7WIX

Cryo-EM structure of Mycobacterium tuberculosis irtAB in complex with ADP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.53 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

Cryo-EM structures for the Mycobacterium tuberculosis iron-loaded siderophore transporter IrtAB.

Sun, S.Gao, Y.Yang, X.Yang, X.Hu, T.Liang, J.Xiong, Z.Ran, Y.Ren, P.Bai, F.Guddat, L.W.Yang, H.Rao, Z.Zhang, B.

(2023) Protein Cell 14: 448-458

  • DOI: https://doi.org/10.1093/procel/pwac060
  • Primary Citation of Related Structures:  
    7WIU, 7WIV, 7WIW, 7WIX

  • PubMed Abstract: 

    The adenosine 5'-triphosphate (ATP)-binding cassette (ABC) transporter, IrtAB, plays a vital role in the replication and viability of Mycobacterium tuberculosis (Mtb), where its function is to import iron-loaded siderophores. Unusually, it adopts the canonical type IV exporter fold. Herein, we report the structure of unliganded Mtb IrtAB and its structure in complex with ATP, ADP, or ATP analogue (AMP-PNP) at resolutions ranging from 2.8 to 3.5 Å. The structure of IrtAB bound ATP-Mg2+ shows a "head-to-tail" dimer of nucleotide-binding domains (NBDs), a closed amphipathic cavity within the transmembrane domains (TMDs), and a metal ion liganded to three histidine residues of IrtA in the cavity. Cryo-electron microscopy (Cryo-EM) structures and ATP hydrolysis assays show that the NBD of IrtA has a higher affinity for nucleotides and increased ATPase activity compared with IrtB. Moreover, the metal ion located in the TM region of IrtA is critical for the stabilization of the conformation of IrtAB during the transport cycle. This study provides a structural basis to explain the ATP-driven conformational changes that occur in IrtAB.


  • Organizational Affiliation

    Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mycobactin import ATP-binding/permease protein IrtA859Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: irtARv1348MTCY02B10.12
EC: 7.2.2
Membrane Entity: Yes 
UniProt
Find proteins for P9WQJ9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WQJ9 
Go to UniProtKB:  P9WQJ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WQJ9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mycobactin import ATP-binding/permease protein IrtB579Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: irtBRv1349MTCY02B10.13
EC: 7.2.2
Membrane Entity: Yes 
UniProt
Find proteins for P9WQJ7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WQJ7 
Go to UniProtKB:  P9WQJ7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WQJ7
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.53 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)China81520108019
National Natural Science Foundation of China (NSFC)China81772204
National Natural Science Foundation of China (NSFC)China32171217
Ministry of Science and Technology (MoST, China)China2017YFC0840300

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-25
    Type: Initial release
  • Version 1.1: 2024-04-10
    Changes: Data collection, Database references