3HYT

Structural Basis of GDP Release and Gating in G Protein Coupled Fe2+ Transport

• PDB DOI: https://doi.org/10.2210/pdb3HYT/pdb

• Classification: METAL TRANSPORT
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-06-23 Released: 2009-08-25 
• Deposition Author(s): Maher, M.J., Jormakka, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.74 Å
• R-Value Free: 0.294 
• R-Value Work: 0.227 
• R-Value Observed: 0.230 

Literature

Structural basis of GDP release and gating in G protein coupled Fe(2+) transport.

Guilfoyle, A., Maher, M.J., Rapp, M., Clarke, R., Harrop, S., Jormakka, M.

(2009) EMBO J 

• PubMed: 19629046 
• DOI: https://doi.org/10.1038/emboj.2009.208
• Primary Citation of Related Structures:  
  3HYR, 3HYT


• PubMed Abstract: 
  

  G proteins are key molecular switches in the regulation of membrane protein function and signal transduction. The prokaryotic membrane protein FeoB is involved in G protein coupled Fe(2+) transport, and is unique in that the G protein is directly tethered to the membrane domain. Here, we report the structure of the soluble domain of FeoB, including the G protein domain, and its assembly into an unexpected trimer. Comparisons between nucleotide free and liganded structures reveal the closed and open state of a central cytoplasmic pore, respectively. In addition, these data provide the first observation of a conformational switch in the nucleotide-binding G5 motif, defining the structural basis for GDP release. From these results, structural parallels are drawn to eukaryotic G protein coupled membrane processes.

---

Organizational Affiliation: 

Centenary Institute, Sydney, New South Wales, Australia.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 91.17 kDa 
• Atom Count: 5,722 
• Modelled Residue Count: 730 
• Deposited Residue Count: 810 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferrous iron transport protein B	A, B, C	270	Escherichia coli	Mutation(s): 0  Gene Names: feoB, b3409, JW3372
UniProt
Find proteins for P33650 (Escherichia coli (strain K12)) Explore P33650  Go to UniProtKB:  P33650

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AGO	D [auth A], F [auth B], H [auth C]	2-amino-9-(5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]-3-O-{[2-(methylamino)phenyl]carbonyl}-beta-D-erythro-pentofuranosyl-2-ulose)-1,9-dihydro-6H-purin-6-one C18 H22 N7 O14 P3 RVBPPAHXMWBKDD-CKUKBARFSA-N
MG	E [auth A], G [auth B], I [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.74 Å
• R-Value Free: 0.294 
• R-Value Work: 0.227 
• R-Value Observed: 0.230 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76	α = 90
b = 46.41	β = 94.95
c = 120.07	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-25 
Deposition Author(s): Maher, M.J., Jormakka, M.

Revision History  

• Version 1.0: 2009-08-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations