Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 12-mer - A8B4 Local Symmetry: Helical - H  (3D View)
Local Stoichiometry: Homo 4-mer - B4 

Local Symmetry: Helical - H  (3D View)
Local Stoichiometry: Homo 4-mer - B4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 163.92 kDa 
• Atom Count: 10,926 
• Modelled Residue Count: 1,369 
• Deposited Residue Count: 1,440 
• Unique protein chains: 2

 7DNJ

K63-polyUb MDA5CARDs complex

• PDB DOI: 10.2210/pdb7DNJ/pdb
• EM Map EMD-30785: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-12-09 Released: 2021-10-13 
• Deposition Author(s): Song, B., Chen, Y., Luo, D.H., Zheng, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Ordered assembly of the cytosolic RNA-sensing MDA5-MAVS signaling complex via binding to unanchored K63-linked poly-ubiquitin chains.

Song, B., Chen, Y., Liu, X., Yuan, F., Tan, E.Y.J., Lei, Y., Song, N., Han, Y., Pascal, B.D., Griffin, P.R., Luo, C., Wu, B., Luo, D., Zheng, J.

(2021) Immunity 54: 2218

• PubMed: 34644557 
• DOI: 10.1016/j.immuni.2021.09.008
• Primary Citation of Related Structures:  
  7DNI, 7DNJ


• PubMed Abstract: 
  

The RNA sensor MDA5 recruits the signaling adaptor MAVS to initiate type I interferon signaling and downstream antiviral responses, a process that requires K63-linked polyubiquitin chains. Here, we examined the mechanisms whereby K63-polyUb chain regulate MDA5 activation. Only long unanchored K63-polyUb _n (n ≥ 8) could mediate tetramerization of the caspase activation and recruitment domains of MDA5 ( ^MDA5 CARDs). Cryoelectron microscopy structures of a polyUb ₁₃ -bound ^MDA5 CARDs tetramer and a polyUb ₁₁ -bound ^MDA5 CARDs- ^MAVS CARD assembly revealed a tower-like formation, wherein eight Ubs tethered along the outer rim of the helical shell, bridging ^MDA5 CARDs and ^MAVS CARD tetramers into proximity. ATP binding and hydrolysis promoted the stabilization of RNA-bound MDA5 prior to MAVS activation via allosteric effects on CARDs-polyUb complex. Abundant ATP prevented basal activation of apo MDA5. Our findings reveal the ordered assembly of a MDA5 signaling complex competent to recruit and activate MAVS and highlight differences with RIG-I in terms of CARD orientation and Ub sensing that suggest different abilities to induce antiviral responses.

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Organizational Affiliation: 

Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interferon-induced helicase C domain-containing protein 1	A, B, C, D	208	Homo sapiens	Mutation(s): 0  Gene Names: MDA5, IFIH1, RH116 EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYX4 (Homo sapiens) Explore Q9BYX4  Go to UniProtKB:  Q9BYX4
PHAROS:  Q9BYX4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	E, F, G, H, I, J, K, L	76	Homo sapiens	Mutation(s): 0  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-10-13 
Deposition Author(s): Song, B., Chen, Y., Luo, D.H., Zheng, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81971538

Revision History  

• Version 1.0: 2021-10-13
  Type: Initial release
  
• Version 1.1: 2022-02-16
  Changes: Database references