Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 13.26 kDa 
• Atom Count: 926 
• Modelled Residue Count: 97 
• Deposited Residue Count: 111 
• Unique protein chains: 1

6AC5

Crystal structure of RIPK1 death domain GlcNAcylated by EPEC effector NleB

• DOI: 10.2210/pdb6AC5/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-07-25 Released: 2019-05-01 
• Deposition Author(s): Ding, J., Shao, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.189 
• R-Value Work: 0.156 
• R-Value Observed: 0.157 

Literature

Structural and Functional Insights into Host Death Domains Inactivation by the Bacterial Arginine GlcNAcyltransferase Effector.

Ding, J., Pan, X., Du, L., Yao, Q., Xue, J., Yao, H., Wang, D.C., Li, S., Shao, F.

(2019) Mol Cell 74: 922

• PubMed: 30979585 
• DOI: 10.1016/j.molcel.2019.03.028
• Primary Citation of Related Structures:  
  6E66, 6AC0, 6AC5, 6ACI


• PubMed Abstract: 
  

Enteropathogenic E. coli NleB and related type III effectors catalyze arginine GlcNAcylation of death domain (DD) proteins to block host defense, but the underlying mechanism is unknown. Here we solve crystal structures of NleB alone and in complex with FADD-DD, UDP, and Mn ²⁺ as well as NleB-GlcNAcylated DDs of TRADD and RIPK1. NleB adopts a GT-A fold with a unique helix-pair insertion to hold FADD-DD; the interface contacts explain the selectivity of NleB for certain DDs. The acceptor arginine is fixed into a cleft, in which Glu253 serves as a base to activate the guanidinium. Analyses of the enzyme-substrate complex and the product structures reveal an inverting sugar-transfer reaction and a detailed catalytic mechanism. These structural insights are validated by mutagenesis analyses of NleB-mediated GlcNAcylation in vitro and its function in mouse infection. Our study builds a structural framework for understanding of NleB-catalyzed arginine GlcNAcylation of host death domain.

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Organizational Affiliation: 

National Institute of Biological Sciences, Beijing 102206, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor-interacting serine/threonine-protein kinase 1	A	111	Homo sapiens	Mutation(s): 0  Gene Names: RIPK1, RIP, RIP1 EC: 2.7.11.1
Find proteins for Q13546 (Homo sapiens) Explore Q13546  Go to UniProtKB:  Q13546
NIH Common Fund Data Resources
PHAROS:  Q13546 GTEx:  ENSG00000137275

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.189 
• R-Value Work: 0.156 
• R-Value Observed: 0.157 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.75	α = 90
b = 55.75	β = 90
c = 59.15	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-07-25 
• Released Date: 2019-05-01 
Deposition Author(s): Ding, J., Shao, F.

Revision History  

• Version 1.0: 2019-05-01
  Type: Initial release
  
• Version 1.1: 2019-06-26
  Changes: Data collection, Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary