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- PDB-5e3h: Structural Basis for RNA Recognition and Activation of RIG-I -

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Basic information

Entry
Database: PDB / ID: 5e3h
TitleStructural Basis for RNA Recognition and Activation of RIG-I
Components
  • Probable ATP-dependent RNA helicase DDX58
  • RNA (5'-R(*CP*GP*AP*CP*GP*CP*UP*AP*GP*CP*GP*U)-3')
KeywordsHYDROLASE/RNA / Adenosine Triphosphatases / Adenosine Triphosphate / DEAD-box RNA Helicases / Enzyme Activation / Fluorometry / Humans / Immunity / Innate / Models / Molecular / Nucleic Acid Conformation / Pliability / Protein Binding / Protein Structure / Tertiary / Proteolysis / RNA / Double-Stranded / RNA-Binding Proteins / Scattering / Small Angle / Structure-Activity Relationship / Substrate Specificity / Trypsin / HYDROLASE / 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 / cytoplasmic pattern recognition receptor signaling pathway / cellular response to exogenous dsRNA / response to exogenous dsRNA / 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 / positive regulation of interleukin-6 production / ruffle membrane / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of DNA-binding transcription factor activity / Ovarian tumor domain proteases / actin cytoskeleton / positive regulation of tumor necrosis factor production / double-stranded RNA binding / 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
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / 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: 2.7 Å
AuthorsJiang, F. / Miller, M.T. / Marcotrigiano, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nature / Year: 2011
Title: Structural basis of RNA recognition and activation by innate immune receptor RIG-I.
Authors: Jiang, F. / Ramanathan, A. / Miller, M.T. / Tang, G.Q. / Gale, M. / Patel, S.S. / Marcotrigiano, J.
History
DepositionOct 2, 2015Deposition site: RCSB / Processing site: RCSB
SupersessionNov 18, 2015ID: 3TMI
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Derived calculations / Category: pdbx_struct_oper_list / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable ATP-dependent RNA helicase DDX58
B: RNA (5'-R(*CP*GP*AP*CP*GP*CP*UP*AP*GP*CP*GP*U)-3')
C: RNA (5'-R(*CP*GP*AP*CP*GP*CP*UP*AP*GP*CP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,27410
Polymers88,5503
Non-polymers7247
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-60 kcal/mol
Surface area32530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.030, 176.030, 108.071
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein / RNA chain , 2 types, 3 molecules ABC

#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.: 1 / Fragment: UNP residues 232-925
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX58 / Plasmid: RIG-I (232-925), RIG-I DeltaCARD / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(de3) / References: UniProt: O95786, RNA helicase
#2: RNA chain RNA (5'-R(*CP*GP*AP*CP*GP*CP*UP*AP*GP*CP*GP*U)-3')


Mass: 4477.723 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 7 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


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


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% w/v PEG3350, 0.25 M sodium thiocyanate, 100 mM MOPS, pH 7.8, 3% v/v 2,2,2-trifluoroethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 27622 / % possible obs: 100 % / Redundancy: 38.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.24 / Rpim(I) all: 0.039 / Net I/σ(I): 16.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allCC1/2Rpim(I) all% possible all
2.7-2.85352.841.613810939490.4150.48100
8.54-5035.40.06657.53545810020.9990.01199.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TMI

3tmi
PDB Unreleased entry


Resolution: 2.7→34.974 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2679 3721 7.24 %Random selection
Rwork0.2335 ---
obs0.2361 27571 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→34.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4967 509 41 0 5517
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025667
X-RAY DIFFRACTIONf_angle_d0.6297795
X-RAY DIFFRACTIONf_dihedral_angle_d11.2612103
X-RAY DIFFRACTIONf_chiral_restr0.026913
X-RAY DIFFRACTIONf_plane_restr0.003909
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.73420.45021330.38821757X-RAY DIFFRACTION100
2.7342-2.77020.39061370.36981769X-RAY DIFFRACTION100
2.7702-2.80810.38931380.3561770X-RAY DIFFRACTION100
2.8081-2.84820.38321410.35471761X-RAY DIFFRACTION100
2.8482-2.89070.38921360.33621753X-RAY DIFFRACTION100
2.8907-2.93590.32711420.33481796X-RAY DIFFRACTION100
2.9359-2.9840.36191360.31971757X-RAY DIFFRACTION100
2.984-3.03540.35481430.30191785X-RAY DIFFRACTION100
3.0354-3.09060.31091330.30351762X-RAY DIFFRACTION100
3.0906-3.150.39731350.28491759X-RAY DIFFRACTION100
3.15-3.21420.34131380.28811756X-RAY DIFFRACTION100
3.2142-3.28410.3661430.29051784X-RAY DIFFRACTION100
3.2841-3.36040.31581410.26121753X-RAY DIFFRACTION100
3.3604-3.44440.2741390.26031788X-RAY DIFFRACTION100
3.4444-3.53740.3271330.25341727X-RAY DIFFRACTION100
3.5374-3.64140.30221400.25431781X-RAY DIFFRACTION100
3.6414-3.75880.31241390.23571782X-RAY DIFFRACTION100
3.7588-3.8930.23511350.22451766X-RAY DIFFRACTION100
3.893-4.04860.25821420.22181778X-RAY DIFFRACTION100
4.0486-4.23260.27391350.20551749X-RAY DIFFRACTION100
4.2326-4.45530.26311380.19151753X-RAY DIFFRACTION100
4.4553-4.73380.22131310.18181785X-RAY DIFFRACTION100
4.7338-5.09830.22881420.18321746X-RAY DIFFRACTION100
5.0983-5.60950.21461410.19411783X-RAY DIFFRACTION100
5.6095-6.41680.2381430.22921756X-RAY DIFFRACTION100
6.4168-8.06810.22841310.20991775X-RAY DIFFRACTION100
8.0681-34.97650.20421360.20391778X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.59930.58660.48921.09540.21321.0861-0.03550.03870.05320.0372-0.12910.11540.1736-0.3185-0.04650.4626-0.32910.01550.8414-0.06760.540616.6005-77.34497.2609
21.9178-0.9930.87190.6394-0.23611.5553-0.25990.69310.5965-0.2161-0.16670.2225-0.787-0.226-0.00570.8218-0.0937-0.36171.0610.16341.001318.4674-45.761-7.8881
31.94171.20070.27092.3362-0.87831.1838-0.2736-0.11180.0955-0.1635-0.03380.13520.0316-0.3658-0.02870.5336-0.2213-0.02521.0423-0.06970.667222.6486-67.052511.289
41.57760.19691.00251.56170.09860.6375-0.11340.03970.3474-0.0325-0.05190.3481-0.0472-0.3506-0.19180.5053-0.0206-0.24781.5703-0.18451.1097-7.6565-64.6061-13.4125
51.97180.41130.99062.5506-1.50091.6805-0.2135-0.0931.06180.4793-0.71320.7171-0.5746-1.3562-0.14840.5996-0.0079-0.12071.245-0.32171.10335.1587-59.36656.2361
60.2090.10990.37441.174-0.20660.8166-0.1483-0.32110.40210.8977-0.25030.1669-0.0012-1.1420.01420.6653-0.0781-0.15651.2164-0.17960.94166.5397-61.5013.1908
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 241 through 506 )
2X-RAY DIFFRACTION2chain 'A' and (resid 507 through 674 )
3X-RAY DIFFRACTION3chain 'A' and (resid 675 through 792 )
4X-RAY DIFFRACTION4chain 'A' and (resid 793 through 922 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 12 )
6X-RAY DIFFRACTION6chain 'C' and (resid 3 through 14 )

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