6SM3

Structure of the RagAB peptide importer in the 'closed-closed' state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



Literature

Structural and functional insights into oligopeptide acquisition by the RagAB transporter from Porphyromonas gingivalis.

Madej, M.White, J.B.R.Nowakowska, Z.Rawson, S.Scavenius, C.Enghild, J.J.Bereta, G.P.Pothula, K.Kleinekathoefer, U.Basle, A.Ranson, N.A.Potempa, J.van den Berg, B.

(2020) Nat Microbiol 

  • DOI: 10.1038/s41564-020-0716-y
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Porphyromonas gingivalis, an asaccharolytic member of the Bacteroidetes, is a keystone pathogen in human periodontitis that may also contribute to the development of other chronic inflammatory diseases. P. gingivalis utilizes protease-generated pepti ...

    Porphyromonas gingivalis, an asaccharolytic member of the Bacteroidetes, is a keystone pathogen in human periodontitis that may also contribute to the development of other chronic inflammatory diseases. P. gingivalis utilizes protease-generated peptides derived from extracellular proteins for growth, but how these peptides enter the cell is not clear. Here, we identify RagAB as the outer-membrane importer for these peptides. X-ray crystal structures show that the transporter forms a dimeric RagA 2 B 2 complex, with the RagB substrate-binding surface-anchored lipoprotein forming a closed lid on the RagA TonB-dependent transporter. Cryo-electron microscopy structures reveal the opening of the RagB lid and thus provide direct evidence for a 'pedal bin' mechanism of nutrient uptake. Together with mutagenesis, peptide-binding studies and RagAB peptidomics, our work identifies RagAB as a dynamic, selective outer-membrane oligopeptide-acquisition machine that is essential for the efficient utilization of proteinaceous nutrients by P. gingivalis.


    Organizational Affiliation

    Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK. bert.van-den-berg@ncl.ac.uk.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lipoprotein RagB
A
482Porphyromonas gingivalis W83Mutation(s): 0 
Gene Names: ragBPG_0186
Find proteins for F5H948 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
Go to UniProtKB:  F5H948

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RagA protein
B
903Porphyromonas gingivalis W83Mutation(s): 0 
Gene Names: ragAPG_0185
Find proteins for Q7MXJ7 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
Go to UniProtKB:  Q7MXJ7
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
GLY-GLY-ALA-THR-THR-ALA-THR-THR-THR-THR-SER-THR-SER
C
13Porphyromonas gingivalis W83Mutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5PL
Query on 5PL

Download CCD File 
A
(1R,4S,6R)-6-({[2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-GLUCOPYRANOSYL]OXY}METHYL)-4-HYDROXY-1-{[(15-METHYLHEXADECANOYL)OXY]METHYL}-4-OXIDO-7-OXO-3,5-DIOXA-8-AZA-4-PHOSPHAHEPTACOS-1-YL 15-METHYLHEXADECANOATE
C67 H129 N2 O15 P
LEQHPGOQHCQGAI-TYASGWLASA-N
 Ligand Interaction
PLM
Query on PLM

Download CCD File 
A
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom214222/Z/18/Z
Wellcome TrustUnited Kingdom215064/Z/18/Z
Polish National Science CentrePolandUMO-2015/19/N/NZ1/00322
Polish National Science CentrePolandUMO-2018/28/T/NZ1/00348 to MM
Polish National Science CentrePolandUMO-2016/23/N/NZ1/01513
Polish National Science CentrePolandUMO-2018/31/B/NZ1/03968
Polish National Science CentrePolandNIDCR/DE 022597

Revision History 

  • Version 1.0: 2020-05-20
    Type: Initial release