12KL | pdb_000012kl

SSNMR Structure of Anti-necroptosis Viral:Human Functional Hetero-amyloid M45:RIPK3


Experimental Data Snapshot

  • Method: SOLID-STATE NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structural studies of an antinecroptosis viral:human functional heteroamyloid M45:RIPK3 using SSNMR.

He, C.Varghese, N.R.Keeler, E.G.Pham, C.L.L.Xie, T.Williams, B.Tetter, S.Semaan, C.Wilde, K.L.Brown, S.H.J.Bouwer, J.C.Gambin, Y.Sierecki, E.Steain, M.Zhou, R.Sunde, M.McDermott, A.E.

(2026) Proc Natl Acad Sci U S A 123: e2426811123-e2426811123

  • DOI: https://doi.org/10.1073/pnas.2426811123
  • Primary Citation Related Structures: 
    12KL

  • PubMed Abstract: 

    The formation of RIP-homotypic interaction motif (RHIM)-based heteromeric amyloid assemblies between effector proteins such as receptor-interacting protein kinases 1, Z-DNA Binding Protein 1, or TRIF and the kinase RIPK3 serves as regulating signals for the necroptosis process, a key element of innate immune defense. Murine cytomegalovirus expresses the M45-encoded viral inhibitor of RIP activation which inhibits necroptosis in a RHIM-dependent manner. A pivotal question is how viral M45 forms heteroamyloids with RIPK3 to effectively create an inhibitory assembly. We report a high-resolution structure of the M45:RIPK3 complex where M45 and RIPK3 alternately stack in an amyloid-state structure. Mutagenesis of the residues flanking the IQIG tetrad in M45 results in specific impacts on coassembly with RIPK3, indicating an extended interface in the heteromeric fibrils. Other key interactions support the formation of stable viral:host fibrils. The M45:RIPK3 heteroamyloid is likely to act as an antinecroptotic signal by competing with formation of other pronecroptotic species and introducing a barrier to RIPK3 autophosphorylation.


  • Organizational Affiliation
    • Department of Chemistry, Columbia University, New York, NY 10027.

Macromolecule Content 

  • Total Structure Weight: 96.02 kDa 
  • Atom Count: 1,664 
  • Modeled Residue Count: 220 
  • Deposited Residue Count: 900 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Receptor-interacting serine/threonine-protein kinase 3
A, C, E, G
133Homo sapiensMutation(s): 0 
Gene Names: RIPK3RIP3
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y572 (Homo sapiens)
Explore Q9Y572 
Go to UniProtKB:  Q9Y572
PHAROS:  Q9Y572
GTEx:  ENSG00000129465 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y572
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribonucleoside-diphosphate reductase large subunit-like protein
B, D, F, H
92Murid betaherpesvirus 1Mutation(s): 0 
Gene Names: M45RIR1
UniProt
Find proteins for H2A2P4 (Murid herpesvirus 1)
Explore H2A2P4 
Go to UniProtKB:  H2A2P4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH2A2P4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLID-STATE NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesNSF MCB 24-27038
Australian Research Council (ARC)AustraliaDP DP200102463

Revision History  (Full details and data files)

  • Version 1.0: 2026-04-22
    Type: Initial release
  • Version 1.1: 2026-05-06
    Changes: Database references
  • Version 1.2: 2026-05-13
    Changes: Database references