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- PDB-7jl3: Cryo-EM structure of RIG-I:dsRNA filament in complex with RIPLET ... -

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Basic information

Entry
Database: PDB / ID: 7jl3
TitleCryo-EM structure of RIG-I:dsRNA filament in complex with RIPLET PrySpry domain (trimer)
Components
  • Antiviral innate immune response receptor RIG-I
  • E3 ubiquitin-protein ligase RNF135
  • dsRNA strand 2
  • dsRNA strand1
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 / 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
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 / helical reconstruction / cryo EM / Resolution: 4.2 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 1.1Jan 20, 2021Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 17, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Antiviral innate immune response receptor RIG-I
B: E3 ubiquitin-protein ligase RNF135
C: Antiviral innate immune response receptor RIG-I
D: E3 ubiquitin-protein ligase RNF135
E: Antiviral innate immune response receptor RIG-I
F: E3 ubiquitin-protein ligase RNF135
X: dsRNA strand1
Y: dsRNA strand 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)340,00920
Polymers338,1498
Non-polymers1,86012
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain "C"
21chain "A"
31chain "E"
12chain "B"
22chain "D"
32chain "F"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
111SERPHEG1 - 650
121ADPADPH
131ALFALFI
141MGMGJ
211SERPHEA1 - 650
221ADPADPB
231ALFALFC
241MGMGD
311SERPHEM1 - 650
321ADPADPN
331ALFALFO
341MGMGP
112GLNVALF1 - 169
212GLNVALL1 - 169
312GLNVALR1 - 169

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.238512344136, -0.9711374443, 0.00198140662128), (0.971139094738, 0.238513539755, 0.000387330950736), (-0.000848743896532, 0.00183183821949, 0.999997961999)281.348843203, -34.2087870785, 46.1153192331
2given(-0.884121260797, -0.467251219212, 0.00242782878392), (0.467253967815, -0.884122871664, 0.000690913146667), (0.0018236689462, 0.00174526363479, 0.999996814138)382.081527685, 230.228150745, 91.931983386
3given(0.243279105848, 0.969937941903, -0.00597206124758), (-0.969940292298, 0.243305876019, 0.00425206674451), (0.00557727846049, 0.00475810383649, 0.999973126845)-33.9066111802, 280.040274517, -47.837515793
4given(0.236687425243, -0.971568801065, -0.00575565186604), (0.97153919779, 0.236729959358, -0.00839723166331), (0.00952102353172, -0.00360432225513, 0.999948178143)282.970805898, -32.6701209476, 45.0966440749

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Components

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Protein , 2 types, 6 molecules ACEBDF

#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.: 3 / 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
#2: 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.: 3 / 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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RNA chain , 2 types, 2 molecules XY

#3: RNA chain dsRNA strand1


Mass: 13550.107 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: RNA chain dsRNA strand 2


Mass: 13360.916 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 12 molecules

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


Mass: 427.201 Da / Num. of mol.: 3 / 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.: 3 / Source method: obtained synthetically / Formula: AlF4
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Ternary complex of dsRNA-bound RIG-I filament with RIPLET PrySpry domain
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 FIELDBright-field microscopy
Image recordingElectron dose: 19.424 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 76.1005 ° / Axial rise/subunit: 46.2706 Å / Axial symmetry: C1
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39718 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 98.75 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007521826
ELECTRON MICROSCOPYf_angle_d0.867829932
ELECTRON MICROSCOPYf_chiral_restr0.04743462
ELECTRON MICROSCOPYf_plane_restr0.00453435
ELECTRON MICROSCOPYf_dihedral_angle_d14.40933633
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
12AELECTRON MICROSCOPYNCS constraints0.000709447079495
13EELECTRON MICROSCOPYNCS constraints0.0007023311317
22DELECTRON MICROSCOPYNCS constraints0.000711277415258
23FELECTRON MICROSCOPYNCS constraints0.000714121215817

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