3GYZ

Crystal structure of IpgC from Shigella flexneri

PDB DOI: https://doi.org/10.2210/pdb3GYZ/pdb

Classification: CHAPERONE
Organism(s): Shigella flexneri
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-04-06 Released: 2009-06-16
Deposition Author(s): Lunelli, M., Lokareddy, R.K., Zychlinsky, A., Kolbe, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.214
R-Value Work: 0.191
R-Value Observed: 0.192

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

IpaB-IpgC interaction defines binding motif for type III secretion translocator

Lunelli, M., Lokareddy, R.K., Zychlinsky, A., Kolbe, M.

(2009) Proc Natl Acad Sci U S A 106: 9661-9666

PubMed: 19478065 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1073/pnas.0812900106
Primary Citation of Related Structures:
3GYZ, 3GZ1

PubMed Abstract:
The delivery of virulence factors into host cells through type III secretion systems is essential for enterobacterial pathogenesis. Molecular chaperones bind specifically to virulence factors in the bacterial cytosol before secretion. Invasion plasmid gene C (IpgC) is a chaperone that binds 2 essential virulence factors of Shigella: invasion plasmid antigens (Ipa) B and C. Here, we report the crystal structure of IpgC alone and in complex with the chaperone binding domain (CBD) of IpaB. The chaperone captures the CBD in an extended conformation that is stabilized by conserved residues lining the cleft. Analysis of the cocrystal structure reveals a sequence motif that is functional in the IpaB translocator class from different bacteria as determined by isothermal titration calorimetry. Our results show how translocators are chaperoned and may allow the design of inhibitors of enterobacterial diseases.

Organizational Affiliation

Department of Cellular Microbiology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117 Berlin, Germany.

Macromolecule Content

Total Structure Weight: 35.28 kDa
Atom Count: 2,447
Modelled Residue Count: 286
Deposited Residue Count: 302
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chaperone protein ipgC	A, B	151	Shigella flexneri	Mutation(s): 1 Gene Names: ipgC
UniProt
Find proteins for P0A2U4 (Shigella flexneri) Explore P0A2U4 Go to UniProtKB: P0A2U4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A2U4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	D [auth A] E [auth A] F [auth A] H [auth B] I [auth B] D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]