6BL6 | pdb_00006bl6

Crystallization of lipid A transporter MsbA from Salmonella typhimurium

• PDB DOI: https://doi.org/10.2210/pdb6BL6/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2017-11-09 Released: 2019-01-09 
• Deposition Author(s): Padayatti, P.S., Stanfield, R.L., Zhang, Q., Wilson, I.A., Lee, S.C.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.301 (Depositor), 0.304 (DCC) 
• R-Value Work: 
  0.270 (Depositor), 0.277 (DCC) 
• R-Value Observed: 
  0.271 (Depositor) 

Starting Model: experimental

Literature

Structural Insights into the Lipid A Transport Pathway in MsbA.

Padayatti, P.S., Lee, S.C., Stanfield, R.L., Wen, P.C., Tajkhorshid, E., Wilson, I.A., Zhang, Q.

(2019) Structure 27: 1114

• PubMed: 31130486 
• DOI: https://doi.org/10.1016/j.str.2019.04.007
• Primary Citation Related Structures: 
  6BL6, 6O30


• PubMed Abstract: 
  

  MsbA is an essential ATP-binding cassette transporter in Gram-negative bacteria that transports lipid A and lipopolysaccharide from the cytoplasmic leaflet to the periplasmic leaflet of the inner membrane. Here we report the X-ray structure of MsbA from Salmonella typhimurium at 2.8-Å resolution in an inward-facing conformation after cocrystallization with lipid A and using a stabilizing facial amphiphile. The structure displays a large amplitude opening in the transmembrane portal, which is likely required for lipid A to pass from its site of synthesis into the protein-enclosed transport pathway. Putative lipid A density is observed further inside the transmembrane cavity, consistent with a trap and flip model. Additional electron density attributed to lipid A is observed near an outer surface cleft at the periplasmic ends of the transmembrane helices. These findings provide new structural insights into the lipid A transport pathway through comparative analysis with existing MsbA structures.

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Organizational Affiliation: 
• Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 127.22 kDa 
• Atom Count: 8,894 
• Modeled Residue Count: 1,150 
• Deposited Residue Count: 1,152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipid A export ATP-binding/permease protein MsbA	A, B	576	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 1  Gene Names: msbA, STM0984 EC: 3.6.3 (PDB Primary Data), 7.5.2.6 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P63359 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P63359  Go to UniProtKB:  P63359

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.301 (Depositor), 0.304 (DCC) 
• R-Value Work:  0.270 (Depositor), 0.277 (DCC) 
• R-Value Observed: 0.271 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.052	α = 90
b = 154.819	β = 90
c = 228.886	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-01-09 
Deposition Author(s): Padayatti, P.S., Stanfield, R.L., Zhang, Q., Wilson, I.A., Lee, S.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM118594
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM098538

Revision History  

• Version 1.0: 2019-01-09
  Type: Initial release
  
• Version 1.1: 2019-01-16
  Changes: Author supporting evidence, Data collection, Structure summary
• Version 1.2: 2019-06-12
  Changes: Data collection, Database references, Structure summary
• Version 1.3: 2019-07-17
  Changes: Data collection, Database references
• Version 1.4: 2020-01-01
  Changes: Author supporting evidence
• Version 1.5: 2023-10-04
  Changes: Data collection, Database references, Refinement description