5M87 | pdb_00005m87

Crystal structure of Eremococcus coleocola manganese transporter


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.277 (Depositor), 0.320 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 
    0.234 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.3 of the entry. See complete history


Literature

Structural and mechanistic basis of proton-coupled metal ion transport in the SLC11/NRAMP family.

Ehrnstorfer, I.A.Manatschal, C.Arnold, F.M.Laederach, J.Dutzler, R.

(2017) Nat Commun 8: 14033-14033

  • DOI: https://doi.org/10.1038/ncomms14033
  • Primary Citation of Related Structures:  
    5M87, 5M8A, 5M8J, 5M8K

  • PubMed Abstract: 

    Secondary active transporters of the SLC11/NRAMP family catalyse the uptake of iron and manganese into cells. These proteins are highly conserved across all kingdoms of life and thus likely share a common transport mechanism. Here we describe the structural and functional properties of the prokaryotic SLC11 transporter EcoDMT. Its crystal structure reveals a previously unknown outward-facing state of the protein family. In proteoliposomes EcoDMT mediates proton-coupled uptake of manganese at low micromolar concentrations. Mutants of residues in the transition-metal ion-binding site severely affect transport, whereas a mutation of a conserved histidine located near this site results in metal ion transport that appears uncoupled to proton transport. Combined with previous results, our study defines the conformational changes underlying transition-metal ion transport in the SLC11 family and it provides molecular insight to its coupling to protons.


  • Organizational Affiliation

    Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Divalent metal cation transporter MntH519Eremococcus coleocola ACS-139-V-Col8Mutation(s): 0 
Gene Names: mntHHMPREF9257_1603
Membrane Entity: Yes 
UniProt
Find proteins for E4KPW4 (Eremococcus coleocola ACS-139-V-Col8)
Explore E4KPW4 
Go to UniProtKB:  E4KPW4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE4KPW4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DMU
Query on DMU

Download Ideal Coordinates CCD File 
B [auth A]DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free:  0.277 (Depositor), 0.320 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 0.234 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.2α = 90
b = 81.65β = 107.57
c = 96.23γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
SHELXCDphasing
SHARPphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted DMUClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-01-18
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references