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- EMDB-30567: Structure of Mrp complex from Dietzia sp. DQ12-45-1b -

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Basic information

Entry
Database: EMDB / ID: EMD-30567
TitleStructure of Mrp complex from Dietzia sp. DQ12-45-1b
Map data
Sample
  • Complex: Mrp complex of Dietzia sp. DQ12-45-1b
    • Protein or peptide: Monovalent Na+/H+ antiporter subunit D
    • Protein or peptide: Monovalent Na+/H+ antiporter subunit A
    • Protein or peptide: Monovalent Na+/H+ antiporter subunit C
    • Protein or peptide: Monovalent Na+/H+ antiporter subunit F
    • Protein or peptide: Monovalent Na+/H+ antiporter subunit G
    • Protein or peptide: Cation antiporter
  • Ligand: DODECYL-BETA-D-MALTOSIDE
KeywordsSodium/proton antiporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


: / 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
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 ...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
Monovalent Na+/H+ antiporter subunit D / Cation antiporter / Monovalent Na+/H+ antiporter subunit A / Monovalent Na+/H+ antiporter subunit C / Monovalent Na+/H+ antiporter subunit F / Monovalent Na+/H+ antiporter subunit G
Similarity search - Component
Biological speciesDietzia sp. DQ12-45-1b (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsLi B / Zhang KD
Funding support China, 2 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31971134 China
National Science Foundation (NSF, China)31770120 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
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
DepositionSep 21, 2020-
Header (metadata) releaseDec 9, 2020-
Map releaseDec 9, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7d3u
  • Surface level: 6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30567.png

Downloads & links

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Map

FileDownload / File: emd_30567.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 6.0 / Movie #1: 6
Minimum - Maximum-18.336582 - 33.112729999999999
Average (Standard dev.)-0.000000000002462 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z312.000312.000312.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-18.33733.113-0.000

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Supplemental data

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Sample components

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Entire : Mrp complex of Dietzia sp. DQ12-45-1b

EntireName: Mrp complex of Dietzia sp. DQ12-45-1b
Components
  • Complex: Mrp complex of Dietzia sp. DQ12-45-1b
    • Protein or peptide: Monovalent Na+/H+ antiporter subunit D
    • Protein or peptide: Monovalent Na+/H+ antiporter subunit A
    • Protein or peptide: Monovalent Na+/H+ antiporter subunit C
    • Protein or peptide: Monovalent Na+/H+ antiporter subunit F
    • Protein or peptide: Monovalent Na+/H+ antiporter subunit G
    • Protein or peptide: Cation antiporter
  • Ligand: DODECYL-BETA-D-MALTOSIDE

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Supramolecule #1: Mrp complex of Dietzia sp. DQ12-45-1b

SupramoleculeName: Mrp complex of Dietzia sp. DQ12-45-1b / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Dietzia sp. DQ12-45-1b (bacteria)

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

MacromoleculeName: Monovalent Na+/H+ antiporter subunit D / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dietzia sp. DQ12-45-1b (bacteria)
Molecular weightTheoretical: 59.028 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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

MacromoleculeName: Monovalent Na+/H+ antiporter subunit A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dietzia sp. DQ12-45-1b (bacteria)
Molecular weightTheoretical: 100.097484 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #3: Monovalent Na+/H+ antiporter subunit C

MacromoleculeName: Monovalent Na+/H+ antiporter subunit C / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dietzia sp. DQ12-45-1b (bacteria)
Molecular weightTheoretical: 14.310331 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MTLAISVGVL MAGFVFLVLQ RGMVRVILGF ILLSHAAHLT LMAAGGASRR EAPLVSDPDP ALTSDGLPQA FVLTAIVIAF AITIYLLVL AVIGGDDDDT DIGDLDPLDL LPETPGGAHP EDPEPDEPST HDAEGVHR

UniProtKB: Monovalent Na+/H+ antiporter subunit C

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Macromolecule #4: Monovalent Na+/H+ antiporter subunit F

MacromoleculeName: Monovalent Na+/H+ antiporter subunit F / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dietzia sp. DQ12-45-1b (bacteria)
Molecular weightTheoretical: 8.9608 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MIVVDIAIVL VAIAAVLSSY RMIRGPHAGD RAIAADLLFF AFIALLALVG VRVDSPFVYD LVLVATLVGL VSALSLARLM SGGRR

UniProtKB: Monovalent Na+/H+ antiporter subunit F

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Macromolecule #5: Monovalent Na+/H+ antiporter subunit G

MacromoleculeName: Monovalent Na+/H+ antiporter subunit G / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dietzia sp. DQ12-45-1b (bacteria)
Molecular weightTheoretical: 12.780665 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSWELVATVL GSVSVLVGAV VFLGGAIGLL RFPDLYVRSS AIGAAAGLGL VFVIAGAFLL HPTWEAAPKV AVAAILQFAS SAIGAMYIA RAGFLSGAAP TTATRYSQIE FTTGPPTDST EVTRDD

UniProtKB: Monovalent Na+/H+ antiporter subunit G

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Macromolecule #6: Cation antiporter

MacromoleculeName: Cation antiporter / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dietzia sp. DQ12-45-1b (bacteria)
Molecular weightTheoretical: 13.878893 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MTSTLTWPLR IAWFLLWFFW QQTTTSAKVV RDAFLPHASI TPGFVRFPTR CRSELEVTML SSLITLTPGT LTLGAHHPGE GEDWEIVVH GMYFPDPDDL TASLHDLENH MLRAIRREGL TR

UniProtKB: Cation antiporter

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Macromolecule #7: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 7 / Number of copies: 28 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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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: 7.5
GridMaterial: COPPER
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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 93505

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