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- PDB-3zd6: Snapshot 1 of RIG-I scanning on RNA duplex -

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Basic information

Entry
Database: PDB / ID: 3zd6
TitleSnapshot 1 of RIG-I scanning on RNA duplex
Components
  • PROBABLE ATP-DEPENDENT RNA HELICASE DDX58
  • RNA DUPLEX
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
RNA / Antiviral innate immune response receptor RIG-I
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLuo, D. / Pyle, A.M.
CitationJournal: Embo Rep. / Year: 2013
Title: Defining the Functional Determinants for RNA Surveillance by Rig-I.
Authors: Kohlway, A. / Luo, D. / Rawling, D.C. / Ding, S.C. / Pyle, A.M.
History
DepositionNov 25, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Dec 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_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.pdbx_dist_value / _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_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_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: RNA DUPLEX
D: RNA DUPLEX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2174
Polymers86,1523
Non-polymers651
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-29 kcal/mol
Surface area34650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.474, 78.017, 225.104
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: 79737.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: O95786, RNA helicase
#2: RNA chain RNA DUPLEX


Mass: 3206.980 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.36 Å3/Da / Density % sol: 53.6 % / Description: NONE
Crystal growpH: 9 / Details: pH 9

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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→48 Å / Num. obs: 21820 / % possible obs: 99.5 % / Observed criterion σ(I): 1.8 / Redundancy: 5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.2
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.8 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YKG

2ykg


Resolution: 2.8→25 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.889 / SU B: 36.739 / SU ML: 0.331 / Cross valid method: THROUGHOUT / ESU R Free: 0.407 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27896 1102 5.1 %RANDOM
Rwork0.22155 ---
obs0.22444 20593 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.678 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20 Å20 Å2
2--2.14 Å20 Å2
3----3.26 Å2
Refinement stepCycle: LAST / Resolution: 2.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4946 424 1 9 5380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225522
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5622.067571
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9475627
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.48524.612219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.20815876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9671521
X-RAY DIFFRACTIONr_chiral_restr0.0990.2877
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213972
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_it0.5211.53157
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.01525084
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.47832365
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3644.52487
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
Rfree0.534 57 -
Rwork0.438 1515 -
obs--98.31 %
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)
14.77690.39592.7716.3754.37248.1561-0.32180.59010.6696-0.46790.5162-0.8759-0.99340.7768-0.19440.1232-0.07460.01990.45810.14580.298310.6778-11.197-9.5813
23.84680.49470.39813.0389-0.23834.9584-0.06780.46910.0387-0.29150.0527-0.04010.01280.31680.01510.0467-0.0298-0.01440.29690.16570.16931.6128-15.9915-19.1345
32.94640.41051.47883.5708-0.33016.9692-0.4163-0.10430.06740.08480.1059-0.0988-0.3752-0.10230.31040.75740.0389-0.08270.29580.12990.5169-9.644727.1603-27.274
41.5606-0.5249-0.00075.6421-0.49563.2288-0.0985-0.01790.3254-0.11510.05880.0126-0.6145-0.30790.03960.16790.00650.01760.44990.20010.3957-12.0099-7.2875-9.0077
58.01043.2343-0.19511.6282-1.5529.31040.04990.0925-0.1987-1.23030.0085-0.00260.39260.1455-0.05850.53540.0321-0.13670.40110.02430.2049-19.537-9.341-48.5846
68.25381.73051.02616.2416-2.80552.72160.2189-0.11710.82360.54220.00030.5996-0.2581-0.6652-0.21920.207-0.02050.00690.42850.14370.3659-17.7835-4.0832-28.8119
725.1263-7.05012.89138.16991.49163.62230.2781-0.15091.65160.5501-0.13340.3101-0.4345-0.5801-0.14460.3476-0.06720.20450.57270.27090.431-16.2349-2.3646-31.5206
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A235 - 285
2X-RAY DIFFRACTION2A286 - 455
3X-RAY DIFFRACTION3A456 - 716
4X-RAY DIFFRACTION4A717 - 798
5X-RAY DIFFRACTION5A799 - 919
6X-RAY DIFFRACTION6C1 - 10
7X-RAY DIFFRACTION7D1 - 10

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