7D3U

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the Dietzia Mrp complex reveals molecular mechanism of this giant bacterial sodium proton pump.

Li, B.Zhang, K.Nie, Y.Wang, X.Zhao, Y.Zhang, X.C.Wu, X.L.

(2020) Proc Natl Acad Sci U S A 117: 31166-31176

  • DOI: https://doi.org/10.1073/pnas.2006276117
  • Primary Citation of Related Structures:  
    7D3U

  • PubMed 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 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 Dietzia 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.


  • Organizational Affiliation

    National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Monovalent Na+/H+ antiporter subunit DA [auth D]574Dietzia sp. DQ12-45-1bMutation(s): 0 
Gene Names: amnhDGJR88_00771
Membrane Entity: Yes 
UniProt
Find proteins for A0A221C8X0 (Dietzia sp. DQ12-45-1b)
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A221C8X0
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Monovalent Na+/H+ antiporter subunit AB [auth A]958Dietzia sp. DQ12-45-1bMutation(s): 0 
Gene Names: amnhAGJR88_00777
Membrane Entity: Yes 
UniProt
Find proteins for A0A221C8X2 (Dietzia sp. DQ12-45-1b)
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UniProt GroupA0A221C8X2
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Monovalent Na+/H+ antiporter subunit C137Dietzia sp. DQ12-45-1bMutation(s): 0 
Gene Names: amnhCGJR88_00774
Membrane Entity: Yes 
UniProt
Find proteins for A0A221C8X5 (Dietzia sp. DQ12-45-1b)
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UniProt GroupA0A221C8X5
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Monovalent Na+/H+ antiporter subunit FD [auth F]85Dietzia sp. DQ12-45-1bMutation(s): 0 
Gene Names: amnhFGJR88_00768
Membrane Entity: Yes 
UniProt
Find proteins for A0A221C8X7 (Dietzia sp. DQ12-45-1b)
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UniProt GroupA0A221C8X7
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Monovalent Na+/H+ antiporter subunit GE [auth G]125Dietzia sp. DQ12-45-1bMutation(s): 0 
Gene Names: amnhGGJR88_00766
Membrane Entity: Yes 
UniProt
Find proteins for A0A221C8Y4 (Dietzia sp. DQ12-45-1b)
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UniProt GroupA0A221C8Y4
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cation antiporterF [auth E]121Dietzia sp. DQ12-45-1bMutation(s): 0 
Gene Names: amnhEGJR88_00770
Membrane Entity: Yes 
UniProt
Find proteins for A0A221C8X1 (Dietzia sp. DQ12-45-1b)
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UniProt GroupA0A221C8X1
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LMT
Query on LMT

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
CA [auth A]
DA [auth A]
EA [auth A]
AA [auth A],
BA [auth A],
CA [auth A],
DA [auth A],
EA [auth A],
FA [auth A],
G [auth D],
GA [auth C],
H [auth D],
HA [auth C],
I [auth D],
J [auth D],
K [auth D],
L [auth D],
M [auth D],
N [auth D],
O [auth D],
P [auth D],
Q [auth D],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China31971134
National Science Foundation (NSF, China)China31770120

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-09
    Type: Initial release
  • Version 1.1: 2020-12-23
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references