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- PDB-7jl1: Cryo-EM structure of RIG-I:dsRNA in complex with RIPLET PrySpry d... -

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Basic information

Entry
Database: PDB / ID: 7jl1
TitleCryo-EM structure of RIG-I:dsRNA in complex with RIPLET PrySpry domain (monomer)
Components
  • (dsRNA strand ...) x 2
  • Antiviral innate immune response receptor RIG-I
  • E3 ubiquitin-protein ligase RNF135
KeywordsHYDROLASE/TRANSFERASE/RNA / Innate immunity / E3 ligase / helicase / antiviral signaling / RLR / dsRNA sensor / HYDROLASE-TRANSFERASE-RNA complex
Function / homology
Function and homology information


RIG-I binding / regulation of type III interferon production / free ubiquitin chain polymerization / RIG-I signaling pathway / positive regulation of myeloid dendritic cell cytokine production / OAS antiviral response / detection of virus / positive regulation of response to cytokine stimulus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of granulocyte macrophage colony-stimulating factor production ...RIG-I binding / regulation of type III interferon production / free ubiquitin chain polymerization / RIG-I signaling pathway / positive regulation of myeloid dendritic cell cytokine production / OAS antiviral response / detection of virus / positive regulation of response to cytokine stimulus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of granulocyte macrophage colony-stimulating factor production / Modulation of host responses by IFN-stimulated genes / TRAF6 mediated IRF7 activation / cytoplasmic pattern recognition receptor signaling pathway / regulation of innate immune response / pattern recognition receptor activity / cellular response to exogenous dsRNA / RSV-host interactions / response to exogenous dsRNA / TRAF6 mediated NF-kB activation / positive regulation of interferon-alpha production / protein K63-linked ubiquitination / bicellular tight junction / ribonucleoprotein complex binding / positive regulation of defense response to virus by host / antiviral innate immune response / positive regulation of interferon-beta production / regulation of cell migration / positive regulation of interleukin-8 production / Negative regulators of DDX58/IFIH1 signaling / protein homooligomerization / DDX58/IFIH1-mediated induction of interferon-alpha/beta / RING-type E3 ubiquitin transferase / Evasion by RSV of host interferon responses / positive regulation of interleukin-6 production / ISG15 antiviral mechanism / response to virus / ruffle membrane / protein polyubiquitination / cytoplasmic stress granule / ubiquitin-protein transferase activity / positive regulation of tumor necrosis factor production / SARS-CoV-1 activates/modulates innate immune responses / ubiquitin protein ligase activity / Ovarian tumor domain proteases / actin cytoskeleton / double-stranded RNA binding / TRAF3-dependent IRF activation pathway / double-stranded DNA binding / defense response to virus / gene expression / 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 / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / zinc ion binding / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
RNF135, PRY/SPRY domain / : / zinc finger of C3HC4-type, RING / SPRY domain / RIG-I, CARD domain repeat 2 / 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 / : ...RNF135, PRY/SPRY domain / : / zinc finger of C3HC4-type, RING / SPRY domain / RIG-I, CARD domain repeat 2 / 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 / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Death-like domain superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Ring finger / Helicase conserved C-terminal domain / Zinc finger RING-type profile. / Zinc finger, RING-type / helicase superfamily c-terminal domain / Concanavalin A-like lectin/glucanase domain superfamily / 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 / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / RNA / RNA (> 10) / Antiviral innate immune response receptor RIG-I / E3 ubiquitin-protein ligase RNF135
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsKato, K. / Ahmad, S. / Hur, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Mol Cell / Year: 2021
Title: Structural analysis of RIG-I-like receptors reveals ancient rules of engagement between diverse RNA helicases and TRIM ubiquitin ligases.
Authors: Kazuki Kato / Sadeem Ahmad / Zixiang Zhu / Janet M Young / Xin Mu / Sehoon Park / Harmit S Malik / Sun Hur /
Abstract: RNA helicases and E3 ubiquitin ligases mediate many critical functions in cells, but their actions have largely been studied in distinct biological contexts. Here, we uncover evolutionarily conserved ...RNA helicases and E3 ubiquitin ligases mediate many critical functions in cells, but their actions have largely been studied in distinct biological contexts. Here, we uncover evolutionarily conserved rules of engagement between RNA helicases and tripartite motif (TRIM) E3 ligases that lead to their functional coordination in vertebrate innate immunity. Using cryoelectron microscopy and biochemistry, we show that RIG-I-like receptors (RLRs), viral RNA receptors with helicase domains, interact with their cognate TRIM/TRIM-like E3 ligases through similar epitopes in the helicase domains. Their interactions are avidity driven, restricting the actions of TRIM/TRIM-like proteins and consequent immune activation to RLR multimers. Mass spectrometry and phylogeny-guided biochemical analyses further reveal that similar rules of engagement may apply to diverse RNA helicases and TRIM/TRIM-like proteins. Our analyses suggest not only conserved substrates for TRIM proteins but also, unexpectedly, deep evolutionary connections between TRIM proteins and RNA helicases, linking ubiquitin and RNA biology throughout animal evolution.
History
DepositionJul 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.0Dec 9, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 9, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.0Dec 9, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.1Jan 20, 2021Group: Database references / Category: citation
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Structure visualization

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Assembly

Deposited unit
A: Antiviral innate immune response receptor RIG-I
X: dsRNA strand 1
Y: dsRNA strand 2
B: E3 ubiquitin-protein ligase RNF135
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,2768
Polymers112,6564
Non-polymers6204
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area7910 Å2
ΔGint-77 kcal/mol
Surface area42420 Å2

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Antiviral innate immune response receptor RIG-I / DEAD box protein 58 / Probable ATP-dependent RNA helicase DDX58 / RIG-I-like receptor 1 / RLR-1 / ...DEAD box protein 58 / Probable ATP-dependent RNA helicase DDX58 / RIG-I-like receptor 1 / RLR-1 / Retinoic acid-inducible gene 1 protein / RIG-1 / Retinoic acid-inducible gene I protein / RIG-I


Mass: 82724.070 Da / Num. of mol.: 1 / Fragment: UNP residues 159-880
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX58 / Production host: Escherichia coli (E. coli) / References: UniProt: O95786, RNA helicase
#4: Protein E3 ubiquitin-protein ligase RNF135 / RIG-I E3 ubiquitin ligase / REUL / RING finger protein 135 / RING finger protein leading to RIG-I ...RIG-I E3 ubiquitin ligase / REUL / RING finger protein 135 / RING finger protein leading to RIG-I activation / Riplet / RING-type E3 ubiquitin transferase RNF135


Mass: 21021.904 Da / Num. of mol.: 1 / Fragment: RIPLET PrySpry domain (UNP residues 249-432)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF135, L13 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IUD6, RING-type E3 ubiquitin transferase

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DsRNA strand ... , 2 types, 2 molecules XY

#2: RNA chain dsRNA strand 1


Mass: 4486.731 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: RNA chain dsRNA strand 2


Mass: 4423.667 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 4 molecules

#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ternary complex of RIG-I:dsRNA:RIPLET PrySpry / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
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
Image recordingElectron dose: 19.424 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18rc6_3830: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74079 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.017335
ELECTRON MICROSCOPYf_angle_d0.87510058
ELECTRON MICROSCOPYf_dihedral_angle_d14.9571216
ELECTRON MICROSCOPYf_chiral_restr0.0541164
ELECTRON MICROSCOPYf_plane_restr0.0051158

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