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- PDB-5jaj: Structure of chicken LGP2 witha 5'p 10-mer dsRNA and ADP-AlF4-Mg. -

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Basic information

Entry
Database: PDB / ID: 5jaj
TitleStructure of chicken LGP2 witha 5'p 10-mer dsRNA and ADP-AlF4-Mg.
Components
  • LGP2
  • RNA (5'-R(P*GP*GP*UP*AP*CP*GP*UP*AP*CP*C)-3')
  • RNA (5'-R(P*GP*GP*UP*AP*CP*GP*UP*AP*CP*CP*C)-3')
KeywordsRNA BINDING PROTEIN / Innate immune pattern recognition receptor / RIG-I like helcase / dsRNA binding / dsRNA-dependent ATPase
Function / homology
Function and homology information


negative regulation of RIG-I signaling pathway / antiviral innate immune response / double-stranded RNA binding / RNA helicase activity / single-stranded RNA binding / hydrolase activity / RNA helicase / DNA binding / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
phosphoenolpyruvate carboxylase, domain 3 - #30 / phosphoenolpyruvate carboxylase, domain 3 / 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 ...phosphoenolpyruvate carboxylase, domain 3 - #30 / phosphoenolpyruvate carboxylase, domain 3 / 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 / 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 Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / TRIFLUOROMAGNESATE / RNA / RNA (> 10) / RNA helicase
Similarity search - Component
Biological speciesGallus gallus (chicken)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 12, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Derived calculations / Source and taxonomy
Category: pdbx_audit_support / pdbx_entity_src_syn / struct_conn
Item: _pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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

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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*CP*GP*UP*AP*CP*CP*C)-3')
Y: RNA (5'-R(P*GP*GP*UP*AP*CP*GP*UP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,06311
Polymers84,1753
Non-polymers8878
Water10,142563
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7950 Å2
ΔGint-52 kcal/mol
Surface area30650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.590, 97.050, 122.520
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 , 1 types, 1 molecules A

#1: Protein LGP2


Mass: 77516.055 Da / Num. of mol.: 1
Mutation: GAMGGGGS at N-terminus from tag replaces methionine.
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pETM11SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: G0YYQ5

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RNA chain , 2 types, 2 molecules XY

#2: RNA chain RNA (5'-R(P*GP*GP*UP*AP*CP*GP*UP*AP*CP*CP*C)-3')


Mass: 3482.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA (5'-R(P*GP*GP*UP*AP*CP*GP*UP*AP*CP*C)-3')


Mass: 3176.948 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 7 types, 571 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: 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
#6: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-MGF / TRIFLUOROMAGNESATE


Mass: 81.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F3Mg
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 563 / 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: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 5prime monophosphate 10-mer dsRNA:ADP:AlF4:mg complex was mixed with reservoir buffer (0.1 M tri-sodium citrate dihydrate pH 6.1, 0.04-0.08 M ammonium dihydrogen phosphate) 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: 1.5→76.1 Å / Num. obs: 132907 / % possible obs: 99.9 % / Redundancy: 5.25 % / Rsym value: 0.048 / Net I/σ(I): 17.6
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 5.27 % / Rmerge(I) obs: 0.746 / Mean I/σ(I) obs: 2.31 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TMI

3tmi
PDB Unreleased entry


Resolution: 1.5→76.08 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.413 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.059 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16847 6681 5 %RANDOM
Rwork0.13305 ---
obs0.13483 126226 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.159 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20 Å2-0 Å2
2---0.62 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.5→76.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5228 448 50 563 6289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196254
X-RAY DIFFRACTIONr_bond_other_d0.0020.025670
X-RAY DIFFRACTIONr_angle_refined_deg1.511.8878612
X-RAY DIFFRACTIONr_angle_other_deg1.014313039
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8265721
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29623.693287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.321151021
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6341554
X-RAY DIFFRACTIONr_chiral_restr0.0950.2944
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026950
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021536
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_it2.992.5612791
X-RAY DIFFRACTIONr_mcbond_other2.9912.5592790
X-RAY DIFFRACTIONr_mcangle_it3.6583.843543
X-RAY DIFFRACTIONr_mcangle_other3.6573.8433544
X-RAY DIFFRACTIONr_scbond_it4.2522.9833463
X-RAY DIFFRACTIONr_scbond_other4.2522.9833463
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9294.3085070
X-RAY DIFFRACTIONr_long_range_B_refined5.57822.3387800
X-RAY DIFFRACTIONr_long_range_B_other5.27621.8667562
X-RAY DIFFRACTIONr_rigid_bond_restr2.681311924
X-RAY DIFFRACTIONr_sphericity_free36.2945170
X-RAY DIFFRACTIONr_sphericity_bonded14.583512138
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 514 -
Rwork0.244 9206 -
obs--99.74 %

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