5ZCK

Structure of the RIP3 core region

  • Classification: PROTEIN FIBRIL
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2018-02-18 Released: 2018-04-18 
  • Deposition Author(s): Li, J., Wu, H.
  • Funding Organization(s): Natural Science Foundation of China

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.139 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Structure of the Necrosome RIPK1-RIPK3 Core, a Human Hetero-Amyloid Signaling Complex.

Mompean, M.Li, W.Li, J.Laage, S.Siemer, A.B.Bozkurt, G.Wu, H.McDermott, A.E.

(2018) Cell 173: 1244-1253.e10

  • DOI: 10.1016/j.cell.2018.03.032
  • Primary Citation of Related Structures:  
    5ZCK, 5V7Z

  • PubMed Abstract: 
  • The RIPK1-RIPK3 necrosome is an amyloid signaling complex that initiates TNF-induced necroptosis, serving in human immune defense, cancer, and neurodegenerative diseases. RIPK1 and RIPK3 associate through their RIP homotypic interaction motifs with consensus sequences IQIG (RIPK1) and VQVG (RIPK3) ...

    The RIPK1-RIPK3 necrosome is an amyloid signaling complex that initiates TNF-induced necroptosis, serving in human immune defense, cancer, and neurodegenerative diseases. RIPK1 and RIPK3 associate through their RIP homotypic interaction motifs with consensus sequences IQIG (RIPK1) and VQVG (RIPK3). Using solid-state nuclear magnetic resonance, we determined the high-resolution structure of the RIPK1-RIPK3 core. RIPK1 and RIPK3 alternately stack (RIPK1, RIPK3, RIPK1, RIPK3, etc.) to form heterotypic β sheets. Two such β sheets bind together along a compact hydrophobic interface featuring an unusual ladder of alternating Ser (from RIPK1) and Cys (from RIPK3). The crystal structure of a four-residue RIPK3 consensus sequence is consistent with the architecture determined by NMR. The RIPK1-RIPK3 core is the first detailed structure of a hetero-amyloid and provides a potential explanation for the specificity of hetero- over homo-amyloid formation and a structural basis for understanding the mechanisms of signal transduction.


    Organizational Affiliation

    Department of Chemistry, Columbia University, New York, NY 10027, USA. Electronic address: aem5@columbia.edu.



Macromolecules
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
peptide from Receptor-interacting serine/threonine-protein kinase 3A4Homo sapiensMutation(s): 0 
Gene Names: RIPK3RIP3
EC: 2.7.11.1
Find proteins for Q9Y572 (Homo sapiens)
Explore Q9Y572 
Go to UniProtKB:  Q9Y572
NIH Common Fund Data Resources
PHAROS:  Q9Y572
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download Ideal Coordinates CCD File 
B [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.139 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 4.813α = 90
b = 17.151β = 90
c = 29.564γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-02-18 
  • Released Date: 2018-04-18 
  • Deposition Author(s): Li, J., Wu, H.

Funding OrganizationLocationGrant Number
Natural Science Foundation of ChinaChina31470724

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-18
    Type: Initial release
  • Version 1.1: 2018-05-23
    Changes: Data collection, Database references
  • Version 1.2: 2018-05-30
    Changes: Data collection, Database references