9G2K

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

• PDB DOI: https://doi.org/10.2210/pdb9G2K/pdb
• EM Map EMD-50977: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Mycolicibacterium thermoresistibile ATCC 19527
• Expression System: Escherichia coli MC1061
• Mutation(s): No 


• Deposited: 2024-07-11 Released: 2024-12-18 
• Deposition Author(s): Gonda, I., Seeger, M.A.
• Funding Organization(s): University of Zurich, European Research Council (ERC), Swiss National Science Foundation

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Experimental Data Snapshot

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

Starting Model: experimental

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.

(2024) Nature 

• DOI: https://doi.org/10.1038/s41467-024-55136-7

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy, gel filtration

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mycobactin import ATP-binding/permease protein IrtA	A	900	Mycolicibacterium thermoresistibile ATCC 19527	Mutation(s): 0  Gene Names: irtA, KEK_01485 EC: 7.2.2
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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mycobactin import ATP-binding/permease protein IrtB	B	586	Mycolicibacterium thermoresistibile ATCC 19527	Mutation(s): 0  Gene Names: irtB, KEK_01490 EC: 7.2.2
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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AOV (Subject of Investigation/LOI)	C [auth A], F [auth B]	ADP ORTHOVANADATE C10 H17 N5 O14 P2 V SWCHWRVRYDCWAN-AZGWGOJFSA-J
ZN (Subject of Investigation/LOI)	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	v3.0
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-18 
Deposition Author(s): Gonda, I., Seeger, M.A.

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Funding Organization	Location	Grant Number
University of Zurich	Switzerland	FK-19-028
European Research Council (ERC)	European Union	consolidator grant 772190
Swiss National Science Foundation	Switzerland	PP00P3_144823
Swiss National Science Foundation	Switzerland	310030_188817

Revision History  

• Version 1.0: 2024-12-18
  Type: Initial release