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- EMDB-29824: Cryo-EM structure of RNP end 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-29824
TitleCryo-EM structure of RNP end 2
Map dataCryo-EM structure of RNP end 2
Sample
  • Complex: Complex of RNP end 2
    • Protein or peptide: Antiviral innate immune response receptor RIG-I
    • Protein or peptide: E3 ubiquitin-protein ligase RNF135
    • RNA: p3dsRNA24a
    • RNA: p3dsRNA24b
  • Ligand: ZINC ION
Keywordsribonucleoprotein complex / RNA sensor / RIG-I like receptor / Ubiquitination / E3 ligase / TRIM family / ANTIVIRAL PROTEIN / Transferase-Hydrolase-RNA complex
Function / homology
Function and homology information


RIG-I binding / free ubiquitin chain polymerization / regulation of type III interferon production / RIG-I signaling pathway / positive regulation of myeloid dendritic cell cytokine production / OAS antiviral response / detection of virus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of response to cytokine stimulus / positive regulation of granulocyte macrophage colony-stimulating factor production ...RIG-I binding / free ubiquitin chain polymerization / regulation of type III interferon production / RIG-I signaling pathway / positive regulation of myeloid dendritic cell cytokine production / OAS antiviral response / detection of virus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of response to cytokine stimulus / positive regulation of granulocyte macrophage colony-stimulating factor production / RSV-host interactions / pattern recognition receptor activity / TRAF6 mediated IRF7 activation / regulation of innate immune response / cytoplasmic pattern recognition receptor signaling pathway / cellular response to exogenous dsRNA / response to exogenous dsRNA / protein K63-linked ubiquitination / antiviral innate immune response / TRAF6 mediated NF-kB activation / positive regulation of interferon-alpha production / bicellular tight junction / ribonucleoprotein complex binding / regulation of cell migration / positive regulation of defense response to virus by host / positive regulation of interferon-beta production / Evasion by RSV of host interferon responses / Negative regulators of DDX58/IFIH1 signaling / positive regulation of interleukin-8 production / response to virus / RING-type E3 ubiquitin transferase / DDX58/IFIH1-mediated induction of interferon-alpha/beta / protein homooligomerization / ISG15 antiviral mechanism / ruffle membrane / cytoplasmic stress granule / protein polyubiquitination / ubiquitin-protein transferase activity / positive regulation of interleukin-6 production / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of tumor necrosis factor production / ubiquitin protein ligase activity / double-stranded RNA binding / Ovarian tumor domain proteases / actin cytoskeleton / TRAF3-dependent IRF activation pathway / gene expression / double-stranded DNA binding / defense response to virus / RNA helicase activity / single-stranded RNA binding / Ub-specific processing proteases / protein ubiquitination / RNA helicase / ribonucleoprotein complex / innate immune response / ubiquitin protein ligase binding / positive regulation of gene expression / GTP binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / zinc ion binding / ATP binding / identical protein binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
RNF135, PRY/SPRY domain / zinc finger of C3HC4-type, RING / RIG-I, CARD domain repeat 2 / SPRY-associated / PRY / 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 ...RNF135, PRY/SPRY domain / zinc finger of C3HC4-type, RING / RIG-I, CARD domain repeat 2 / SPRY-associated / PRY / 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. / Butyrophylin-like, SPRY domain / Caspase recruitment domain / Caspase recruitment domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Death-like domain superfamily / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Ring finger / Helicase conserved C-terminal domain / Zinc finger RING-type profile. / Zinc finger, RING-type / 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 / Concanavalin A-like lectin/glucanase domain superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Antiviral innate immune response receptor RIG-I / E3 ubiquitin-protein ligase RNF135
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsWang W / Pyle AM
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI131518 United States
CitationJournal: Nat Commun / Year: 2023
Title: The E3 ligase Riplet promotes RIG-I signaling independent of RIG-I oligomerization.
Authors: Wenshuai Wang / Benjamin Götte / Rong Guo / Anna Marie Pyle /
Abstract: RIG-I is an essential innate immune receptor that responds to infection by RNA viruses. The RIG-I signaling cascade is mediated by a series of post-translational modifications, the most important of ...RIG-I is an essential innate immune receptor that responds to infection by RNA viruses. The RIG-I signaling cascade is mediated by a series of post-translational modifications, the most important of which is ubiquitination of the RIG-I Caspase Recruitment Domains (CARDs) by E3 ligase Riplet. This is required for interaction between RIG-I and its downstream adapter protein MAVS, but the mechanism of action remains unclear. Here we show that Riplet is required for RIG-I signaling in the presence of both short and long dsRNAs, establishing that Riplet activation does not depend upon RIG-I filament formation on long dsRNAs. Likewise, quantitative Riplet-RIG-I affinity measurements establish that Riplet interacts with RIG-I regardless of whether the receptor is bound to RNA. To understand this, we solved high-resolution cryo-EM structures of RIG-I/RNA/Riplet complexes, revealing molecular interfaces that control Riplet-mediated activation and enabling the formulation of a unified model for the role of Riplet in signaling.
History
DepositionFeb 17, 2023-
Header (metadata) releaseNov 15, 2023-
Map releaseNov 15, 2023-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29824.png

Downloads & links

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Map

FileDownload / File: emd_29824.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of RNP end 2
Voxel sizeX=Y=Z: 0.839 Å
Density
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.03486959 - 0.07158984
Average (Standard dev.)-0.0000025592362 (±0.0022160045)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions264264264
Spacing264264264
CellA=B=C: 221.496 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_29824_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 1

Fileemd_29824_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_29824_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of RNP end 2

EntireName: Complex of RNP end 2
Components
  • Complex: Complex of RNP end 2
    • Protein or peptide: Antiviral innate immune response receptor RIG-I
    • Protein or peptide: E3 ubiquitin-protein ligase RNF135
    • RNA: p3dsRNA24a
    • RNA: p3dsRNA24b
  • Ligand: ZINC ION

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Supramolecule #1: Complex of RNP end 2

SupramoleculeName: Complex of RNP end 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Antiviral innate immune response receptor RIG-I

MacromoleculeName: Antiviral innate immune response receptor RIG-I / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 106.740555 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTTEQRRSLQ AFQDYIRKTL DPTYILSYMA PWFREEEVQY IQAEKNNKGP MEAATLFLKF LLELQEEGWF RGFLDALDHA GYSGLYEAI ESWDFKKIEK LEEYRLLLKR LQPEFKTRII PTDIISDLSE CLINQECEEI LQICSTKGMM AGAEKLVECL L RSDKENWP ...String:
MTTEQRRSLQ AFQDYIRKTL DPTYILSYMA PWFREEEVQY IQAEKNNKGP MEAATLFLKF LLELQEEGWF RGFLDALDHA GYSGLYEAI ESWDFKKIEK LEEYRLLLKR LQPEFKTRII PTDIISDLSE CLINQECEEI LQICSTKGMM AGAEKLVECL L RSDKENWP KTLKLALEKE RNKFSELWIV EKGIKDVETE DLEDKMETSD IQIFYQEDPE CQNLSENSCP PSEVSDTNLY SP FKPRNYQ LELALPAMKG KNTIICAPTG CGKTFVSLLI CEHHLKKFPQ GQKGKVVFFA NQIPVYEQQK SVFSKYFERH GYR VTGISG ATAENVPVEQ IVENNDIIIL TPQILVNNLK KGTIPSLSIF TLMIFDECHN TSKQHPYNMI MFNYLDQKLG GSSG PLPQV IGLTASVGVG DAKNTDEALD YICKLCASLD ASVIATVKHN LEELEQVVYK PQKFFRKVES RISDKFKYII AQLMR DTES LAKRICKDLE NLSQIQNREF GTQKYEQWIV TVQKACMVFQ MPDKDEESRI CKALFLYTSH LRKYNDALII SEHARM KDA LDYLKDFFSN VRAAGFDEIE QDLTQRFEEK LQELESVSRD PSNENPKLED LCFILQEEYH LNPETITILF VKTRALV DA LKNWIEGNPK LSFLKPGILT GRGKTNQNTG MTLPAQKCIL DAFKASGDHN ILIATSVADE GIDIAQCNLV ILYEYVGN V IKMIQTRGRG RARGSKCFLL TSNAGVIEKE QINMYKEKMM NDSILRLQTW DEAVFREKIL HIQTHEKFIR DSQEKPKPV PDKENKKLLC RKCKALACYT ADVRVIEECH YTVLGDAFKE CFVSRPHPKP KQFSSFEKRA KIFCARQNCS HDWGIHVKYK TFEIPVIKI ESFVVEDIAT GVQTLYSKWK DFHFEKIPFD PAEMSK

UniProtKB: Antiviral innate immune response receptor RIG-I

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Macromolecule #2: E3 ubiquitin-protein ligase RNF135

MacromoleculeName: E3 ubiquitin-protein ligase RNF135 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.946305 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAGLGLGSAV PVWLAEDDLG CIICQGLLDW PATLPCGHSF CRHCLEALWG ARDARRWACP TCRQGAAQQP HLRKNTLLQD LADKYRRAA REIQAGSDPA HCPCPGSSSL SSAAARPRRR PELQRVAVEK SITEVAQELT ELVEHLVDIV RSLQNQRPLS E SGPDNELS ...String:
MAGLGLGSAV PVWLAEDDLG CIICQGLLDW PATLPCGHSF CRHCLEALWG ARDARRWACP TCRQGAAQQP HLRKNTLLQD LADKYRRAA REIQAGSDPA HCPCPGSSSL SSAAARPRRR PELQRVAVEK SITEVAQELT ELVEHLVDIV RSLQNQRPLS E SGPDNELS ILGKAFSSGV DLSMASPKLV TSDTAAGKIR DILHDLEEIQ EKLQESVTWK EAPEAQMQGE LLEAPSSSSC PL PDQSHPA LRRASRFAQW AIHPTFNLKS LSCSLEVSKD SRTVTVSHRP QPYRWSCERF STSQVLCSQA LSSGKHYWEV DTR NCSHWA VGVASWEMSR DQVLGRTMDS CCVEWKGTSQ LSAWHMVKET VLGSDRPGVV GIWLNLEEGK LAFYSVDNQE KLLY ECTIS ASSPLYPAFW LYGLHPGNYL IIKQVKV

UniProtKB: E3 ubiquitin-protein ligase RNF135

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Macromolecule #3: p3dsRNA24a

MacromoleculeName: p3dsRNA24a / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.885581 KDa
SequenceString:
(GTP)GACGUACGU UUCGCGACUG UAGA

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Macromolecule #4: p3dsRNA24b

MacromoleculeName: p3dsRNA24b / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.788551 KDa
SequenceString:
(UTP)CUACAGUCG CGAAACGUAC GUCC

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 68414
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8g7t


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Overall B value: 131.389
Output model

PDB-8g7u:
Cryo-EM structure of Riplet:RIG-I:dsRNA complex (end-semi-closed end)

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