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- EMDB-22369: Cryo-EM structure of RIG-I:dsRNA in complex with RIPLET PrySpry d... -

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Basic information

Entry
Database: EMDB / ID: EMD-22369
TitleCryo-EM structure of RIG-I:dsRNA in complex with RIPLET PrySpry domain (monomer)
Map data
Sample
  • Complex: Ternary complex of RIG-I:dsRNA:RIPLET PrySpry
    • Protein or peptide: Antiviral innate immune response receptor RIG-I
    • RNA: dsRNA strand 1
    • RNA: dsRNA strand 2
    • Protein or peptide: E3 ubiquitin-protein ligase RNF135
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: TETRAFLUOROALUMINATE ION
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
KeywordsInnate 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 / 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 / RING-type E3 ubiquitin transferase / DDX58/IFIH1-mediated induction of interferon-alpha/beta / protein homooligomerization / response to virus / Evasion by RSV of host interferon responses / ISG15 antiviral mechanism / positive regulation of interleukin-6 production / ruffle membrane / protein polyubiquitination / ubiquitin-protein transferase activity / cytoplasmic stress granule / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of tumor necrosis factor production / ubiquitin protein ligase activity / Ovarian tumor domain proteases / actin cytoskeleton / double-stranded RNA binding / TRAF3-dependent IRF activation pathway / double-stranded DNA binding / chromatin extrusion motor activity / gene expression / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / defense response to virus / DNA clamp loader activity / single-stranded RNA binding / RNA helicase activity / 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 / metal ion binding / cytosol / cytoplasm
Similarity search - Function
RNF135, PRY/SPRY domain / : / zinc finger of C3HC4-type, RING / 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 ...RNF135, PRY/SPRY domain / : / zinc finger of C3HC4-type, RING / 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 / 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: 3.9 Å
AuthorsKato K / Ahmad S
Funding support United States, 1 items
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, 2020-
Header (metadata) releaseDec 9, 2020-
Map releaseDec 9, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.107
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.107
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7jl1
  • Surface level: 0.107
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7jl1
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22369.png

Downloads & links

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Map

FileDownload / File: emd_22369.map.gz / Format: CCP4 / Size: 12.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.04 Å/pix.
x 114 pix.
= 118.791 Å		1.04 Å/pix.
x 126 pix.
= 131.296 Å		1.04 Å/pix.
x 230 pix.
= 239.667 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.04203 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.107 / Movie #1: 0.107
Minimum - Maximum-0.5968274 - 0.8471623
Average (Standard dev.)0.000000000000628 (±0.032499462)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin764393
Dimensions126230114
Spacing114126230
CellA: 118.79142 Å / B: 131.29578 Å / C: 239.6669 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.04202631578951.04203174603171.0420304347826
M x/y/z114126230
origin x/y/z0.0000.0000.000
length x/y/z118.791131.296239.667
α/β/γ90.00090.00090.000
start NX/NY/NZ937643
NX/NY/NZ114126230
MAP C/R/S321
start NC/NR/NS437693
NC/NR/NS230126114
D min/max/mean-0.5970.8470.000

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Supplemental data

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Sample components

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Entire : Ternary complex of RIG-I:dsRNA:RIPLET PrySpry

EntireName: Ternary complex of RIG-I:dsRNA:RIPLET PrySpry
Components
  • Complex: Ternary complex of RIG-I:dsRNA:RIPLET PrySpry
    • Protein or peptide: Antiviral innate immune response receptor RIG-I
    • RNA: dsRNA strand 1
    • RNA: dsRNA strand 2
    • Protein or peptide: E3 ubiquitin-protein ligase RNF135
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: TETRAFLUOROALUMINATE ION
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: Ternary complex of RIG-I:dsRNA:RIPLET PrySpry

SupramoleculeName: Ternary complex of RIG-I:dsRNA:RIPLET PrySpry / 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: 1 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 82.72407 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: METSDIQIFY QEDPECQNLS ENSCPPSEVS DTNLYSPFKP RNYQLELALP AMKGKNTIIC APTGCGKTFV SLLICEHHLK KFPQGQKGK VVFFANQIPV YEQQKSVFSK YFERHGYRVT GISGATAENV PVEQIVENND IIILTPQILV NNLKKGTIPS L SIFTLMIF ...String:
METSDIQIFY QEDPECQNLS ENSCPPSEVS DTNLYSPFKP RNYQLELALP AMKGKNTIIC APTGCGKTFV SLLICEHHLK KFPQGQKGK VVFFANQIPV YEQQKSVFSK YFERHGYRVT GISGATAENV PVEQIVENND IIILTPQILV NNLKKGTIPS L SIFTLMIF DECHNTSKQH PYNMIMFNYL DQKLGGSSGP LPQVIGLTAS VGVGDAKNTD EALDYICKLC ASLDASVIAT VK HNLEELE QVVYKPQKFF RKVESRISDK FKYIIAQLMR DTESLAKRIC KDLENLSQIQ NREFGTQKYE QWIVTVQKAC MVF QMPDKD EESRICKALF LYTSHLRKYN DALIISEHAR MKDALDYLKD FFSNVRAAGF DEIEQDLTQR FEEKLQELES VSRD PSNEN PKLEDLCFIL QEEYHLNPET ITILFVKTRA LVDALKNWIE GNPKLSFLKP GILTGRGKTN QNTGMTLPAQ KCILD AFKA SGDHNILIAT SVADEGIDIA QCNLVILYEY VGNVIKMIQT RGRGRARGSK CFLLTSNAGV IEKEQINMYK EKMMND SIL RLQTWDEAVF REKILHIQTH EKFIRDSQEK PKPVPDKENK KLLCRKCKAL ACYTADVRVI EECHYTVLGD AFKECFV SR PHPKPKQFSS FEKRAKIFCA RQNCSHDWGI HVKYKTFEIP VIKIESFVVE DIATGVQTLY SKWKDFHFEK IPFDPAEM S K

UniProtKB: Antiviral innate immune response receptor RIG-I

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Macromolecule #4: E3 ubiquitin-protein ligase RNF135

MacromoleculeName: E3 ubiquitin-protein ligase RNF135 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.021904 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
RRASRFAQWA IHPTFNLKSL SCSLEVSKDS RTVTVSHRPQ PYRWSCERFS TSQVLCSQAL SSGKHYWEVD TRNCSHWAVG VASWEMSRD QVLGRTMDSC CVEWKGTSQL SAWHMVKETV LGSDRPGVVG IWLNLEEGKL AFYSVDNQEK LLYECTISAS S PLYPAFWL YGLHPGNYLI IKQVKV

UniProtKB: E3 ubiquitin-protein ligase RNF135

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Macromolecule #2: dsRNA strand 1

MacromoleculeName: dsRNA strand 1 / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.486731 KDa
SequenceString:
GACUGACUGA CUGA

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Macromolecule #3: dsRNA strand 2

MacromoleculeName: dsRNA strand 2 / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.423667 KDa
SequenceString:
UCAGUCAGUC AGUC

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Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

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Macromolecule #6: TETRAFLUOROALUMINATE ION

MacromoleculeName: TETRAFLUOROALUMINATE ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: ALF
Molecular weightTheoretical: 102.975 Da
Chemical component information

ChemComp-ALF:
TETRAFLUOROALUMINATE ION

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 1 / 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 statefilament

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Sample preparation

BufferpH: 7.5
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 19.424 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Featureless cylinder
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 74079
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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