9G2K | pdb_00009g2k

Cryo-EM structure of IrtAB in outward-occluded state in nanodisc in complex with ADP-vanadate


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9G2K

This is version 1.1 of the entry. See complete history

Literature

The mycobacterial ABC transporter IrtAB employs a membrane-facing crevice for siderophore-mediated iron uptake.

Gonda, I.Sorrentino, S.Galazzo, L.Lichti, N.P.Arnold, F.M.Mehdipour, A.R.Bordignon, E.Seeger, M.A.

(2025) Nat Commun 16: 1133-1133

  • DOI: https://doi.org/10.1038/s41467-024-55136-7
  • Primary Citation Related Structures: 
    9FW3, 9FXC, 9G2K, 9G2L, 9G2M, 9G2P, 9G2S, 9G2T, 9G2V, 9G2X, 9G2Y, 9G2Z, 9G36, 9G37, 9GL3

  • PubMed Abstract: 

    The mycobacterial ABC transporter IrtAB features an ABC exporter fold, yet it imports iron-charged siderophores called mycobactins. Here, we present extensive cryo-EM analyses and DEER measurements, revealing that IrtAB alternates between an inward-facing and an outward-occluded conformation, but does not sample an outward-facing conformation. When IrtAB is locked in its outward-occluded conformation in nanodiscs, mycobactin is bound in the middle of the lipid bilayer at a membrane-facing crevice opening at the heterodimeric interface. Mutations introduced at the crevice abrogate mycobactin import and in corresponding structures, the crevice is collapsed. A conserved triple histidine motif coordinating a zinc ion is present below the mycobactin binding site. Substitution of these histidine residues with alanine results in a decoupled transporter, which hydrolyzes ATP, but lost its capacity to import mycobactins. Our data suggest that IrtAB imports mycobactin via a credit-card mechanism in a transport cycle that is coupled to the presence of zinc.


  • Organizational Affiliation
    • Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 160.13 kDa 
  • Atom Count: 8,516 
  • Modeled Residue Count: 1,122 
  • Deposited Residue Count: 1,486 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Mycobactin import ATP-binding/permease protein IrtA900Mycolicibacterium thermoresistibile ATCC 19527Mutation(s): 0 
Gene Names: irtAKEK_01485
EC: 7.2.2
Membrane Entity: Yes 
UniProt
Find proteins for G7CBF5 (Mycolicibacterium thermoresistibile (strain ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316))
Explore G7CBF5 
Go to UniProtKB:  G7CBF5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG7CBF5
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Mycobactin import ATP-binding/permease protein IrtB586Mycolicibacterium thermoresistibile ATCC 19527Mutation(s): 0 
Gene Names: irtBKEK_01490
EC: 7.2.2
Membrane Entity: Yes 
UniProt
Find proteins for G7CBF6 (Mycolicibacterium thermoresistibile (strain ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316))
Explore G7CBF6 
Go to UniProtKB:  G7CBF6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG7CBF6
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARCv3.0
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
University of ZurichSwitzerlandFK-19-028
European Research Council (ERC)European Unionconsolidator grant 772190
Swiss National Science FoundationSwitzerlandPP00P3_144823
Swiss National Science FoundationSwitzerland310030_188817

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-18
    Type: Initial release
  • Version 1.1: 2025-02-12
    Changes: Data collection, Database references