6D9W

Crystal structure of Deinococcus radiodurans MntH, an Nramp-family transition metal transporter, in the inward-open apo state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.94 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.275 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 5KTE


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: https://doi.org/10.7554/eLife.41124
  • Primary Citation of Related Structures:  
    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. 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
MoleculeChains Sequence LengthOrganismDetailsImage
Divalent metal cation transporter MntH420Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 7 
Gene Names: mntHDR_1709
Membrane Entity: Yes 
UniProt
Find proteins for Q9RTP8 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
Explore Q9RTP8 
Go to UniProtKB:  Q9RTP8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RTP8
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab Heavy ChainB [auth H]213Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab Light ChainC [auth L]213Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.94 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.275 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.131α = 90
b = 132.077β = 90
c = 220.995γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States9P41GM104601
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM120996
National Science Foundation (NSF, United States)United StatesNSF-MCA93S028

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-13
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence