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- PDB-5jbj: Crystal structure of chicken LGP2 with 5'p 12-mer dsRNA at 3.6 A ... -

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Basic information

Entry
Database: PDB / ID: 5jbj
TitleCrystal structure of chicken LGP2 with 5'p 12-mer dsRNA at 3.6 A resolution
Components
  • LGP2
  • RNA (5'-R(P*GP*GP*UP*AP*GP*CP*GP*CP*UP*AP*CP*C)-3')
KeywordsIMMUNE SYSTEM / Innate immune pattern recognition receptor / RIG-I like helicase / dsRNA dependent ATPase / zinc-containing CTD domain
Function / homology
Function and homology information


defense response to virus / RNA helicase activity / hydrolase activity / RNA helicase / innate immune response / DNA binding / RNA binding / ATP binding / metal ion binding / 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-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-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. / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA helicase
Similarity search - Component
Biological speciesGallus gallus (chicken)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.58 Å
AuthorsCusack, S. / Uchikawa, E. / Lethier, M.
Funding support France, 1items
OrganizationGrant numberCountry
European Research Council322586 France
CitationJournal: Mol.Cell / Year: 2016
Title: Structural Analysis of dsRNA Binding to Anti-viral Pattern Recognition Receptors LGP2 and MDA5.
Authors: Uchikawa, E. / Lethier, M. / Malet, H. / Brunel, J. / Gerlier, D. / Cusack, S.
History
DepositionApr 13, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / ndb_struct_na_base_pair / pdbx_audit_support / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _ndb_struct_na_base_pair.hbond_type_28 / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LGP2
X: RNA (5'-R(P*GP*GP*UP*AP*GP*CP*GP*CP*UP*AP*CP*C)-3')
Y: RNA (5'-R(P*GP*GP*UP*AP*GP*CP*GP*CP*UP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1794
Polymers85,1143
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-56 kcal/mol
Surface area33110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.090, 90.090, 196.730
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein LGP2


Mass: 77459.000 Da / Num. of mol.: 1
Mutation: GAMGGGS from tag replaces the N-terminal methionine
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: G0YYQ5
#2: RNA chain RNA (5'-R(P*GP*GP*UP*AP*GP*CP*GP*CP*UP*AP*CP*C)-3')


Mass: 3827.336 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic RNA 5 prime mono phosphate / 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

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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: 2.71 Å3/Da / Density % sol: 54.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: chLGP2, directly after size exclusion chromatography, was mixed with dsRNA in a 1:1 ratio and incubated for 30 minutes on ice. The complex was concentrated with an Amicon Ultra concentrator ...Details: chLGP2, directly after size exclusion chromatography, was mixed with dsRNA in a 1:1 ratio and incubated for 30 minutes on ice. The complex was concentrated with an Amicon Ultra concentrator to around 10 mg/ml and then 2 mM ADP:AlF4 and 2 mM MgCl2 were added. chLGP2:12bp dsRNA:ADP:AlF4 complex was mixed with reservoir buffer (0.1 M Bis-Tris propane pH 6.5, 0.05-0.1 M magnesium formate) in a 2:1 ratio

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 3.58→78.02 Å / Num. obs: 10663 / % possible obs: 78.02 % / Redundancy: 11.51 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 20.74
Reflection shellResolution: 3.58→3.73 Å / Redundancy: 10.32 % / Rmerge(I) obs: 1.18 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JB2

5jb2


Resolution: 3.58→78.02 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.905 / SU B: 59.059 / SU ML: 0.855 / Cross valid method: THROUGHOUT / ESU R Free: 0.86 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31881 542 5.1 %RANDOM
Rwork0.25312 ---
obs0.25647 10121 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 202.316 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20.22 Å20 Å2
2--0.43 Å2-0 Å2
3----1.4 Å2
Refinement stepCycle: LAST / Resolution: 3.58→78.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5007 512 1 0 5520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0185694
X-RAY DIFFRACTIONr_bond_other_d0.0010.025152
X-RAY DIFFRACTIONr_angle_refined_deg0.9541.8697799
X-RAY DIFFRACTIONr_angle_other_deg0.8573.00111823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1595628
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.07823.566258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87615916
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0381548
X-RAY DIFFRACTIONr_chiral_restr0.0550.2860
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026138
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021384
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_it4.58520.6662518
X-RAY DIFFRACTIONr_mcbond_other4.58520.6652517
X-RAY DIFFRACTIONr_mcangle_it7.89730.9893144
X-RAY DIFFRACTIONr_mcangle_other7.89630.993145
X-RAY DIFFRACTIONr_scbond_it3.61220.2343174
X-RAY DIFFRACTIONr_scbond_other3.60820.2353173
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.34430.2134653
X-RAY DIFFRACTIONr_long_range_B_refined11.4426310
X-RAY DIFFRACTIONr_long_range_B_other11.4416311
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.58→3.673 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 42 -
Rwork0.359 738 -
obs--99.11 %

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