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- PDB-5f98: Crystal structure of RIG-I in complex with Cap-0 RNA -

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Basic information

Entry
Database: PDB / ID: 5f98
TitleCrystal structure of RIG-I in complex with Cap-0 RNA
Components
  • Probable ATP-dependent RNA helicase DDX58
  • RNA (5'-R(P*GP*AP*AP*UP*AP*UP*AP*AP*UP*AP*GP*UP*GP*AP*UP*AP*UP*UP*AP*UP*AP*UP*UP*C)-3')
Keywordshydrolase/rna / Complex / RIG-I / capped RNA / self versus non-self / innate immunity / hydrolase-rna complex
Function / homology
Function and homology information


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 / pattern recognition receptor activity / TRAF6 mediated IRF7 activation ...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 / pattern recognition receptor activity / TRAF6 mediated IRF7 activation / response to exogenous dsRNA / cellular response to exogenous dsRNA / cytoplasmic pattern recognition receptor signaling pathway / positive regulation of interferon-alpha production / antiviral innate immune response / TRAF6 mediated NF-kB activation / bicellular tight junction / regulation of cell migration / positive regulation of defense response to virus by host / positive regulation of interferon-beta production / Negative regulators of DDX58/IFIH1 signaling / positive regulation of interleukin-8 production / response to virus / DDX58/IFIH1-mediated induction of interferon-alpha/beta / ISG15 antiviral mechanism / ruffle membrane / positive regulation of interleukin-6 production / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of DNA-binding transcription factor activity / Ovarian tumor domain proteases / actin cytoskeleton / double-stranded RNA binding / positive regulation of tumor necrosis factor production / gene expression / TRAF3-dependent IRF activation pathway / double-stranded DNA binding / defense response to virus / RNA helicase activity / single-stranded RNA binding / RNA helicase / Ub-specific processing proteases / ribonucleoprotein complex / innate immune response / ubiquitin protein ligase binding / GTP binding / positive regulation of gene expression / 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 / cytosol / cytoplasm
Similarity search - Function
phosphoenolpyruvate carboxylase, domain 3 - #30 / phosphoenolpyruvate carboxylase, domain 3 / RIG-I-like receptor, C-terminal regulatory domain / RIG-I, CARD domain repeat 2 / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / 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 ...phosphoenolpyruvate carboxylase, domain 3 - #30 / phosphoenolpyruvate carboxylase, domain 3 / RIG-I-like receptor, C-terminal regulatory domain / RIG-I, CARD domain repeat 2 / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / 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 / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Death-like domain superfamily / Beta Complex / 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 nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE / RNA / RNA (> 10) / Antiviral innate immune response receptor RIG-I
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.28 Å
AuthorsWang, C. / Marcotrigiano, J. / Miller, M. / Jiang, F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structural basis for m7G recognition and 2'-O-methyl discrimination in capped RNAs by the innate immune receptor RIG-I.
Authors: Devarkar, S.C. / Wang, C. / Miller, M.T. / Ramanathan, A. / Jiang, F. / Khan, A.G. / Patel, S.S. / Marcotrigiano, J.
History
DepositionDec 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references / Structure summary
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Revision 2.0Mar 6, 2024Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable ATP-dependent RNA helicase DDX58
B: RNA (5'-R(P*GP*AP*AP*UP*AP*UP*AP*AP*UP*AP*GP*UP*GP*AP*UP*AP*UP*UP*AP*UP*AP*UP*UP*C)-3')
C: Probable ATP-dependent RNA helicase DDX58
D: RNA (5'-R(P*GP*AP*AP*UP*AP*UP*AP*AP*UP*AP*GP*UP*GP*AP*UP*AP*UP*UP*AP*UP*AP*UP*UP*C)-3')
E: Probable ATP-dependent RNA helicase DDX58
F: RNA (5'-R(P*GP*AP*AP*UP*AP*UP*AP*AP*UP*AP*GP*UP*GP*AP*UP*AP*UP*UP*AP*UP*AP*UP*UP*C)-3')
G: Probable ATP-dependent RNA helicase DDX58
H: RNA (5'-R(P*GP*AP*AP*UP*AP*UP*AP*AP*UP*AP*GP*UP*GP*AP*UP*AP*UP*UP*AP*UP*AP*UP*UP*C)-3')
I: Probable ATP-dependent RNA helicase DDX58
J: RNA (5'-R(P*GP*AP*AP*UP*AP*UP*AP*AP*UP*AP*GP*UP*GP*AP*UP*AP*UP*UP*AP*UP*AP*UP*UP*C)-3')
K: Probable ATP-dependent RNA helicase DDX58
L: RNA (5'-R(P*GP*AP*AP*UP*AP*UP*AP*AP*UP*AP*GP*UP*GP*AP*UP*AP*UP*UP*AP*UP*AP*UP*UP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)526,75330
Polymers523,46612
Non-polymers3,28818
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32090 Å2
ΔGint-321 kcal/mol
Surface area183490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.180, 174.570, 309.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 79594.734 Da / Num. of mol.: 6
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: RNA chain
RNA (5'-R(P*GP*AP*AP*UP*AP*UP*AP*AP*UP*AP*GP*UP*GP*AP*UP*AP*UP*UP*AP*UP*AP*UP*UP*C)-3')


Mass: 7649.559 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: Cap-0 HP RNA (24-MER) / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-M7G / 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE


Mass: 458.235 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C11H18N5O11P2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 20% (w/v) PEG 3350, 0.2 M NaSCN, 100 mM MOPS (pH 7.8), 3.5% (v/v) 2,2,2-trifluoroethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 3.1→84.003 Å / Num. obs: 92301 / % possible obs: 99.8 % / Redundancy: 14 % / Rmerge(I) obs: 0.56 / Net I/σ(I): 7.1
Reflection shellResolution: 3.3→3.4 Å / Redundancy: 11.8 % / Mean I/σ(I) obs: 1.9 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E3H

5e3h


Resolution: 3.28→84.003 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2774 1999 2.17 %
Rwork0.221 --
obs0.2222 92301 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.28→84.003 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29492 3054 162 0 32708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00233702
X-RAY DIFFRACTIONf_angle_d0.54146489
X-RAY DIFFRACTIONf_dihedral_angle_d11.00912394
X-RAY DIFFRACTIONf_chiral_restr0.0225469
X-RAY DIFFRACTIONf_plane_restr0.0035427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.28-3.3620.3571410.29496384X-RAY DIFFRACTION99
3.362-3.45290.35231420.28376384X-RAY DIFFRACTION100
3.4529-3.55450.31511400.27926358X-RAY DIFFRACTION99
3.5545-3.66930.3421410.26396365X-RAY DIFFRACTION99
3.6693-3.80040.31881410.24746368X-RAY DIFFRACTION99
3.8004-3.95260.29391420.23626422X-RAY DIFFRACTION99
3.9526-4.13250.30061420.23046394X-RAY DIFFRACTION99
4.1325-4.35030.2761420.22036399X-RAY DIFFRACTION100
4.3503-4.62290.28971430.18826458X-RAY DIFFRACTION99
4.6229-4.97980.221430.1776444X-RAY DIFFRACTION100
4.9798-5.48080.23381430.19326489X-RAY DIFFRACTION99
5.4808-6.27370.27731440.22146501X-RAY DIFFRACTION99
6.2737-7.90320.26821460.21476575X-RAY DIFFRACTION99
7.9032-84.03080.2171490.18716761X-RAY DIFFRACTION99

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