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- PDB-9y4l: CryoEM Structure of human MDA5 in complex with dsRNA (two protein... -

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Basic information

Entry
Database: PDB / ID: 9y4l
TitleCryoEM Structure of human MDA5 in complex with dsRNA (two protein subunits on dsRNA)
Components
  • (RNA (30-MER)) x 2
  • Interferon-induced helicase C domain-containing protein 1
KeywordsIMMUNE SYSTEM / RLR / MDA5 / filament / dsRNA
Function / homology
Function and homology information


MDA-5 signaling pathway / regulation of type III interferon production / detection of virus / positive regulation of response to cytokine stimulus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / Modulation of host responses by IFN-stimulated genes / TRAF6 mediated IRF7 activation / negative regulation of viral genome replication / cellular response to exogenous dsRNA / pattern recognition receptor activity ...MDA-5 signaling pathway / regulation of type III interferon production / detection of virus / positive regulation of response to cytokine stimulus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / Modulation of host responses by IFN-stimulated genes / TRAF6 mediated IRF7 activation / negative regulation of viral genome replication / cellular response to exogenous dsRNA / pattern recognition receptor activity / cytoplasmic pattern recognition receptor signaling pathway / TRAF6 mediated NF-kB activation / positive regulation of interferon-alpha production / protein complex oligomerization / protein sumoylation / ribonucleoprotein complex binding / Dengue virus activates/modulates innate and adaptive immune responses / positive regulation of interferon-beta production / antiviral innate immune response / cellular response to virus / Negative regulators of DDX58/IFIH1 signaling / positive regulation of interleukin-6 production / response to virus / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Evasion by RSV of host interferon responses / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of tumor necrosis factor production / Ovarian tumor domain proteases / double-stranded RNA binding / TRAF3-dependent IRF activation pathway / defense response to virus / RNA helicase activity / single-stranded RNA binding / Ub-specific processing proteases / RNA helicase / innate immune response / protein domain specific binding / 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
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 ...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 / Death-like domain superfamily / Helicase conserved C-terminal domain / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / RNA / RNA (> 10) / Interferon-induced helicase C domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
in vitro transcription vector pT7-Fluc
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsXu, L. / Chung, K. / Pyle, A.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Unraveling the molecular basis for MDA5 T331I disease-linked mutation
Authors: Xu, L. / Chung, K. / Guo, R. / Pan, A. / Pyle, A.M.
History
DepositionSep 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 9, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interferon-induced helicase C domain-containing protein 1
G: Interferon-induced helicase C domain-containing protein 1
B: RNA (30-MER)
C: RNA (30-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,5996
Polymers186,5864
Non-polymers1,0122
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Interferon-induced helicase C domain-containing protein 1 / Clinically amyopathic dermatomyositis autoantigen 140 kDa / CADM-140 autoantigen / Helicase with 2 ...Clinically amyopathic dermatomyositis autoantigen 140 kDa / CADM-140 autoantigen / Helicase with 2 CARD domains / Helicard / Interferon-induced with helicase C domain protein 1 / Melanoma differentiation-associated protein 5 / MDA-5 / Murabutide down-regulated protein / RIG-I-like receptor 2 / RLR-2 / RNA helicase-DEAD box protein 116


Mass: 83702.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFIH1, MDA5, RH116
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9BYX4, RNA helicase
#2: RNA chain RNA (30-MER)


Mass: 9664.721 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) in vitro transcription vector pT7-Fluc(deltai) (others)
#3: RNA chain RNA (30-MER)


Mass: 9516.735 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) in vitro transcription vector pT7-Fluc(deltai) (others)
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
Has ligand of interestY
Has protein modificationY

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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

ComponentName: Complex of human MDA5 with dsRNA / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 51.98 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 402040 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00312380
ELECTRON MICROSCOPYf_angle_d0.60216956
ELECTRON MICROSCOPYf_dihedral_angle_d10.4472150
ELECTRON MICROSCOPYf_chiral_restr0.0451956
ELECTRON MICROSCOPYf_plane_restr0.0041922

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