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- PDB-5jbg: Crystal structure of chicken LGP2 with 5'ppp 26-mer hairpin RNA w... -

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Basic information

Entry
Database: PDB / ID: 5jbg
TitleCrystal structure of chicken LGP2 with 5'ppp 26-mer hairpin RNA with 3' GG overhang and ADP-AlF4-Mg2+ at 2.0 A resolution.
Components
  • LGP2
  • RNA (5'-R(*GPPP*GP*AP*GP*CP*GP*UP*GP*CP*CP*GP*GP*GP*CP*AP*CP*GP*CP*UP*CP*CP*GP*G)-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
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / RNA / RNA (> 10) / RNA helicase
Similarity search - Component
Biological speciesGallus gallus (chicken)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCusack, S. / Uchikawa, E.
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 / pdbx_audit_support / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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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(*GPPP*GP*AP*GP*CP*GP*UP*GP*CP*CP*GP*GP*GP*CP*AP*CP*GP*CP*UP*CP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,12411
Polymers86,0242
Non-polymers1,1009
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint-107 kcal/mol
Surface area31560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.860, 97.430, 122.580
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 AX

#1: Protein LGP2


Mass: 77459.000 Da / Num. of mol.: 1 / Mutation: GAMGGGS from tag replaces 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(*GPPP*GP*AP*GP*CP*GP*UP*GP*CP*CP*GP*GP*GP*CP*AP*CP*GP*CP*UP*CP*CP*GP*G)-3')


Mass: 8565.016 Da / Num. of mol.: 1 / Mutation: 5' triphosphate / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 277 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


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.43 Å3/Da / Density % sol: 49.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 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. 5 prime triphosphate, 3 prime GG overhang 26-mer hairpin RNA:ADP:AlF4 complex was mixed with reservoir buffer containing 0.1 M citric acid pH 5.0, 0.8 M ammonium sulphate in a 1:1 ratio.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2→76.27 Å / Num. obs: 56661 / % possible obs: 99.9 % / Redundancy: 4.47 % / Rmerge(I) obs: 0.259 / Net I/σ(I): 6.31
Reflection shellResolution: 2→2.1 Å / Redundancy: 4.35 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 1.38 / % possible all: 98.7

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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: 2→76.27 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.593 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.176 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 2814 5 %RANDOM
Rwork0.21758 ---
obs0.21945 53847 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.664 Å2
Baniso -1Baniso -2Baniso -3
1-2.5 Å2-0 Å20 Å2
2---0.76 Å20 Å2
3----1.75 Å2
Refinement stepCycle: 1 / Resolution: 2→76.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5290 506 59 268 6123
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0196075
X-RAY DIFFRACTIONr_bond_other_d0.0020.025466
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.8968330
X-RAY DIFFRACTIONr_angle_other_deg0.933.00112545
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8455670
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.75123.688282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.28915985
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9821553
X-RAY DIFFRACTIONr_chiral_restr0.070.2909
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026573
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021475
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_it1.9953.7342674
X-RAY DIFFRACTIONr_mcbond_other1.9893.7322673
X-RAY DIFFRACTIONr_mcangle_it3.2865.5783346
X-RAY DIFFRACTIONr_mcangle_other3.2865.5813347
X-RAY DIFFRACTIONr_scbond_it2.14.0173401
X-RAY DIFFRACTIONr_scbond_other2.0913.9983380
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5275.8884955
X-RAY DIFFRACTIONr_long_range_B_refined6.43730.327114
X-RAY DIFFRACTIONr_long_range_B_other6.18130.247024
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 201 -
Rwork0.333 3904 -
obs--98.63 %

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