Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - ABC Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer -A2B 

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

Biological Assembly Evidence: gel filtration, surface plasmon resonance

Macromolecule Content

• Total Structure Weight: 92990.35 
• Atom Count: 6139 
• Residue Count: 860 
• Unique protein chains: 3

6GV1

Crystal structure of E.coli Multidrug/H+ antiporter MdfA in outward open conformation with bound Fab fragment

• DOI: 10.2210/pdb6GV1/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli (strain K12)
• Expression System: Mus musculus, Escherichia coli


• Deposited: 2018-06-20 Released: 2018-10-03 
• Deposition Author(s): Nagarathinam, K., Parthier, C., Stubbs, M.T., Tanabe, M.
• Funding Organization(s): Other government; Japan Agency for Medical Research and Development (AMED) 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.4 Å
• R-Value Free: 0.283 
• R-Value Work: 0.258 

Literature

Outward open conformation of a Major Facilitator Superfamily multidrug/H+antiporter provides insights into switching mechanism.

Nagarathinam, K., Nakada-Nakura, Y., Parthier, C., Terada, T., Juge, N., Jaenecke, F., Liu, K., Hotta, Y., Miyaji, T., Omote, H., Iwata, S., Nomura, N., Stubbs, M.T., Tanabe, M.

(2018) Nat Commun 9: 4005-4005

• PubMed: 30275448 

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Major Facilitator Superfamily multidrug/H+ antiporter MdfA from E.coli	A	410	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: mdfA (cmlA, cmr)
Find proteins for P0AEY8 (Escherichia coli (strain K12)) Go to UniProtKB:  P0AEY8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Fab fragment YN1074 heavy chain	H	236	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Fab fragment YN1074 light chain	L	214	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.4 Å
• R-Value Free: 0.283 
• R-Value Work: 0.258 
• Space Group: P 6₁ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 73.258	α = 90.00
b = 73.258	β = 90.00
c = 927.920	γ = 120.00

Software Package:

Software Name	Purpose
XDS	data reduction
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-06-20 
• Released Date: 2018-10-03 
• Deposition Author(s): Nagarathinam, K., Parthier, C., Stubbs, M.T., Tanabe, M.

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Funding Organization	Location	Grant Number
Other government	Germany	BMBF 03Z2HN21
Japan Agency for Medical Research and Development (AMED)	Japan	JP18am0101071j0001

Revision History 

• Version 1.0: 2018-10-03
  Type: Initial release
• Version 1.1: 2018-10-10
  Type: Data collection, Database references, Structure summary