8J5S

Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the pre-catalytic intermediate state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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

An oligopeptide permease, OppABCD, requires an iron-sulfur cluster domain for functionality.

Yang, X.Hu, T.Liang, J.Xiong, Z.Lin, Z.Zhao, Y.Zhou, X.Gao, Y.Sun, S.Yang, X.Guddat, L.W.Yang, H.Rao, Z.Zhang, B.

(2024) Nat Struct Mol Biol 

  • DOI: https://doi.org/10.1038/s41594-024-01256-z
  • Primary Citation of Related Structures:  
    8J5Q, 8J5R, 8J5S, 8J5T, 8J5U

  • PubMed Abstract: 

    Oligopeptide permease, OppABCD, belongs to the type I ABC transporter family. Its role is to import oligopeptides into bacteria for nutrient uptake and to modulate the host immune response. OppABCD consists of a cluster C substrate-binding protein (SBP), OppA, membrane-spanning OppB and OppC subunits, and an ATPase, OppD, that contains two nucleotide-binding domains (NBDs). Here, using cryo-electron microscopy, we determined the high-resolution structures of Mycobacterium tuberculosis OppABCD in the resting state, oligopeptide-bound pre-translocation state, AMPPNP-bound pre-catalytic intermediate state and ATP-bound catalytic intermediate state. The structures show an assembly of a cluster C SBP with its ABC translocator and a functionally required [4Fe-4S] cluster-binding domain in OppD. Moreover, the ATP-bound OppABCD structure has an outward-occluded conformation, although no substrate was observed in the transmembrane cavity. Here, we reveal an oligopeptide recognition and translocation mechanism of OppABCD, which provides a perspective on how this and other type I ABC importers facilitate bulk substrate transfer across the lipid bilayer.


  • Organizational Affiliation

    Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China. yangxl@shanghaitech.edu.cn.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein Rv1280c599Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: Rv1280cMTCY50.02
UniProt
Find proteins for P9WGU5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WGU5 
Go to UniProtKB:  P9WGU5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WGU5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Putative peptide transport permease protein Rv1283c325Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: Rv1283cMTCY373.02c
UniProt
Find proteins for P9WFZ7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WFZ7 
Go to UniProtKB:  P9WFZ7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WFZ7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Putative peptide transport permease protein Rv1282c291Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: Rv1282cMTCY373.01cMTCY3H3.01
UniProt
Find proteins for P9WFZ9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WFZ9 
Go to UniProtKB:  P9WFZ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WFZ9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized ABC transporter ATP-binding protein Rv1281c612Mycobacterium tuberculosis H37RvMutation(s): 2 
Gene Names: Rv1281cMTCY50.01
UniProt
Find proteins for P9WQJ5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WQJ5 
Go to UniProtKB:  P9WQJ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WQJ5
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Endogenous oligopeptide8Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32200996
National Natural Science Foundation of China (NSFC)China32171217

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-03
    Type: Initial release
  • Version 1.1: 2024-04-10
    Changes: Database references