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- PDB-4bpb: STRUCTURAL INSIGHTS INTO RNA RECOGNITION BY RIG-I -

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Basic information

Entry
Database: PDB / ID: 4bpb
TitleSTRUCTURAL INSIGHTS INTO RNA RECOGNITION BY RIG-I
Components
  • 5'-R(*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP)-3'
  • PROBABLE ATP-DEPENDENT RNA HELICASE DDX58
KeywordsHYDROLASE/RNA / HYDROLASE-RNA COMPLEX / ADENOSINE TRIPHOSPHATE / DEAD-BOX RNA HELICASES / DOUBLE-STRANDED / SIGNAL TRANSDUCTION
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 / cellular response to exogenous dsRNA / 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 / 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 / Ub-specific processing proteases / 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 / cytosol / cytoplasm
Similarity search - Function
phosphoenolpyruvate carboxylase, domain 3 - #30 / phosphoenolpyruvate carboxylase, domain 3 / RIG-I-like receptor, C-terminal regulatory domain / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / 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 ...phosphoenolpyruvate carboxylase, domain 3 - #30 / phosphoenolpyruvate carboxylase, domain 3 / RIG-I-like receptor, C-terminal regulatory domain / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / 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 / Death-like domain superfamily / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / 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
RNA / Antiviral innate immune response receptor RIG-I
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.584 Å
AuthorsLuo, D. / Pyle, A.M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: Structural Insights Into RNA Recognition by Rig-I.
Authors: Luo, D. / Ding, S.C. / Vela, A. / Kohlway, A. / Lindenbach, B.D. / Pyle, A.M.
History
DepositionMay 23, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROBABLE ATP-DEPENDENT RNA HELICASE DDX58
C: 5'-R(*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP)-3'
D: 5'-R(*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5535
Polymers86,3913
Non-polymers1612
Water1,928107
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-47.9 kcal/mol
Surface area34560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.618, 76.208, 219.825
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 / RETINOIC ACID-INDUCIBLE GENE 1 PROTEIN / RIG-1 / RETINOIC ACID-INDUCIBLE GENE ...DEAD BOX PROTEIN 58 / RETINOIC ACID-INDUCIBLE GENE 1 PROTEIN / RIG-1 / RETINOIC ACID-INDUCIBLE GENE I PROTEIN / RIG-I


Mass: 79977.141 Da / Num. of mol.: 1 / Fragment: RESIDUES 230-925
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O95786, RNA helicase
#2: RNA chain 5'-R(*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP)-3'


Mass: 3206.980 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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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: 2.31 Å3/Da / Density % sol: 46.72 % / Description: NONE
Crystal growpH: 9
Details: 0.1 M BICINE, PH 9.0, 22.5 % POLYETHYLENE GLYCOL 6,000

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→45 Å / Num. obs: 25750 / % possible obs: 99 % / Observed criterion σ(I): 1.56 / Redundancy: 5.2 % / Biso Wilson estimate: 52.91 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.22
Reflection shellResolution: 2.58→2.68 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.56 / % possible all: 92

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.584→39.928 Å / SU ML: 0.35 / σ(F): 1.36 / Phase error: 26.58 / Stereochemistry target values: ML / Details: BETTER REFINEMENT OF PDB ENTRY 2YKG
RfactorNum. reflection% reflection
Rfree0.2554 1311 5.1 %
Rwork0.1947 --
obs0.1978 25746 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.584→39.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4978 424 6 107 5515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035566
X-RAY DIFFRACTIONf_angle_d0.7357622
X-RAY DIFFRACTIONf_dihedral_angle_d13.672102
X-RAY DIFFRACTIONf_chiral_restr0.053879
X-RAY DIFFRACTIONf_plane_restr0.003894
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.584-2.68750.32881410.27522478X-RAY DIFFRACTION93
2.6875-2.80980.37131330.28152722X-RAY DIFFRACTION99
2.8098-2.95780.30261480.25342675X-RAY DIFFRACTION100
2.9578-3.14310.32381600.2292670X-RAY DIFFRACTION100
3.1431-3.38570.27511260.21312739X-RAY DIFFRACTION100
3.3857-3.72610.26911520.18962699X-RAY DIFFRACTION100
3.7261-4.26480.25371510.16462756X-RAY DIFFRACTION100
4.2648-5.37110.19651520.15472770X-RAY DIFFRACTION100
5.3711-39.93240.22641480.19162926X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4450.3061-0.32961.8883-0.28422.17860.0013-0.1837-0.14580.05040.0573-0.14820.00770.2033-0.02380.10810.00520.00580.13630.09470.18949.349813.354116.4757
20.39940.2776-0.48182.0049-0.73751.1576-0.13120.0317-0.0953-0.00060.01730.140.421-0.06680.09530.3222-0.0892-0.00090.33850.02770.3062-9.0759-18.886522.6294
32.76050.1736-0.70782.7936-0.00073.7796-0.1373-0.0619-0.42160.3693-0.34510.07170.1384-0.05240.4530.47820.02690.08910.45060.01370.2925-11.82377.105749.851
43.2411-0.8778-1.05451.6438-0.49350.76090.23820.2294-0.4774-0.36340.38280.73910.3567-1.191-0.30010.3971-0.096-0.10120.50650.12610.4262-11.66741.937428.0065
51.25840.47510.0570.50860.46910.6101-0.0014-0.0242-0.1958-0.24960.50780.5287-0.1244-0.61020.12530.33730.0021-0.29470.59520.48890.6783-9.52850.404130.8073
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 236 THROUGH 455 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 456 THROUGH 795 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 796 THROUGH 927 )
4X-RAY DIFFRACTION4CHAIN C AND (RESID 1 THROUGH 10 )
5X-RAY DIFFRACTION5CHAIN D AND (RESID 1 THROUGH 10 )

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