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- EMDB-37609: Structure of MAVS-CARD Filament -

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Basic information

Entry
Database: EMDB / ID: EMD-37609
TitleStructure of MAVS-CARD Filament
Map data
Sample
  • Organelle or cellular component: MAVS-CARD
    • Protein or peptide: Mitochondrial antiviral-signaling protein
KeywordsFilament / IMMUNE SYSTEM
Function / homology
Function and homology information


positive regulation of IP-10 production / regulation of peroxisome organization / RIG-I binding / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of myeloid dendritic cell cytokine production / CARD domain binding / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of response to cytokine stimulus / protein localization to mitochondrion / positive regulation of type I interferon-mediated signaling pathway ...positive regulation of IP-10 production / regulation of peroxisome organization / RIG-I binding / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of myeloid dendritic cell cytokine production / CARD domain binding / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of response to cytokine stimulus / protein localization to mitochondrion / positive regulation of type I interferon-mediated signaling pathway / peroxisomal membrane / TRAF6 mediated IRF7 activation / negative regulation of type I interferon-mediated signaling pathway / type I interferon-mediated signaling pathway / negative regulation of viral genome replication / cytoplasmic pattern recognition receptor signaling pathway / cellular response to exogenous dsRNA / positive regulation of NLRP3 inflammasome complex assembly / TRAF6 mediated NF-kB activation / positive regulation of interferon-alpha production / positive regulation of type I interferon production / ubiquitin ligase complex / signaling adaptor activity / positive regulation of defense response to virus by host / antiviral innate immune response / activation of innate immune response / positive regulation of interferon-beta production / positive regulation of DNA-binding transcription factor activity / positive regulation of interleukin-8 production / Negative regulators of DDX58/IFIH1 signaling / molecular condensate scaffold activity / mitochondrial membrane / PKR-mediated signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Evasion by RSV of host interferon responses / positive regulation of interleukin-6 production / positive regulation of protein import into nucleus / positive regulation of tumor necrosis factor production / SARS-CoV-1 activates/modulates innate immune responses / Ovarian tumor domain proteases / TRAF3-dependent IRF activation pathway / protein-macromolecule adaptor activity / molecular adaptor activity / defense response to virus / mitochondrial outer membrane / positive regulation of canonical NF-kappaB signal transduction / intracellular signal transduction / defense response to bacterium / innate immune response / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / identical protein binding
Similarity search - Function
IPS1, CARD domain / : / Caspase recruitment domain / Caspase recruitment domain / Death-like domain superfamily
Similarity search - Domain/homology
Mitochondrial antiviral-signaling protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsShi M / Gao P
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32130057, 31922037, 81921005, 32271275 China
CitationJournal: Mol Cell / Year: 2025
Title: Nucleic-acid-induced ZCCHC3 condensation promotes broad innate immune responses.
Authors: Miao Shi / Tao Jiang / Mengfan Zhang / Quanjin Li / Kexin Liu / Ni Lin / Xinlu Wang / Amin Jiang / Yina Gao / Yong Wang / Songqing Liu / Liguo Zhang / Dong Li / Pu Gao /
Abstract: Retinoic acid-inducible gene-I (RIG-I)-like receptors (RLRs) and cyclic GMP-AMP synthase (cGAS) recognize aberrant nucleic acids and initiate antiviral responses. Host factor zinc finger CCHC domain- ...Retinoic acid-inducible gene-I (RIG-I)-like receptors (RLRs) and cyclic GMP-AMP synthase (cGAS) recognize aberrant nucleic acids and initiate antiviral responses. Host factor zinc finger CCHC domain-containing protein 3 (ZCCHC3) positively regulates both RLRs- and cGAS-mediated signaling through unknown mechanisms. Here, we show that ZCCHC3 employs a broad and unified strategy to promote these pathways in human cell lines. Rather than developing strong protein-protein interactions, ZCCHC3 harbors multiple nucleic-acid-binding modules and undergoes robust liquid phase condensation with nucleic acids. RNA-induced ZCCHC3 condensates enrich and activate RLRs, which then facilitate the interaction of RLRs with the downstream adaptor mitochondrial antiviral-signaling (MAVS). Direct and high-resolution structure determination of liquid condensates confirms the assembly of active-form MAVS filaments. Furthermore, ZCCHC3 efficiently promotes the condensation and enrichment of DNA, cGAS, ATP, and GTP, thereby enhancing cGAS signaling. ZCCHC3 mutants defective in RNA/DNA-induced condensation lost their regulatory efficiency in both pathways. These results highlight unexpectedly broad connections between biomolecular condensation and innate immunity.
History
DepositionSep 28, 2023-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37609.png

Downloads & links

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Map

FileDownload / File: emd_37609.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 256 pix.
= 348.16 Å		1.36 Å/pix.
x 256 pix.
= 348.16 Å		1.36 Å/pix.
x 256 pix.
= 348.16 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-2.0144262 - 4.056377
Average (Standard dev.)0.004051038 (±0.16542311)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 348.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37609_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_37609_half_map_2.map
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Sample components

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Entire : MAVS-CARD

EntireName: MAVS-CARD
Components
  • Organelle or cellular component: MAVS-CARD
    • Protein or peptide: Mitochondrial antiviral-signaling protein

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Supramolecule #1: MAVS-CARD

SupramoleculeName: MAVS-CARD / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Mitochondrial antiviral-signaling protein

MacromoleculeName: Mitochondrial antiviral-signaling protein / type: protein_or_peptide / ID: 1 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.327857 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPFAEDKTYK YICRNFSNFC NVDVVEILPY LPCLTARDQD RLRATCTLSG NRDTLWHLFN TLQRRPGWVE YFIAALRGCE LVDLADEVA SVYQSYQP

UniProtKB: Mitochondrial antiviral-signaling protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2vgq

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 80454
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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