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- PDB-7dnj: K63-polyUb MDA5CARDs complex -

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Basic information

Entry
Database: PDB / ID: 7dnj
TitleK63-polyUb MDA5CARDs complex
Components
  • Interferon-induced helicase C domain-containing protein 1
  • Ubiquitin
KeywordsIMMUNE SYSTEM / signaling complex
Function / homology
Function and homology information


MDA-5 signaling pathway / regulation of type III interferon production / detection of virus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of response to cytokine stimulus / Modulation of host responses by IFN-stimulated genes / symbiont entry into host cell via disruption of host cell glycocalyx / TRAF6 mediated IRF7 activation / negative regulation of viral genome replication / symbiont entry into host cell via disruption of host cell envelope ...MDA-5 signaling pathway / regulation of type III interferon production / detection of virus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of response to cytokine stimulus / Modulation of host responses by IFN-stimulated genes / symbiont entry into host cell via disruption of host cell glycocalyx / TRAF6 mediated IRF7 activation / negative regulation of viral genome replication / symbiont entry into host cell via disruption of host cell envelope / cytoplasmic pattern recognition receptor signaling pathway / type I interferon-mediated signaling pathway / pattern recognition receptor activity / virus tail / cellular response to exogenous dsRNA / protein complex oligomerization / TRAF6 mediated NF-kB activation / positive regulation of interferon-alpha production / protein sumoylation / ribonucleoprotein complex binding / antiviral innate immune response / Negative regulators of DDX58/IFIH1 signaling / positive regulation of interferon-beta production / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Evasion by RSV of host interferon responses / cellular response to virus / positive regulation of interleukin-6 production / response to virus / SARS-CoV-1 activates/modulates innate immune responses / Ovarian tumor domain proteases / positive regulation of tumor necrosis factor production / double-stranded RNA binding / TRAF3-dependent IRF activation pathway / defense response to virus / single-stranded RNA binding / Ub-specific processing proteases / RNA helicase activity / RNA helicase / innate immune response / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / mitochondrion / DNA binding / RNA binding / zinc ion binding / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Death Domain, Fas / Death Domain, Fas / RIG-I-like receptor, C-terminal / RIG-I receptor C-terminal domain / RIG-I-like receptor, C-terminal regulatory domain / RIG-I-like receptor, C-terminal domain superfamily / : / C-terminal domain of RIG-I / RIG-I-like receptor (RLR) C-terminal regulatory (CTR) domain profile. / Caspase recruitment domain ...Death Domain, Fas / Death Domain, Fas / RIG-I-like receptor, C-terminal / RIG-I receptor C-terminal domain / RIG-I-like receptor, C-terminal regulatory domain / RIG-I-like receptor, C-terminal domain superfamily / : / C-terminal domain of RIG-I / RIG-I-like receptor (RLR) C-terminal regulatory (CTR) domain profile. / Caspase recruitment domain / Caspase recruitment domain / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Pectin lyase fold / Pectin lyase fold/virulence factor / Death-like domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Helicase conserved C-terminal domain / Ubiquitin-like (UB roll) / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Roll / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Tail fiber / Interferon-induced helicase C domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSong, B. / Chen, Y. / Luo, D.H. / Zheng, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81971538 China
CitationJournal: Immunity / Year: 2021
Title: Ordered assembly of the cytosolic RNA-sensing MDA5-MAVS signaling complex via binding to unanchored K63-linked poly-ubiquitin chains.
Authors: Bin Song / Yun Chen / Xin Liu / Fei Yuan / Eddie Yong Jun Tan / Yixuan Lei / Ning Song / Yinqi Han / Bruce D Pascal / Patrick R Griffin / Cheng Luo / Bin Wu / Dahai Luo / Jie Zheng /
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 ...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 ≥ 8) could mediate tetramerization of the caspase activation and recruitment domains of MDA5 (CARDs). Cryoelectron microscopy structures of a polyUb-bound CARDs tetramer and a polyUb-bound CARDs-CARD assembly revealed a tower-like formation, wherein eight Ubs tethered along the outer rim of the helical shell, bridging CARDs and 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.
History
DepositionDec 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.0Oct 13, 2021Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 13, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 13, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Oct 13, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 13, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Oct 13, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 13, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3Jul 2, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

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Assembly

Deposited unit
A: Interferon-induced helicase C domain-containing protein 1
B: Interferon-induced helicase C domain-containing protein 1
C: Interferon-induced helicase C domain-containing protein 1
D: Interferon-induced helicase C domain-containing protein 1
E: Ubiquitin
F: Ubiquitin
G: Ubiquitin
H: Ubiquitin
I: Ubiquitin
J: Ubiquitin
K: Ubiquitin
L: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)163,91812
Polymers163,91812
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry, HDX-MS
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area22620 Å2
ΔGint-64 kcal/mol
Surface area52010 Å2

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Components

#1: Protein
Interferon-induced helicase C domain-containing protein 1


Mass: 23825.883 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MDA5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BYX4, RNA helicase
#2: Protein
Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1k63polyUb bound MDA5 CARDs complexCOMPLEXall0RECOMBINANT
2k63polyUbCOMPLEXall1RECOMBINANT
3MDA5 CARDsCOMPLEXall1RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli (E. coli)562
32Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: OTHER

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 70 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 143814 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00811082
ELECTRON MICROSCOPYf_angle_d0.71314991
ELECTRON MICROSCOPYf_dihedral_angle_d16.5351467
ELECTRON MICROSCOPYf_chiral_restr0.0481765
ELECTRON MICROSCOPYf_plane_restr0.0051932

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