5M8J | pdb_00005m8j

Crystal structure of Eremococcus coleocola manganese transporter mutant H236A

• PDB DOI: https://doi.org/10.2210/pdb5M8J/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Eremococcus coleocola ACS-139-V-Col8
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2016-10-29 Released: 2017-01-11 
• Deposition Author(s): Manatschal, C., Ehrnstorfer, I.A., Arnold, F.M., Laederach, J., Dutzler, R.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 Å
• R-Value Free: 
  0.257 (Depositor), 0.334 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.266 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

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

• PubMed: 28059071 
• DOI: https://doi.org/10.1038/ncomms14033
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 56.56 kDa 
• Atom Count: 3,775 
• Modeled Residue Count: 494 
• Deposited Residue Count: 519 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Divalent metal cation transporter MntH	A	519	Eremococcus coleocola ACS-139-V-Col8	Mutation(s): 1  Gene Names: mntH, HMPREF9257_1603 Membrane Entity: Yes
UniProt
Find proteins for E4KPW4 (Eremococcus coleocola ACS-139-V-Col8) Explore E4KPW4  Go to UniProtKB:  E4KPW4

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 Å
• R-Value Free:  0.257 (Depositor), 0.334 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.266 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.4	α = 90
b = 81.79	β = 107.47
c = 96.44	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
PHENIX	refinement
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-01-11 
Deposition Author(s): Manatschal, C., Ehrnstorfer, I.A., Arnold, F.M., Laederach, J., Dutzler, R.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	--

Revision History  

• 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: 2024-01-17
  Changes: Data collection, Database references, Refinement description