4WGV

Crystal structure of Staphylococcus capitis divalent metal ion transporter (DMT) in complex with nanobody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.101 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.250 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of a SLC11 (NRAMP) transporter reveals the basis for transition-metal ion transport.

Ehrnstorfer, I.A.Geertsma, E.R.Pardon, E.Steyaert, J.Dutzler, R.

(2014) Nat.Struct.Mol.Biol. 21: 990-996

  • DOI: 10.1038/nsmb.2904
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Members of the SLC11 (NRAMP) family transport iron and other transition-metal ions across cellular membranes. These membrane proteins are present in all kingdoms of life with a high degree of sequence conservation. To gain insight into the determinan ...

    Members of the SLC11 (NRAMP) family transport iron and other transition-metal ions across cellular membranes. These membrane proteins are present in all kingdoms of life with a high degree of sequence conservation. To gain insight into the determinants of ion selectivity, we have determined the crystal structure of Staphylococcus capitis DMT (ScaDMT), a close prokaryotic homolog of the family. ScaDMT shows a familiar architecture that was previously identified in the amino acid permease LeuT. The protein adopts an inward-facing conformation with a substrate-binding site located in the center of the transporter. This site is composed of conserved residues, which coordinate Mn2+, Fe2+ and Cd2+ but not Ca2+. Mutations of interacting residues affect ion binding and transport in both ScaDMT and human DMT1. Our study thus reveals a conserved mechanism for transition-metal ion selectivity within the SLC11 family.


    Organizational Affiliation

    Department of Biochemistry, University of Zurich, Zurich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Divalent metal cation transporter MntH
A, C
415N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Camelid antibody fragment, nanobody
B, D
124N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.101 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.250 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 114.350α = 90.00
b = 114.350β = 90.00
c = 257.870γ = 120.00
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
SHARPphasing
SHELXDEphasing
SHELXDphasing
DMphasing
XSCALEdata scaling
XDSdata reduction
XSCALEdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerlandNCCR TransCure

Revision History 

  • Version 1.0: 2014-10-22
    Type: Initial release
  • Version 1.1: 2014-10-29
    Type: Database references
  • Version 1.2: 2014-11-19
    Type: Database references
  • Version 1.3: 2017-09-13
    Type: Author supporting evidence, Data collection, Derived calculations