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- EMDB-72484: CryoEM Structure of human MDA5 with dsRNA (one protein subunit on... -

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Basic information

Entry
Database: EMDB / ID: EMD-72484
TitleCryoEM Structure of human MDA5 with dsRNA (one protein subunit on dsRNA)
Map datasharpened map
Sample
  • Complex: CryoEM structure of MDA5 binds to dsRNA in presence of AMPPNP - one protein subunit on dsRNA
    • Protein or peptide: Interferon-induced helicase C domain-containing protein 1
    • RNA: RNA 13mer
    • RNA: RNA 13mer
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: water
KeywordsRLR / MDA5 / signaling / filament / dsRNA / IMMUNE SYSTEM
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
Interferon-induced helicase C domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human) / in vitro transcription vector pT7-Fluc(deltai) (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsXu L / Chung K / Pyle A
Funding support United States, 1 items
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 AM
History
DepositionSep 3, 2025-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72484.png

Downloads & links

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Map

FileDownload / File: emd_72484.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 425.984 Å		0.83 Å/pix.
x 512 pix.
= 425.984 Å		0.83 Å/pix.
x 512 pix.
= 425.984 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-2.2740946 - 3.1371214
Average (Standard dev.)-0.00002045723 (±0.037724037)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 425.984 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: raw map

Fileemd_72484_additional_1.map
Annotationraw map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A for monoMDA5/dsRNA

Fileemd_72484_half_map_1.map
Annotationhalf map A for monoMDA5/dsRNA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B for monoMDA5/dsRNA

Fileemd_72484_half_map_2.map
Annotationhalf map B for monoMDA5/dsRNA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CryoEM structure of MDA5 binds to dsRNA in presence of AMPPNP - o...

EntireName: CryoEM structure of MDA5 binds to dsRNA in presence of AMPPNP - one protein subunit on dsRNA
Components
  • Complex: CryoEM structure of MDA5 binds to dsRNA in presence of AMPPNP - one protein subunit on dsRNA
    • Protein or peptide: Interferon-induced helicase C domain-containing protein 1
    • RNA: RNA 13mer
    • RNA: RNA 13mer
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: CryoEM structure of MDA5 binds to dsRNA in presence of AMPPNP - o...

SupramoleculeName: CryoEM structure of MDA5 binds to dsRNA in presence of AMPPNP - one protein subunit on dsRNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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

MacromoleculeName: Interferon-induced helicase C domain-containing protein 1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 83.702422 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: ARASPEPELQ LRPYQMEVAQ PALEGKNIII CLPTGSGKTR VAVYIAKDHL DKKKKASEPG KVIVLVNKVL LVEQLFRKEF QPFLKKWYR VIGLSGDTQL KISFPEVVKS CDIIISTAQI LENSLLNLEN GEDAGVQLSD FSLIIIDECH HTNKEAVYNN I MRHYLMQK ...String:
ARASPEPELQ LRPYQMEVAQ PALEGKNIII CLPTGSGKTR VAVYIAKDHL DKKKKASEPG KVIVLVNKVL LVEQLFRKEF QPFLKKWYR VIGLSGDTQL KISFPEVVKS CDIIISTAQI LENSLLNLEN GEDAGVQLSD FSLIIIDECH HTNKEAVYNN I MRHYLMQK LKNNRLKKEN KPVIPLPQIL GLTASPGVGG ATKQAKAEEH ILKLCANLDA FTIKTVKENL DQLKNQIQEP CK KFAIADA TREDPFKEKL LEIMTRIQTY CQMSPMSDFG TQPYEQWAIQ MEKKAAKEGN RKERVCAEHL RKYNEALQIN DTI RMIDAY THLETFYNEE KDKKFAVIED DSDEGGDDEY CDGDEDEDDL KKPLKLDETD RFLMTLFFEN NKMLKRLAEN PEYE NEKLT KLRNTIMEQY TRTEESARGI IFTKTRQSAY ALSQWITENE KFAEVGVKAH HLIGAGHSSE FKPMTQNEQK EVISK FRTG KINLLIATTV AEEGLDIKEC NIVIRYGLVT NEIAMVQARG RARADESTYV LVAHSGSGVI EHETVNDFRE KMMYKA IHC VQNMKPEEYA HKILELQMQS IMEKKMKTKR NIAKHYKNNP SLITFLCKNC SVLACSGEDI HVIEKMHHVN MTPEFKE LY IVRENKALQK KCADYQINGE IICKCGQAWG TMMVHKGLDL PCLKIRNFVV VFKNNSTKKQ YKKWVELPIT FPNLDYSE C CLFSDED

UniProtKB: Interferon-induced helicase C domain-containing protein 1

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Macromolecule #2: RNA 13mer

MacromoleculeName: RNA 13mer / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: in vitro transcription vector pT7-Fluc(deltai) (others)
Molecular weightTheoretical: 4.21355 KDa
SequenceString:
CGGUUAGGGG CUA

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Macromolecule #3: RNA 13mer

MacromoleculeName: RNA 13mer / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: in vitro transcription vector pT7-Fluc(deltai) (others)
Molecular weightTheoretical: 4.076494 KDa
SequenceString:
UAGCCCCUAA CCG

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Macromolecule #4: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 4 / Number of copies: 1 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.98 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 402040
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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