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- PDB-4ay2: Capturing 5' tri-phosphorylated RNA duplex by RIG-I -

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Basic information

Entry
Database: PDB / ID: 4ay2
TitleCapturing 5' tri-phosphorylated RNA duplex by RIG-I
Components
  • 5'-R-PPP(GP*GP*CP*GP*CP*GP*GP*CP*UP*UP*CP*GP*GP*CP *CP*GP*CP*GP*CP*C)-3'
  • PROBABLE ATP-DEPENDENT RNA HELICASE DDX58
KeywordsHYDROLASE/RNA / HYDROLASE-RNA COMPLEX / INNATE IMMUNITY
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
ADENOSINE-5'-DIPHOSPHATE / RNA / RNA (> 10) / Antiviral innate immune response receptor RIG-I
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLuo, D. / Pyle, A.M.
CitationJournal: Structure / Year: 2012
Title: Visualizing the Determinants of Viral RNA Recognition by Innate Immune Sensor Rig-I.
Authors: Luo, D. / Kohlway, A. / Vela, A. / Pyle, A.M.
History
DepositionJun 17, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Nov 28, 2012Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: 5'-R-PPP(GP*GP*CP*GP*CP*GP*GP*CP*UP*UP*CP*GP*GP*CP *CP*GP*CP*GP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7845
Polymers85,2682
Non-polymers5173
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-44.3 kcal/mol
Surface area34220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.745, 76.156, 221.222
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / RNA chain , 2 types, 2 molecules AC

#1: Protein PROBABLE ATP-DEPENDENT RNA HELICASE DDX58 / DDX58 / DEAD BOX PROTEIN 58 / RIG-I-LIKE RECEPTOR 1 / RLR-1 / RETINOIC ACID-INDUCIBLE GENE 1 ...DDX58 / 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: 78686.758 Da / Num. of mol.: 1 / Fragment: RESIDUES 239-925 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: O95786, RNA helicase
#2: RNA chain 5'-R-PPP(GP*GP*CP*GP*CP*GP*GP*CP*UP*UP*CP*GP*GP*CP *CP*GP*CP*GP*CP*C)-3' / 5' TRI-PHOSPHORYLATED RNA


Mass: 6580.821 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 4 types, 73 molecules

#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.34 Å3/Da / Density % sol: 53 % / Description: NONE

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / 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: 2.8→47.7 Å / Num. obs: 20333 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 11.4
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 3 / % possible all: 98.6

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Processing

SoftwareName: REFMAC / Version: 5.7.0029 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YKG

2ykg


Resolution: 2.8→24.9 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.861 / SU B: 33.592 / SU ML: 0.318 / Cross valid method: THROUGHOUT / ESU R Free: 0.44 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.28583 1036 5.1 %RANDOM
Rwork0.21816 ---
obs0.22153 19224 97.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.699 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2---1.97 Å20 Å2
3---1.66 Å2
Refinement stepCycle: LAST / Resolution: 2.8→24.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5007 436 29 70 5542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195624
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1351.9127701
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1125623
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.8224.675231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.17115929
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6171523
X-RAY DIFFRACTIONr_chiral_restr0.0750.2860
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214012
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 66 -
Rwork0.341 1362 -
obs--98.48 %
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)
13.3372-1.0852-0.19183.2522-0.17783.4686-0.08840.3858-0.0901-0.13840.05040.19640.1106-0.24150.0380.0145-0.0243-0.00670.1924-0.0670.0454-8.521813.4427-16.4463
20.2789-0.5165-0.15242.63651.08380.5736-0.0239-0.0274-0.14530.0234-0.03690.10660.1616-0.02860.06090.27390.02880.02870.4350.01850.26539.4813-18.8195-22.6639
38.06910.2482-1.97965.7236-0.20778.4498-0.01560.0136-0.4002-0.6326-0.4104-0.15910.15790.1970.4260.45650.01350.06390.48880.03440.18311.84637.0072-50.1809
44.4888-3.58460.15855.8158-0.40153.74740.15530.9068-0.52630.3016-0.3914-0.56290.3220.94990.23610.32030.0774-0.0650.566-0.17950.437411.62040.8647-30.3065
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A239 - 455
2X-RAY DIFFRACTION2A456 - 798
3X-RAY DIFFRACTION3A799 - 930
4X-RAY DIFFRACTION4C1 - 20

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