6SML

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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 5: 1016-1025

  • DOI: https://doi.org/10.1038/s41564-020-0716-y
  • Primary Citation of Related Structures:  
    6SLI, 6SLJ, 6SLN, 6SM3, 6SML, 6SMQ

  • 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 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

    Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lipoprotein RagB482Porphyromonas gingivalis W83Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for F5H948 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
Explore F5H948 
Go to UniProtKB:  F5H948
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF5H948
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RagA protein915Porphyromonas gingivalis W83Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q7MXJ7 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
Explore Q7MXJ7 
Go to UniProtKB:  Q7MXJ7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7MXJ7
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
GLY-THR-GLY-GLY-SER-THR-GLY-THR-THR-SER-ALA-GLY12Porphyromonas gingivalis W83Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5PL
Query on 5PL

Download Ideal Coordinates CCD File 
D [auth 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
PLM
Query on PLM

Download Ideal Coordinates CCD File 
E [auth A]PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0

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  (Full details and data files)

  • Version 1.0: 2020-05-20
    Type: Initial release
  • Version 1.1: 2020-08-05
    Changes: Database references, Derived calculations