5B0T

Structure of Shigella effector LRR domain

PDB DOI: https://doi.org/10.2210/pdb5B0T/pdb

Classification: LIGASE
Organism(s): Shigella flexneri
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-11-04 Released: 2016-04-06
Deposition Author(s): Takagi, K., Sasakawa, C., Kim, M., Mizushima, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.265
R-Value Work: 0.211
R-Value Observed: 0.214

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the substrate-recognition domain of the Shigella E3 ligase IpaH9.8

Takagi, K., Kim, M., Sasakawa, C., Mizushima, T.

(2016) Acta Crystallogr F Struct Biol Commun 72: 269-275

PubMed: 27050259 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S2053230X16002715
Primary Citation of Related Structures:
5B0N, 5B0T

PubMed Abstract:
Infectious diseases caused by bacteria have significant impacts on global public health. During infection, pathogenic bacteria deliver a variety of virulence factors, called effectors, into host cells. The Shigella effector IpaH9.8 functions as an ubiquitin ligase, ubiquitinating the NF-κB essential modulator (NEMO)/IKK-γ to inhibit host inflammatory responses. IpaH9.8 contains leucine-rich repeats (LRRs) involved in substrate recognition and an E3 ligase domain. To elucidate the structural basis of the function of IpaH9.8, the crystal structure of the LRR domain of Shigella IpaH9.8 was determined and this structure was compared with the known structures of other IpaH family members. This model provides insights into the structural features involved in substrate specificity.

Organizational Affiliation

Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan.

Macromolecule Content

Total Structure Weight: 25.38 kDa
Atom Count: 1,831
Modelled Residue Count: 220
Deposited Residue Count: 224
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase ipaH9.8	A	224	Shigella flexneri	Mutation(s): 0 Gene Names: ipaH9.8, CP0226, pWR501_0234, SFLP090 EC: 6.3.2
UniProt
Find proteins for Q8VSC3 (Shigella flexneri) Explore Q8VSC3 Go to UniProtKB: Q8VSC3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8VSC3
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.265
R-Value Work: 0.211
R-Value Observed: 0.214
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.271	α = 90
b = 105.011	β = 90
c = 61.596	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2016-04-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-04-06
Type: Initial release
Version 1.1: 2016-04-20
Changes: Database references
Version 1.2: 2020-02-26
Changes: Data collection, Derived calculations
Version 1.3: 2024-03-20
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.