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- EMDB-72284: CryoEM map of human MDA5 filament formed on short dsRNA -

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Basic information

Entry
Database: EMDB / ID: EMD-72284
TitleCryoEM map of human MDA5 filament formed on short dsRNA
Map data
Sample
  • Complex: CryoEM map of human MDA5 filament on short dsRNA
    • Protein or peptide: human MDA5 (Melanoma Differentiation-Associated Protein 5)
KeywordsRLR / MDA5 / signaling / filament / dsRNA / IMMUNE SYSTEM
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsXu L / Chung L / 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
DepositionAug 22, 2025-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72284.png

Downloads & links

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Map

FileDownload / File: emd_72284.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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: 0.14
Minimum - Maximum-0.7619889 - 1.3689834
Average (Standard dev.)-0.000012773965 (±0.018992547)
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: #1

Fileemd_72284_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72284_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72284_half_map_2.map
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 map of human MDA5 filament on short dsRNA

EntireName: CryoEM map of human MDA5 filament on short dsRNA
Components
  • Complex: CryoEM map of human MDA5 filament on short dsRNA
    • Protein or peptide: human MDA5 (Melanoma Differentiation-Associated Protein 5)

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Supramolecule #1: CryoEM map of human MDA5 filament on short dsRNA

SupramoleculeName: CryoEM map of human MDA5 filament on short dsRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: human MDA5 (Melanoma Differentiation-Associated Protein 5)

MacromoleculeName: human MDA5 (Melanoma Differentiation-Associated Protein 5)
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: ARASPEPELQ LRPYQMEVAQ PALEGKNIII CLPTGSGKTR VAVYIAKDHL DKKKKASEPG KVIVLVNKVL LVEQLFRKEF QPFLKKWYRV IGLSGDTQLK ISFPEVVKSC DIIISTAQIL ENSLLNLENG EDAGVQLSDF SLIIIDECHH TNKEAVYNNI MRHYLMQKLK ...String:
ARASPEPELQ LRPYQMEVAQ PALEGKNIII CLPTGSGKTR VAVYIAKDHL DKKKKASEPG KVIVLVNKVL LVEQLFRKEF QPFLKKWYRV IGLSGDTQLK ISFPEVVKSC DIIISTAQIL ENSLLNLENG EDAGVQLSDF SLIIIDECHH TNKEAVYNNI MRHYLMQKLK NNRLKKENKP VIPLPQILGL TASPGVGGAT KQAKAEEHIL KLCANLDAFT IKTVKENLDQ LKNQIQEPCK KFAIADATRE DPFKEKLLEI MTRIQTYCQM SPMSDFGTQP YEQWAIQMEK KAAKEGNRKE RVCAEHLRKY NEALQINDTI RMIDAYTHLE TFYNEEKDKK FAVIEDDSDE GGDDEYCDGD EDEDDLKKPL KLDETDRFLM TLFFENNKML KRLAENPEYE NEKLTKLRNT IMEQYTRTEE SARGIIFTKT RQSAYALSQW ITENEKFAEV GVKAHHLIGA GHSSEFKPMT QNEQKEVISK FRTGKINLLI ATTVAEEGLD IKECNIVIRY GLVTNEIAMV QARGRARADE STYVLVAHSG SGVIEHETVN DFREKMMYKA IHCVQNMKPE EYAHKILELQ MQSIMEKKMK TKRNIAKHYK NNPSLITFLC KNCSVLACSG EDIHVIEKMH HVNMTPEFKE LYIVRENKAL QKKCADYQIN GEIICKCGQA WGTMMVHKGL DLPCLKIRNF VVVFKNNSTK KQYKKWVELP ITFPNLDYSE CCLFSDED

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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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 79446
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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