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- PDB-4a2w: Structure of full-length duck RIG-I -

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Basic information

Entry
Database: PDB / ID: 4a2w
TitleStructure of full-length duck RIG-I
ComponentsRETINOIC ACID INDUCIBLE PROTEIN I
KeywordsHYDROLASE / SUPERFAMILY 2 RNA HELICASE / ATP AND DSRNA BINDING / CARD / ANTIVIRAL SIGNALLING PATHWAY
Function / homology
Function and homology information


RNA helicase activity / hydrolase activity / RNA helicase / innate immune response / RNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
phosphoenolpyruvate carboxylase, domain 3 - #30 / phosphoenolpyruvate carboxylase, domain 3 / RIG-I, CARD domain repeat 2 / Death Domain, Fas / Death Domain, Fas / 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, CARD domain repeat 2 / Death Domain, Fas / Death Domain, Fas / 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 / 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 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesANAS PLATYRHYNCHOS (mallard)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsKowalinski, E. / Lunardi, T. / McCarthy, A.A. / Cusack, S.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: Structural Basis for the Activation of Innate Immune Pattern Recognition Receptor Rig-I by Viral RNA.
Authors: Kowalinski, E. / Lunardi, T. / Mccarthy, A.A. / Louber, J. / Brunel, J. / Grigorov, B. / Gerlier, D. / Cusack, S.
History
DepositionSep 29, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references
Revision 1.2Mar 27, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _pdbx_database_status.recvd_author_approval
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RETINOIC ACID INDUCIBLE PROTEIN I
B: RETINOIC ACID INDUCIBLE PROTEIN I


Theoretical massNumber of molelcules
Total (without water)213,8322
Polymers213,8322
Non-polymers00
Water0
1
A: RETINOIC ACID INDUCIBLE PROTEIN I


Theoretical massNumber of molelcules
Total (without water)106,9161
Polymers106,9161
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RETINOIC ACID INDUCIBLE PROTEIN I


Theoretical massNumber of molelcules
Total (without water)106,9161
Polymers106,9161
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)163.320, 163.320, 152.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A91 - 186
2111B91 - 186
1121A245 - 450
2121B245 - 450
1221A750 - 790
2221B750 - 790
1131A470 - 600
2131B470 - 600
1141A610 - 698
2141B610 - 698
1241A729 - 740
2241B729 - 740
1151A1 - 90
2151B1 - 90

NCS ensembles :
ID
1
2
3
4
5

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999274, -0.00999, 0.036753), (0.009332, -0.999794, -0.018035), (0.036925, -0.017678, 0.999162)34.29549, -33.58417, -0.92796

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Components

#1: Protein RETINOIC ACID INDUCIBLE PROTEIN I / RIG-I


Mass: 106916.117 Da / Num. of mol.: 2 / Fragment: FULL-LENGTH, RESIDUES 2-933
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ANAS PLATYRHYNCHOS (mallard) / Plasmid: PFASTBAC / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: D3TI84
Sequence detailsEXTRA GAM AT N-TERMINUS AFTER HIS-TAG CLEAVAGE

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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: 2.38 Å3/Da / Density % sol: 48.5 % / Description: NONE
Crystal growDetails: 7 MG/ML PROTEIN 0.1 M KCL, 0.01M MGCL2, TRIS PH 8.5, 30% PEG 4000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.037
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.037 Å / Relative weight: 1
ReflectionResolution: 3.7→50 Å / Num. obs: 22592 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 7.93 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.8
Reflection shellResolution: 3.7→4 Å / Redundancy: 8.09 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.3 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.6.0116refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RIG-I HELICASE

Resolution: 3.7→42.77 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.912 / SU B: 96.431 / SU ML: 0.622 / Cross valid method: THROUGHOUT / ESU R Free: 0.736 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.27365 1160 5.1 %RANDOM
Rwork0.21836 ---
obs0.22118 21432 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 148.465 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å20 Å20 Å2
2---1.23 Å20 Å2
3---2.45 Å2
Refinement stepCycle: LAST / Resolution: 3.7→42.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10880 0 0 0 10880
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0211086
X-RAY DIFFRACTIONr_bond_other_d0.0010.027631
X-RAY DIFFRACTIONr_angle_refined_deg1.1291.96714957
X-RAY DIFFRACTIONr_angle_other_deg0.846318641
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16651342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.00124.586532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.152152101
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6271578
X-RAY DIFFRACTIONr_chiral_restr0.0610.21709
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212098
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022156
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1348tight positional0.020.05
12B1348tight positional0.020.05
21A3240tight positional0.020.05
22B3240tight positional0.020.05
31A1688tight positional0.030.05
32B1688tight positional0.030.05
41A896tight positional0.020.05
42B896tight positional0.020.05
51A1229tight positional0.020.05
52B1229tight positional0.020.05
11A1348tight thermal7.170.5
12B1348tight thermal7.170.5
21A3240tight thermal5.90.5
22B3240tight thermal5.90.5
31A1688tight thermal7.10.5
32B1688tight thermal7.10.5
41A896tight thermal8.310.5
42B896tight thermal8.310.5
51A1229tight thermal6.360.5
52B1229tight thermal6.360.5
LS refinement shellResolution: 3.7→3.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 61 -
Rwork0.334 1424 -
obs--99.8 %
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)
17.5539-2.1845-2.45321.7316-1.68596.75420.0688-0.5707-0.5896-0.105-0.1632-0.1310.71290.79820.09440.89140.1764-0.13591.3469-0.14141.452658.6031-21.3627-18.5303
212.87913.7034-0.55443.59211.36239.38010.01880.3710.4678-0.08210.2992-0.854-0.02971.2656-0.31810.1865-0.02540.15260.8645-0.2250.583940.6779-6.5638-20.4581
35.02482.9628-2.76243.8601-1.48172.098-0.28740.26150.52030.65350.2491-0.0142-0.08110.34850.03820.9154-0.2451-0.25220.60590.25960.588324.536442.1836-26.8143
45.4762-2.42543.39645.6003-3.8289.48510.05210.4760.2097-0.23640.2702-0.1056-0.17270.7403-0.32230.0968-0.1430.120.2839-0.15460.168315.32672.2712-14.4368
55.83313.44422.14012.17471.48961.2443-0.46751.93961.2319-0.17010.4710.745-0.199-0.2913-0.00351.16860.1642-0.10973.05080.60481.9354-24.9124-12.4859-16.7536
618.17634.0488-1.7723.2731-3.78075.7374-0.62872.3681-1.5556-0.3191.0170.55630.1753-1.8652-0.38830.8604-0.1969-0.09061.6944-0.99951.2514-6.8476-26.757-19.7585
73.37512.98341.47726.61181.68613.94230.0771-0.6062-0.15260.0805-0.19670.41990.046-0.81210.11970.91490.25230.0480.48670.10711.130216.3383-79.1412-25.7254
86.1865-5.498-3.56988.38175.45118.5774-0.25850.0269-0.6544-0.00290.04650.20720.81030.17250.21210.70680.00320.0320.02820.00970.416818.7258-35.5721-14.1395
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 89
2X-RAY DIFFRACTION2A90 - 186
3X-RAY DIFFRACTION3A245 - 466
4X-RAY DIFFRACTION3A745 - 794
5X-RAY DIFFRACTION4A467 - 744
6X-RAY DIFFRACTION5B1 - 89
7X-RAY DIFFRACTION6B90 - 186
8X-RAY DIFFRACTION7B245 - 466
9X-RAY DIFFRACTION7B745 - 794
10X-RAY DIFFRACTION8B467 - 744

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