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- PDB-7d3u: Structure of Mrp complex from Dietzia sp. DQ12-45-1b -

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Basic information

Entry
Database: PDB / ID: 7d3u
TitleStructure of Mrp complex from Dietzia sp. DQ12-45-1b
Components
  • (Monovalent Na+/H+ antiporter subunit ...) x 5
  • Cation antiporter
KeywordsMEMBRANE PROTEIN / Sodium/proton antiporter
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsLi, B. / Zhang, K.D. / Wu, X.L. / Zhang, X.C.
Funding support China, 2items
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, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
D: Monovalent Na+/H+ antiporter subunit D
A: Monovalent Na+/H+ antiporter subunit A
C: Monovalent Na+/H+ antiporter subunit C
F: Monovalent Na+/H+ antiporter subunit F
G: Monovalent Na+/H+ antiporter subunit G
E: Cation antiporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,35334
Polymers209,0566
Non-polymers14,29728
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area53370 Å2
ΔGint-250 kcal/mol
Surface area54980 Å2

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Components

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Monovalent Na+/H+ antiporter subunit ... , 5 types, 5 molecules DACFG

#1: Protein Monovalent Na+/H+ antiporter subunit D / Putative monovalent cation/H antiporter subunit D


Mass: 59028.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dietzia sp. DQ12-45-1b (bacteria) / Gene: amnhD, GJR88_00771 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A221C8X0
#2: Protein Monovalent Na+/H+ antiporter subunit A / Putative monovalent cation/H antiporter subunit A


Mass: 100097.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dietzia sp. DQ12-45-1b (bacteria) / Gene: amnhA, GJR88_00777 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A221C8X2
#3: Protein Monovalent Na+/H+ antiporter subunit C / Putative monovalent cation/H antiporter subunit C


Mass: 14310.331 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dietzia sp. DQ12-45-1b (bacteria) / Gene: amnhC, GJR88_00774 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A221C8X5
#4: Protein Monovalent Na+/H+ antiporter subunit F / Multiple resistance and pH regulation protein F


Mass: 8960.800 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dietzia sp. DQ12-45-1b (bacteria) / Gene: amnhF, GJR88_00768 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A221C8X7
#5: Protein Monovalent Na+/H+ antiporter subunit G / Monovalent cation/proton antiporter / MnhG/PhaG subunit


Mass: 12780.665 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dietzia sp. DQ12-45-1b (bacteria) / Gene: amnhG, GJR88_00766 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A221C8Y4

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Protein / Sugars , 2 types, 29 molecules E

#6: Protein Cation antiporter / Monovalent Na+/H+ antiporter subunit E


Mass: 13878.893 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dietzia sp. DQ12-45-1b (bacteria) / Gene: amnhE, GJR88_00770 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A221C8X1
#7: Sugar...
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mrp complex of Dietzia sp. DQ12-45-1b / Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT
Source (natural)Organism: Dietzia sp. DQ12-45-1b (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 93505 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00414605
ELECTRON MICROSCOPYf_angle_d0.57419863
ELECTRON MICROSCOPYf_dihedral_angle_d18.1132261
ELECTRON MICROSCOPYf_chiral_restr0.042487
ELECTRON MICROSCOPYf_plane_restr0.0042388

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