6XBD

Cryo-EM structure of MlaFEDB in nanodiscs with phospholipid substrates


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of bacterial phospholipid transporter MlaFEDB with substrate bound.

Coudray, N.Isom, G.L.MacRae, M.R.Saiduddin, M.N.Bhabha, G.Ekiert, D.C.

(2020) Elife 9

  • DOI: 10.7554/eLife.62518
  • Primary Citation of Related Structures:  
    6XBD

  • PubMed Abstract: 
  • In double-membraned bacteria, phospholipid transport across the cell envelope is critical to maintain the outer membrane barrier, which plays a key role in virulence and antibiotic resistance. An MCE transport system called Mla has been implicated in pho ...

    In double-membraned bacteria, phospholipid transport across the cell envelope is critical to maintain the outer membrane barrier, which plays a key role in virulence and antibiotic resistance. An MCE transport system called Mla has been implicated in phospholipid trafficking and outer membrane integrity, and includes an ABC transporter, MlaFEDB. The transmembrane subunit, MlaE, has minimal sequence similarity to other transporters, and the structure of the entire inner-membrane MlaFEDB complex remains unknown. Here, we report the cryo-EM structure of MlaFEDB at 3.05 Å resolution, revealing distant relationships to the LPS and MacAB transporters, as well as the eukaryotic ABCA/ABCG families. A continuous transport pathway extends from the MlaE substrate-binding site, through the channel of MlaD, and into the periplasm. Unexpectedly, two phospholipids are bound to MlaFEDB, suggesting that multiple lipid substrates may be transported each cycle. Our structure provides mechanistic insight into substrate recognition and transport by MlaFEDB.


    Organizational Affiliation

    Department of Microbiology, New York University School of Medicine, New York, United States.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phospholipid ABC transporter-binding protein MlaD ABCDEF201Escherichia coli DEC6AMutation(s): 0 
Gene Names: mlaDECDEC6A_3942
Find proteins for H4UPP8 (Escherichia coli DEC6A)
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Go to UniProtKB:  H4UPP8
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Phospholipid ABC transporter permease protein MlaE GH260Escherichia coli DEC6AMutation(s): 0 
Gene Names: mlaEECDEC6A_3943
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Mammalian Cell Entry (MCE) Proteins
Protein: 
MlaFEDB in nanodiscs with phospholipid substrates
Find proteins for H4UPP9 (Escherichia coli DEC6A)
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Go to UniProtKB:  H4UPP9
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Phospholipid transport system ATP-binding protein MlaF IJ269Escherichia coli DEC6AMutation(s): 0 
Gene Names: mlaFECDEC6A_3944
EC: 3.6.3
Find proteins for H4UPQ0 (Escherichia coli DEC6A)
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Go to UniProtKB:  H4UPQ0
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Phospholipid ABC transporter-binding protein MlaB KL97Escherichia coli K-12Mutation(s): 0 
Gene Names: mlaBECDEC6A_3940
Find proteins for H4UPP6 (Escherichia coli DEC6A)
Explore H4UPP6 
Go to UniProtKB:  H4UPP6
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
MSP1D1 MN164Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEF
Query on PEF

Download Ideal Coordinates CCD File 
G
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
C37 H74 N O8 P
SLKDGVPOSSLUAI-PGUFJCEWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR00GM112982
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM128777
Other privateUnited StatesPEW-00033055
American Heart AssociationUnited States20POST35210202
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32 GM088118
Other privateUnited StatesDFS 20 16
Other privateUnited StatesSF349247
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM103310
Other privateUnited StatesF00316
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesOD019994
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesU24GM129547
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesGM103311

Revision History 

  • Version 1.0: 2020-07-01
    Type: Initial release
  • Version 1.1: 2020-11-25
    Changes: Experimental preparation, Source and taxonomy, Structure summary
  • Version 1.2: 2021-01-13
    Changes: Database references