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- PDB-4a2p: Structure of duck RIG-I helicase domain -

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Basic information

Entry
Database: PDB / ID: 4a2p
TitleStructure of duck RIG-I helicase domain
ComponentsRETINOIC ACID INDUCIBLE PROTEIN I
KeywordsHYDROLASE / SUPERFAMILY 2 RNA HELICASE / ATP AND DSRNA BINDING / ANTIVIRAL SIGNALLING PATHWAY
Function / homology
Function and homology information


antiviral innate immune response / double-stranded RNA binding / RNA helicase activity / single-stranded RNA binding / hydrolase activity / RNA helicase / RNA binding / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
phosphoenolpyruvate carboxylase, domain 3 - #30 / phosphoenolpyruvate carboxylase, domain 3 / 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 ...phosphoenolpyruvate carboxylase, domain 3 - #30 / phosphoenolpyruvate carboxylase, domain 3 / 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 / 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
Biological speciesANAS PLATYRHYNCHOS (mallard)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 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 28, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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

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Assembly

Deposited unit
A: RETINOIC ACID INDUCIBLE PROTEIN I


Theoretical massNumber of molelcules
Total (without water)63,3291
Polymers63,3291
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)192.130, 192.130, 48.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 63329.492 Da / Num. of mol.: 1 / Fragment: HELICASE DOMAIN, RESIDUES 242-794
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 detailsADDITIONAL GAM AT N-TERMINUS AFTER CLEAVAGE OF HIS-TAG

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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: 2.75 Å3/Da / Density % sol: 55.5 % / Description: NONE
Crystal growDetails: 12 MG PER ML PROTEIN AND 0.1 M NACL, 0.1M M TRI-SODIUM CITRATE PH 5.6, 12% PEG 4000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 13392 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.79 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16
Reflection shellResolution: 3→3.1 Å / Redundancy: 3.81 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0116refinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3→33.59 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.901 / SU B: 22.598 / SU ML: 0.41 / Cross valid method: THROUGHOUT / ESU R Free: 0.5 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.29652 646 4.8 %RANDOM
Rwork0.21111 ---
obs0.21511 12746 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 81.432 Å2
Baniso -1Baniso -2Baniso -3
1--3.54 Å2-1.77 Å20 Å2
2---3.54 Å20 Å2
3---5.31 Å2
Refinement stepCycle: LAST / Resolution: 3→33.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3852 0 0 0 3852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.023936
X-RAY DIFFRACTIONr_bond_other_d0.0010.022693
X-RAY DIFFRACTIONr_angle_refined_deg0.9561.9645307
X-RAY DIFFRACTIONr_angle_other_deg0.88936603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1665475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60924.973187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.01315753
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2851523
X-RAY DIFFRACTIONr_chiral_restr0.0950.2616
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024265
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02742
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
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 59 -
Rwork0.342 927 -
obs--99.7 %

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