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- PDB-4s3n: Crystal structure of human OAS3 domain I in complex with dsRNA -

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Basic information

Entry
Database: PDB / ID: 4s3n
TitleCrystal structure of human OAS3 domain I in complex with dsRNA
Components
  • 2'-5'-oligoadenylate synthase 3
  • RNA (5'-R(*GP*GP*CP*UP*UP*UP*UP*GP*AP*CP*CP*UP*UP*UP*AP*UP*GP*AP*A)-3')
  • RNA (5'-R(*UP*UP*CP*AP*UP*AP*AP*AP*GP*GP*UP*CP*AP*AP*AP*AP*GP*CP*C)-3')
KeywordsTransferase/RNA / transferase / dsRNA / Transferase-RNA complex / OAS / OAS1 / OAS2 / OAS3 / OASL / 2-5A / RNase L
Function / homology
Function and homology information


negative regulation of chemokine (C-X-C motif) ligand 9 production / negative regulation of IP-10 production / 2'-5' oligoadenylate synthase / 2'-5'-oligoadenylate synthetase activity / negative regulation of chemokine (C-X-C motif) ligand 2 production / regulation of ribonuclease activity / negative regulation of chemokine (C-C motif) ligand 5 production / MDA-5 signaling pathway / RIG-I signaling pathway / OAS antiviral response ...negative regulation of chemokine (C-X-C motif) ligand 9 production / negative regulation of IP-10 production / 2'-5' oligoadenylate synthase / 2'-5'-oligoadenylate synthetase activity / negative regulation of chemokine (C-X-C motif) ligand 2 production / regulation of ribonuclease activity / negative regulation of chemokine (C-C motif) ligand 5 production / MDA-5 signaling pathway / RIG-I signaling pathway / OAS antiviral response / positive regulation of monocyte chemotactic protein-1 production / nucleobase-containing compound metabolic process / negative regulation of type I interferon-mediated signaling pathway / negative regulation of viral genome replication / positive regulation of interferon-beta production / response to virus / Interferon gamma signaling / positive regulation of tumor necrosis factor production / double-stranded RNA binding / Interferon alpha/beta signaling / defense response to virus / defense response to bacterium / intracellular membrane-bounded organelle / innate immune response / extracellular space / nucleoplasm / ATP binding / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
2'-5'-oligoadenylate synthetase 1, domain 2 / 2-5-oligoadenylate synthetase, N-terminal conserved site / 2'-5'-oligoadenylate synthases signature 1. / 2-5-oligoadenylate synthetase, C-terminal conserved site / 2'-5'-oligoadenylate synthetase 1, domain 2/C-terminal / 2'-5'-oligoadenylate synthetase 1, domain 2, C-terminus / 2'-5'-oligoadenylate synthases signature 2. / 2'-5'-oligoadenylate synthase N-terminal region profile. / 2-5OAS/ClassI-CCAase, nucleotidyltransferase domain / Polymerase, nucleotidyl transferase domain ...2'-5'-oligoadenylate synthetase 1, domain 2 / 2-5-oligoadenylate synthetase, N-terminal conserved site / 2'-5'-oligoadenylate synthases signature 1. / 2-5-oligoadenylate synthetase, C-terminal conserved site / 2'-5'-oligoadenylate synthetase 1, domain 2/C-terminal / 2'-5'-oligoadenylate synthetase 1, domain 2, C-terminus / 2'-5'-oligoadenylate synthases signature 2. / 2'-5'-oligoadenylate synthase N-terminal region profile. / 2-5OAS/ClassI-CCAase, nucleotidyltransferase domain / Polymerase, nucleotidyl transferase domain / Poly(a)-polymerase, middle domain / Nucleotidyltransferase domain / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / 2'-5'-oligoadenylate synthase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDonovan, J. / Whitney, G. / Rath, S. / Korennykh, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structural mechanism of sensing long dsRNA via a noncatalytic domain in human oligoadenylate synthetase 3.
Authors: Donovan, J. / Whitney, G. / Rath, S. / Korennykh, A.
History
DepositionFeb 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2'-5'-oligoadenylate synthase 3
B: RNA (5'-R(*GP*GP*CP*UP*UP*UP*UP*GP*AP*CP*CP*UP*UP*UP*AP*UP*GP*AP*A)-3')
C: RNA (5'-R(*UP*UP*CP*AP*UP*AP*AP*AP*GP*GP*UP*CP*AP*AP*AP*AP*GP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)53,3863
Polymers53,3863
Non-polymers00
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-31 kcal/mol
Surface area20310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.700, 104.700, 63.800
Angle α, β, γ (deg.)90.00, 97.8, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 2'-5'-oligoadenylate synthase 3 / (2-5')oligo(A) synthase 3 / 2-5A synthase 3 / p100 OAS / p100OAS


Mass: 41298.398 Da / Num. of mol.: 1 / Fragment: Domain 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OAS3, P/OKcl.4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6K5, 2'-5' oligoadenylate synthase
#2: RNA chain RNA (5'-R(*GP*GP*CP*UP*UP*UP*UP*GP*AP*CP*CP*UP*UP*UP*AP*UP*GP*AP*A)-3')


Mass: 6017.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic (others)
#3: RNA chain RNA (5'-R(*UP*UP*CP*AP*UP*AP*AP*AP*GP*GP*UP*CP*AP*AP*AP*AP*GP*CP*C)-3')


Mass: 6069.697 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 3.02 Å3/Da / Density % sol: 59.25 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 200 mM trisodium citrate, 150 mM NaCl, 12% PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 20, 2013
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2→43.82 Å / Num. obs: 42802 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.1 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IG8

4ig8


Resolution: 2→35.479 Å / SU ML: 0.2 / Phase error: 24.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2113 2137 5 %5% random
Rwork0.1818 ---
all0.1833 42726 --
obs0.1833 42726 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→35.479 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2704 799 0 292 3795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073665
X-RAY DIFFRACTIONf_angle_d0.9775146
X-RAY DIFFRACTIONf_dihedral_angle_d18.5862147
X-RAY DIFFRACTIONf_chiral_restr0.066594
X-RAY DIFFRACTIONf_plane_restr0.004524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04650.36611420.28542716X-RAY DIFFRACTION100
2.0465-2.09770.28141440.25592696X-RAY DIFFRACTION100
2.0977-2.15440.24761390.22672665X-RAY DIFFRACTION100
2.1544-2.21780.25341460.20922739X-RAY DIFFRACTION100
2.2178-2.28940.22611410.20692684X-RAY DIFFRACTION100
2.2894-2.37120.27231410.20842695X-RAY DIFFRACTION100
2.3712-2.46610.22671420.20322702X-RAY DIFFRACTION100
2.4661-2.57830.26971430.2022703X-RAY DIFFRACTION100
2.5783-2.71420.2491410.20252685X-RAY DIFFRACTION100
2.7142-2.88420.24671420.20352720X-RAY DIFFRACTION100
2.8842-3.10670.2551440.19732699X-RAY DIFFRACTION100
3.1067-3.41920.2191430.1912722X-RAY DIFFRACTION100
3.4192-3.91340.19181420.15852690X-RAY DIFFRACTION100
3.9134-4.92830.16211440.14232741X-RAY DIFFRACTION100
4.9283-35.48430.14731430.1522732X-RAY DIFFRACTION99
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)
11.35360.39330.30093.91190.15161.01480.1008-0.0727-0.19210.2081-0.17930.52660.1668-0.25780.06990.2468-0.05060.04740.3312-0.01560.34969.9121-7.326610.3151
21.228-0.2349-0.08435.10370.56951.15770.02920.03250.0484-0.2256-0.0312-0.6062-0.15310.11840.00420.1865-0.0259-0.00620.25780.0240.336927.75315.2844.1342
34.07563.41781.56925.00723.09032.0742-0.05920.6046-0.940.3344-0.62120.32650.6311-1.23320.56312.1534-0.68620.13491.1745-0.15590.869713.437916.991337.2698
43.2281-1.47314.9063.9803-3.49447.9326-0.3292-0.91290.14411.0045-0.48430.82190.0492-1.430.70590.7217-0.1750.09130.7688-0.20950.392416.20384.380326.3548
56.38921.8805-1.15085.2168-2.56454.03510.3439-1.1643-1.16860.722-0.41190.1710.98220.11480.11861.2819-0.1367-0.04230.65580.29550.985522.9381-8.358732.4876
63.5597-1.0696-0.94244.17512.56232.61910.2657-0.6795-0.26941.1723-0.2979-0.19150.10740.04840.01071.1174-0.1840.18260.63620.11870.657713.2591-21.870926.3639
73.3071.0266-1.2716.479-1.75631.3252-0.3928-0.9387-0.43651.06250.0607-0.60250.46650.56950.28271.0176-0.0977-0.05880.72290.13220.67423.5618-21.904825.8904
82.24981.09591.91490.54541.05452.82080.268-0.9660.2431.5599-0.6320.3496-0.6013-0.15460.44141.2708-0.23220.22730.6689-0.10680.615613.1125-9.785329.2044
90.3506-1.37021.41525.5902-5.92376.3713-0.0217-0.762-0.14921.1212-0.4564-0.17720.0116-0.1520.44261.0859-0.1953-0.05120.73710.01520.295223.94743.578833.9703
102.00942.7391.73645.4973-1.0538.13640.0008-0.76950.670.7344-0.30250.6309-1.4902-1.44070.38261.00650.117-0.09240.7984-0.32070.423816.938816.205426.7964
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:165)
2X-RAY DIFFRACTION2(chain A and resid 166:359)
3X-RAY DIFFRACTION3(chain B and resid 1:4)
4X-RAY DIFFRACTION4(chain B and resid 5:8)
5X-RAY DIFFRACTION5(chain B and resid 9:12)
6X-RAY DIFFRACTION6(chain B and resid 13:19)
7X-RAY DIFFRACTION7(chain C and resid 1:3)
8X-RAY DIFFRACTION8(chain C and resid 4:10)
9X-RAY DIFFRACTION9(chain C and resid 11:14)
10X-RAY DIFFRACTION10(chain C and resid 15:18)

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