X-ray structure of the Deinococcus radiodurans Nramp/MntH divalent transition metal transporter WT in an occluded, manganese-bound state

Experimental Data Snapshot

  • Resolution: 2.38 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.213 

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Ligand Structure Quality Assessment 

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High-resolution structures with bound Mn 2+ and Cd 2+ map the metal import pathway in an Nramp transporter.

Ray, S.Berry, S.P.Wilson, E.A.Zhang, C.H.Shekhar, M.Singharoy, A.Gaudet, R.

(2023) Elife 12

  • DOI: https://doi.org/10.7554/eLife.84006
  • Primary Citation of Related Structures:  
    8E5S, 8E5V, 8E60, 8E6H, 8E6I, 8E6L, 8E6M, 8E6N

  • PubMed Abstract: 

    Transporters of the Nramp (Natural resistance-associated macrophage protein) family import divalent transition metal ions into cells of most organisms. By supporting metal homeostasis, Nramps prevent diseases and disorders related to metal insufficiency or overload. Previous studies revealed that Nramps take on a LeuT fold and identified the metal-binding site. We present high-resolution structures of Deinococcus radiodurans (Dra)Nramp in three stable conformations of the transport cycle revealing that global conformational changes are supported by distinct coordination geometries of its physiological substrate, Mn 2+ , across conformations, and by conserved networks of polar residues lining the inner and outer gates. In addition, a high-resolution Cd 2+ -bound structure highlights differences in how Cd 2+ and Mn 2+ are coordinated by DraNramp. Complementary metal binding studies using isothermal titration calorimetry with a series of mutated DraNramp proteins indicate that the thermodynamic landscape for binding and transporting physiological metals like Mn 2+ is different and more robust to perturbation than for transporting the toxic Cd 2+ metal. Overall, the affinity measurements and high-resolution structural information on metal substrate binding provide a foundation for understanding the substrate selectivity of essential metal ion transporters like Nramps.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Divalent metal cation transporter MntH414Deinococcus radioduransMutation(s): 0 
Gene Names: mntHDR_1709
Membrane Entity: Yes 
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
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on OLC

Download Ideal Coordinates CCD File 
AA [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
AA [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
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]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
Query on PEG

Download Ideal Coordinates CCD File 
BA [auth A],
CA [auth A],
DA [auth A]
C4 H10 O3
Query on GOL

Download Ideal Coordinates CCD File 
C3 H8 O3
Query on MN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
Query on CL

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.076α = 90
b = 71.101β = 90
c = 98.747γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
Cootmodel building

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 StatesGM120996

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-03
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description