLTGFL LEPAV AAAA RASIGEGYEA DFGLWHGFAP ELFMSMIVIT LGIVLVVVRH PVDRFLDREL APITGVATVD ALRRWAIAGG ARVGDV TRT DRISRHVWAV LLVLVALAAV GVVAVRPEPE VGSPVRAEDW IVVVLLVVGT AAMVISRSRL GAVANVGIVG FAMALWF FT LGAVDVALTQ LLVEVLTVVV IVLVLQRLPR AFHTVSRSRT LVSAAVAIVV GLASGAAVWA MTGRRELSDV GRYFLDNA E QDTGGINVVN TVLVDYRALD TLGELTVLGV AGLAVILALH ARRALPRRDV PLAVHADSPL LSAQDNGVFL RTFARILGP LIVLLSLYFL VRGHNAPGGG FNSALIGGAG IAIYYLRAPS DKAARIRVPY VAVIAAGVII GVVTGLAGFV DGSFLLPLHA YLGDVHLTT ALIFDVGVYL AVLGVIMAAI DKLGGDDRSD EPAVPPPPPT GPGAEATAPA ATEDADRVID VTDNREVQA UniProtKB: Monovalent Na+/H+ antiporter subunit A |
-Macromolecule #3: Monovalent Na+/H+ antiporter subunit C
Macromolecule | Name: Monovalent Na+/H+ antiporter subunit C / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 14.310331 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MTLAISVGVL MAGFVFLVLQ RGMVRVILGF ILLSHAAHLT LMAAGGASRR EAPLVSDPDP ALTSDGLPQA FVLTAIVIAF AITIYLLVL AVIGGDDDDT DIGDLDPLDL LPETPGGAHP EDPEPDEPST HDAEGVHR UniProtKB: Monovalent Na+/H+ antiporter subunit C |
-Macromolecule #4: Monovalent Na+/H+ antiporter subunit F
Macromolecule | Name: Monovalent Na+/H+ antiporter subunit F / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 8.9608 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MIVVDIAIVL VAIAAVLSSY RMIRGPHAGD RAIAADLLFF AFIALLALVG VRVDSPFVYD LVLVATLVGL VSALSLARLM SGGRR UniProtKB: Monovalent Na+/H+ antiporter subunit F |
-Macromolecule #5: Monovalent Na+/H+ antiporter subunit G
Macromolecule | Name: Monovalent Na+/H+ antiporter subunit G / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 12.780665 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSWELVATVL GSVSVLVGAV VFLGGAIGLL RFPDLYVRSS AIGAAAGLGL VFVIAGAFLL HPTWEAAPKV AVAAILQFAS SAIGAMYIA RAGFLSGAAP TTATRYSQIE FTTGPPTDST EVTRDD UniProtKB: Monovalent Na+/H+ antiporter subunit G |
-Macromolecule #6: Cation antiporter
Macromolecule | Name: Cation antiporter / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 13.878893 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MTSTLTWPLR IAWFLLWFFW QQTTTSAKVV RDAFLPHASI TPGFVRFPTR CRSELEVTML SSLITLTPGT LTLGAHHPGE GEDWEIVVH GMYFPDPDDL TASLHDLENH MLRAIRREGL TR UniProtKB: Cation antiporter |
-Macromolecule #7: DODECYL-BETA-D-MALTOSIDE
Macromolecule | Name: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 7 / Number of copies: 28 / Formula: LMT |
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Molecular weight | Theoretical: 510.615 Da |
Chemical component information | ![]() ChemComp-LMT: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Grid | Material: COPPER |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 93505 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |