6BU5

Crystal structure of the Deinococcus radiodurans Nramp/MntH divalent transition metal transporter in the outward-open, manganese-bound conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

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This is version 1.2 of the entry. See complete history


Literature

Structures in multiple conformations reveal distinct transition metal and proton pathways in an Nramp transporter.

Bozzi, A.T.Zimanyi, C.M.Nicoludis, J.M.Lee, B.K.Zhang, C.H.Gaudet, R.

(2019) Elife 8

  • DOI: 10.7554/eLife.41124
  • Primary Citation of Related Structures:  
    6BU5, 6C3I, 6D91, 6D9W

  • PubMed Abstract: 
  • Nramp family transporters-expressed in organisms from bacteria to humans-enable uptake of essential divalent transition metals via an alternating-access mechanism that also involves proton transport. We present high-resolution structures of Deinococcus radiodurans (Dra)Nramp in multiple conformations to provide a thorough description of the Nramp transport cycle by identifying the key intramolecular rearrangements and changes to the metal coordination sphere ...

    Nramp family transporters-expressed in organisms from bacteria to humans-enable uptake of essential divalent transition metals via an alternating-access mechanism that also involves proton transport. We present high-resolution structures of Deinococcus radiodurans (Dra)Nramp in multiple conformations to provide a thorough description of the Nramp transport cycle by identifying the key intramolecular rearrangements and changes to the metal coordination sphere. Strikingly, while metal transport requires cycling from outward- to inward-open states, efficient proton transport still occurs in outward-locked (but not inward-locked) DraNramp. We propose a model in which metal and proton enter the transporter via the same external pathway to the binding site, but follow separate routes to the cytoplasm, which could facilitate the co-transport of two cationic species. Our results illustrate the flexibility of the LeuT fold to support a broad range of substrate transport and conformational change mechanisms.


    Organizational Affiliation

    Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Divalent metal cation transporter MntHA412Deinococcus radiodurans R1Mutation(s): 1 
Gene Names: mntHDR_1709
Membrane Entity: Yes 
UniProt
Find proteins for Q9RTP8 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
Explore Q9RTP8 
Go to UniProtKB:  Q9RTP8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RTP8
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 
  • Space Group: C 1 2 1
  • Diffraction Data DOI: 10.15785/SBGRID/564 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.758α = 90
b = 80.389β = 94.72
c = 51.754γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM120996-01A1

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-12
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence