[English] 日本語
Yorodumi
- EMDB-63261: LGP2:MDA5:dsRNA filament -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-63261
TitleLGP2:MDA5:dsRNA filament
Map dataA primary map.
Sample
  • Complex: Filament of LGP2, MDA5 and dsRNA
    • Complex: LGP2
      • Protein or peptide: ATP-dependent RNA helicase DHX58
    • Complex: MDA5
      • Protein or peptide: Interferon-induced helicase C domain-containing protein 1
    • Complex: dsRNA
      • RNA: RNA (45-MER)
      • RNA: RNA (45-MER)
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
KeywordsInnate immune system / RNA receptor / Cryo-EM / Filament / IMMUNE SYSTEM / IMMUNE SYSTEM-RNA complex
Function / homology
Function and homology information


positive regulation of MDA-5 signaling pathway / negative regulation of MDA-5 signaling pathway / negative regulation of RIG-I signaling pathway / MDA-5 signaling pathway / positive regulation of RIG-I 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 ...positive regulation of MDA-5 signaling pathway / negative regulation of MDA-5 signaling pathway / negative regulation of RIG-I signaling pathway / MDA-5 signaling pathway / positive regulation of RIG-I 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 type I interferon production / negative regulation of viral genome replication / cytoplasmic pattern recognition receptor signaling pathway / type I interferon-mediated signaling pathway / regulation of innate immune response / pattern recognition receptor activity / cellular response to exogenous dsRNA / TRAF6 mediated NF-kB activation / protein complex oligomerization / positive regulation of interferon-alpha production / protein sumoylation / positive regulation of type I interferon production / ribonucleoprotein complex binding / antiviral innate immune response / positive regulation of interferon-beta production / negative regulation of innate immune response / response to bacterium / Negative regulators of DDX58/IFIH1 signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / cellular response to virus / Evasion by RSV of host interferon responses / positive regulation of interleukin-6 production / response to virus / positive regulation of tumor necrosis factor production / SARS-CoV-1 activates/modulates innate immune responses / 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 / 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
ATP-dependent RNA helicase DHX58 / Interferon-induced helicase C domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human) / uncultured archaeon (environmental samples)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsKurihara N / Isayama Y / Nureki O / Kato K
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23H04768 Japan
CitationJournal: To Be Published
Title: LGP2:MDA5:dsRNA filament
Authors: Kurihara N / Isayama Y / Nureki O / Kato K
History
DepositionJan 23, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_63261.png

Downloads & links

-
Map

FileDownload / File: emd_63261.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA primary map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 192 pix.
= 239.04 Å		1.25 Å/pix.
x 192 pix.
= 239.04 Å		1.25 Å/pix.
x 192 pix.
= 239.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.245 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.5484381 - 0.8839498
Average (Standard dev.)0.0026058955 (±0.024813881)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 239.04001 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_63261_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: A half map B.

Fileemd_63261_half_map_1.map
AnnotationA half map B.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: A half map A.

Fileemd_63261_half_map_2.map
AnnotationA half map A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Filament of LGP2, MDA5 and dsRNA

EntireName: Filament of LGP2, MDA5 and dsRNA
Components
  • Complex: Filament of LGP2, MDA5 and dsRNA
    • Complex: LGP2
      • Protein or peptide: ATP-dependent RNA helicase DHX58
    • Complex: MDA5
      • Protein or peptide: Interferon-induced helicase C domain-containing protein 1
    • Complex: dsRNA
      • RNA: RNA (45-MER)
      • RNA: RNA (45-MER)
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

+
Supramolecule #1: Filament of LGP2, MDA5 and dsRNA

SupramoleculeName: Filament of LGP2, MDA5 and dsRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

+
Supramolecule #2: LGP2

SupramoleculeName: LGP2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

+
Supramolecule #3: MDA5

SupramoleculeName: MDA5 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Homo sapiens (human)

+
Supramolecule #4: dsRNA

SupramoleculeName: dsRNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: uncultured archaeon (environmental samples)

+
Macromolecule #1: RNA (45-MER)

MacromoleculeName: RNA (45-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: uncultured archaeon (environmental samples)
Molecular weightTheoretical: 14.278429 KDa
SequenceString:
UCUCAGUCAG UCAGUCUCAG UCAGUCAGUC UCAGUCAGUC AGUCU

+
Macromolecule #2: RNA (45-MER)

MacromoleculeName: RNA (45-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: uncultured archaeon (environmental samples)
Molecular weightTheoretical: 14.553724 KDa
SequenceString:
AGACUGACUG ACUGAGACUG ACUGACUGAG ACUGACUGAC UGAGA

+
Macromolecule #3: ATP-dependent RNA helicase DHX58

MacromoleculeName: ATP-dependent RNA helicase DHX58 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 76.742883 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MELRSYQWEV IMPALEGKNI IIWLPTGAGK TRAAAYVAKR HLETVDGAKV VVLVNRVHLV TQHGEEFRRM LDGRWTVTTL SGDMGPRAG FGHLARCHDL LICTAELLQM ALTSPEEEEH VELTVFSLIV VDECHHTHKD TVYNVIMSQY LELKLQRAQP L PQVLGLTA ...String:
MELRSYQWEV IMPALEGKNI IIWLPTGAGK TRAAAYVAKR HLETVDGAKV VVLVNRVHLV TQHGEEFRRM LDGRWTVTTL SGDMGPRAG FGHLARCHDL LICTAELLQM ALTSPEEEEH VELTVFSLIV VDECHHTHKD TVYNVIMSQY LELKLQRAQP L PQVLGLTA SPGTGGASKL DGAINHVLQL CANLDTWCIM SPQNCCPQLQ EHSQQPCKQY NLCHRRSQDP FGDLLKKLMD QI HDHLEMP ELSRKFGTQM YEQQVVKLSE AAALAGLQEQ RVYALHLRRY NDALLIHDTV RAVDALAALQ DFYHREHVTK TQI LCAERR LLALFDDRKN ELAHLATHGP ENPKLEMLEK ILQRQFSSSN SPRGIIFTRT RQSAHSLLLW LQQQQGLQTV DIRA QLLIG AGNSSQSTHM TQRDQQEVIR KFQDGTLNLL VATSVAEEGL DIPHCNVVVR YGLLTNEISM VQARGRARAD QSVYA FVAT EGSRELKREL INEALETLME QAVAAVQKMD QAEYQAKIRD LQQAALTKRA AQAAQRENQR QQFPVEHVQL LCINCM VAV GHGSDLRKVE GTHHVNVNPN FSNYYNVSRD PVVINKVFKD WKPGGVISCR NCGEVWGLQM IYKSVKLPVL KVRSMLL ET PQGRIQAKKW SRVPFSVPDF DFLQHCAENL SDLSLD

UniProtKB: ATP-dependent RNA helicase DHX58

+
Macromolecule #4: Interferon-induced helicase C domain-containing protein 1

MacromoleculeName: Interferon-induced helicase C domain-containing protein 1
type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 84.986758 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSDSDEENV AARASPEPEL QLRPYQMEVA QPALEGKNII ICLPTGSGKT RVAVYIAKDH LDKKKKASEP GKVIVLVNKV LLVEQLFRK EFQPFLKKWY RVIGLSGDTQ LKISFPEVVK SCDIIISTAQ ILENSLLNLE NGEDAGVQLS DFSLIIIDEC H HTNKEAVY ...String:
MGSDSDEENV AARASPEPEL QLRPYQMEVA QPALEGKNII ICLPTGSGKT RVAVYIAKDH LDKKKKASEP GKVIVLVNKV LLVEQLFRK EFQPFLKKWY RVIGLSGDTQ LKISFPEVVK SCDIIISTAQ ILENSLLNLE NGEDAGVQLS DFSLIIIDEC H HTNKEAVY NNIMRHYLMQ KLKNNRLKKE NKPVIPLPQI LGLTASPGVG RATKQAKAEE HILKLCANLD AFTIKTVKEN LD QLKNQIQ EPCKKFAIAD ATREDPFKEK LLEIMTRIQT YCQMSPMSDF GTQPYEQWAI QMEKKAAKEG NRKERVCAEH LRK YNEALQ INDTIRMIDA YTHLETFYNE EKDKKFAVIE DDSDEGGDDE YCDGDEDEDD LKKPLKLDET DRFLMTLFFE NNKM LKRLA ENPEYENEKL TKLRNTIMEQ YTRTEESARG IIFTKTRQSA YALSQWITEN EKFAEVGVKA HHLIGAGHSS EFKPM TQNE QKEVISKFRT GKINLLIATT VAEEGLDIKE CNIVIRYGLV TNEIAMVQAR GRARADESTY VLVAHSGSGV IERETV NDF REKMMYKAIH CVQNMKPEEY AHKILELQMQ SIMEKKMKTK RNIAKHYKNN PSLITFLCKN CSVLACSGED IHVIEKM HH VNMTPEFKEL YIVRENKTLQ KKCADYQING EIICKCGQAW GTMMVHKGLD LPCLKIRNFV VVFKNNSTKK QYKKWVEL P ITFPNLDYSE CCLFSDED

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

+
Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 3 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

+
Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.83 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: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 117189
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more