2GFP | pdb_00002gfp

Structure of the Multidrug Transporter EmrD from Escherichia coli

PDB DOI: https://doi.org/10.2210/pdb2GFP/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPM PDBTM mpstruc

Deposited: 2006-03-22 Released: 2006-05-16
Deposition Author(s): Yin, Y., He, X., Szewczyk, P., Nguyen, T., Chang, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free:
0.350 (Depositor), 0.287 (DCC)
R-Value Work:
0.270 (Depositor), 0.229 (DCC)
R-Value Observed:
0.280 (Depositor)

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This is version 1.3 of the entry. See complete history.

Literature

Structure of the multidrug transporter EmrD from Escherichia coli

Yin, Y., He, X., Szewczyk, P., Nguyen, T., Chang, G.

(2006) Science 312: 741-744

PubMed: 16675700 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.1125629
Primary Citation Related Structures:
2GFP

PubMed Abstract:
EmrD is a multidrug transporter from the Major Facilitator Superfamily that expels amphipathic compounds across the inner membrane of Escherichia coli. Here, we report the x-ray structure of EmrD determined to a resolution of 3.5 angstroms. The structure reveals an interior that is composed mostly of hydrophobic residues, which is consistent with its role transporting amphipathic molecules. Two long loops extend into the inner leaflet side of the cell membrane. This region can serve to recognize and bind substrate directly from the lipid bilayer. We propose that multisubstrate specificity, binding, and transport are facilitated by these loop regions and the internal cavity.

Organizational Affiliation

Scripps Research Institute, Department of Molecular Biology, 10550 North Torrey Pines Road, CB-105, La Jolla, CA 92037, USA.

Macromolecule Content

Total Structure Weight: 80.03 kDa
Atom Count: 5,600
Modeled Residue Count: 750
Deposited Residue Count: 750
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multidrug resistance protein D	A, B	375	Escherichia coli	Mutation(s): 0 Gene Names: emrD Membrane Entity: Yes
UniProt
Find proteins for P31442 (Escherichia coli (strain K12)) Explore P31442 Go to UniProtKB: P31442
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31442
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.350 (Depositor), 0.287 (DCC)
R-Value Work: 0.270 (Depositor), 0.229 (DCC)
R-Value Observed: 0.280 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.5	α = 90
b = 124.5	β = 110.2
c = 109.4	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
HKL-2000	data reduction
PHASES	phasing
X-PLOR	refinement
HKL-2000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-05-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-05-16
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-02-14
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.