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- PDB-4a2x: Structure of duck RIG-I C-terminal domain (CTD) with 14-mer dSRNA -

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Basic information

Entry
Database: PDB / ID: 4a2x
TitleStructure of duck RIG-I C-terminal domain (CTD) with 14-mer dSRNA
Components
  • 5'-R(*CP*GP*CP*GP*UP*UP*GP*UP*UP*CP*UP*CP*CP*CP)-3'
  • 5'-R(*GP*GP*GP*AP*GP*AP*AP*CP*AP*AP*CP*GP*CP*GP)-3'
  • RETINOIC ACID INDUCIBLE PROTEIN I
KeywordsRNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA COMPLEX / SUPERFAMILY 2 RNA HELICASE / ATP AND DSRNA BINDING / ANTIVIRAL SIGNALLING PATHWAY
Function / homology
Function and homology information


cytoplasmic pattern recognition receptor signaling pathway / 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
RIG-I-like receptor, C-terminal regulatory domain / RIG-I, CARD domain repeat 2 / 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. ...RIG-I-like receptor, C-terminal regulatory domain / RIG-I, CARD domain repeat 2 / 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. / Caspase recruitment domain / Caspase recruitment domain / Death-like domain superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / 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 nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA helicase
Similarity search - Component
Biological speciesANAS PLATYRHYNCHOS (mallard)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsKowalinski, E. / Lunardi, T. / McCarthy, A.A. / Cusack, S.
CitationJournal: Cell / 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 1.1Oct 26, 2011Group: Database references
Revision 1.2Jun 13, 2018Group: Data collection / Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: RETINOIC ACID INDUCIBLE PROTEIN I
D: RETINOIC ACID INDUCIBLE PROTEIN I
L: 5'-R(*GP*GP*GP*AP*GP*AP*AP*CP*AP*AP*CP*GP*CP*GP)-3'
M: 5'-R(*CP*GP*CP*GP*UP*UP*GP*UP*UP*CP*UP*CP*CP*CP)-3'
N: 5'-R(*GP*GP*GP*AP*GP*AP*AP*CP*AP*AP*CP*GP*CP*GP)-3'
O: 5'-R(*CP*GP*CP*GP*UP*UP*GP*UP*UP*CP*UP*CP*CP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,86912
Polymers78,6078
Non-polymers2624
Water00
1
A: RETINOIC ACID INDUCIBLE PROTEIN I
B: RETINOIC ACID INDUCIBLE PROTEIN I
L: 5'-R(*GP*GP*GP*AP*GP*AP*AP*CP*AP*AP*CP*GP*CP*GP)-3'
M: 5'-R(*CP*GP*CP*GP*UP*UP*GP*UP*UP*CP*UP*CP*CP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4346
Polymers39,3044
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9060 Å2
ΔGint-8.1 kcal/mol
Surface area21460 Å2
MethodPISA
2
C: RETINOIC ACID INDUCIBLE PROTEIN I
D: RETINOIC ACID INDUCIBLE PROTEIN I
N: 5'-R(*GP*GP*GP*AP*GP*AP*AP*CP*AP*AP*CP*GP*CP*GP)-3'
O: 5'-R(*CP*GP*CP*GP*UP*UP*GP*UP*UP*CP*UP*CP*CP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4346
Polymers39,3044
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint-5.5 kcal/mol
Surface area21640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)216.020, 90.640, 62.960
Angle α, β, γ (deg.)90.00, 90.38, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNTHRTHRAA807 - 8465 - 44
21GLNGLNTHRTHRBB807 - 8465 - 44
31GLNGLNTHRTHRCC807 - 8465 - 44
41GLNGLNTHRTHRDD807 - 8465 - 44
12PHEPHEGLUGLUAA858 - 89856 - 96
22PHEPHEGLUGLUBB858 - 89856 - 96
32PHEPHEGLUGLUCC858 - 89856 - 96
42PHEPHEGLUGLUDD858 - 89856 - 96
13METMETPROPROAA906 - 931104 - 129
23METMETPROPROBB906 - 931104 - 129
33METMETPROPROCC906 - 931104 - 129
43METMETPROPRODD906 - 931104 - 129

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.283065, -0.958885, 0.020318), (-0.957734, 0.283729, 0.047371), (-0.051188, -0.00605, -0.998671)-6.42958, -3.42764, -16.3543
3given(0.284545, 0.957964, 0.036596), (-0.957973, 0.285581, -0.027045), (-0.036359, -0.027363, 0.998964)92.99938, 20.58555, 12.96079
4given(0.842603, -0.538013, 0.023696), (-0.537161, -0.842781, -0.034329), (0.03844, 0.016197, -0.99913)-51.91806, -91.42387, -31.43831

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Components

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


Mass: 15181.542 Da / Num. of mol.: 4 / Fragment: C-TERMINAL DOMAIN, RESIDUES 806-933
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ANAS PLATYRHYNCHOS (mallard) / Plasmid: PET11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): STAR / References: UniProt: D3TI84
#2: RNA chain 5'-R(*GP*GP*GP*AP*GP*AP*AP*CP*AP*AP*CP*GP*CP*GP)-3' / 14-MER RNA


Mass: 4587.852 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: RNA chain 5'-R(*CP*GP*CP*GP*UP*UP*GP*UP*UP*CP*UP*CP*CP*CP)-3'


Mass: 4352.579 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
Sequence detailsADDITIONAL GAM AT N-TERMINUS AFTER CLEAVAGE OF HIS-TAG GENBANK REFERENCE FOR CHAINS A, B, C, D IS ACA61272.

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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: 3.92 Å3/Da / Density % sol: 61.5 % / Description: NONE
Crystal growDetails: 14 MG/ML IN A 2:1 MOLAR RATIO WITH 14-MER DSRNA AND 0.1 M TRIS PH 8.8, 26% (W/V) PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 4→50 Å / Num. obs: 10316 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 4.47 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.3
Reflection shellResolution: 4→4.2 Å / Redundancy: 4.49 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.9 / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.6.0116refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A2V

4a2v


Resolution: 4→108.01 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.913 / SU B: 94.5 / SU ML: 0.553 / Cross valid method: THROUGHOUT / ESU R Free: 0.733 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.24813 495 4.8 %RANDOM
Rwork0.20394 ---
obs0.20603 9821 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.041 Å2
Baniso -1Baniso -2Baniso -3
1--3.25 Å20 Å2-0.02 Å2
2--5.27 Å20 Å2
3----2.01 Å2
Refinement stepCycle: LAST / Resolution: 4→108.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3964 1182 4 0 5150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0175370
X-RAY DIFFRACTIONr_bond_other_d0.0020.023442
X-RAY DIFFRACTIONr_angle_refined_deg1.1311.8097468
X-RAY DIFFRACTIONr_angle_other_deg0.87838402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2945472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.84925192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.06615808
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.5611512
X-RAY DIFFRACTIONr_chiral_restr0.0710.2788
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025006
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021102
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

Ens-ID: 1 / Number: 1519 / Refine-ID: X-RAY DIFFRACTION / Type: tight positional / Weight position: 0.05

Dom-IDAuth asym-IDRms dev position (Å)
1A0.02
2B0.02
3C0.02
4D0.01
LS refinement shellResolution: 4.004→4.108 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 32 -
Rwork0.318 665 -
obs--93.56 %
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)
19.16121.079-3.61936.4657-0.22125.7650.07220.04580.4094-0.2190.3512-0.1525-0.0453-0.3619-0.42330.2451-0.1262-0.08710.32530.08150.161535.1161-36.279313.0507
212.41131.198-2.96969.889-1.63419.3272-0.1975-0.6074-0.8656-0.2071-0.11130.24030.23520.94620.30890.04170.0803-0.00280.43910.20.196218.1851-49.3273-30.0928
39.348-3.56971.078711.0658-2.03056.8872-0.05070.45720.4613-0.15630.13310.3396-0.4778-0.7405-0.08240.39260.35080.12180.51220.12530.220238.0197-71.7184-0.4799
44.8713-0.96860.557412.714-2.07824.80310.1028-0.03-0.44731.3712-0.0852-0.4013-0.3177-0.0354-0.01760.83760.0980.05740.32550.03630.321345.4146-92.5748-44.2779
50.65111.37011.70242.90193.58914.4541-0.0310.0263-0.0313-0.00860.1108-0.1171-0.07910.097-0.07980.63370.061-0.15460.56960.20460.454928.971-44.2121-8.9369
61.0216-2.6687-3.17267.00118.27939.8671-0.0114-0.17170.1766-0.12570.4768-0.49160.13790.6361-0.46541.36590.27320.0221.21410.25080.70843.5484-81.414-22.3116
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A807 - 1000
2X-RAY DIFFRACTION2B807 - 1000
3X-RAY DIFFRACTION3C807 - 1000
4X-RAY DIFFRACTION4D807 - 1000
5X-RAY DIFFRACTION5L1 - 14
6X-RAY DIFFRACTION5M1 - 14
7X-RAY DIFFRACTION6N1 - 14
8X-RAY DIFFRACTION6O1 - 14

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