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- PDB-4rwp: Crystal structure of porcine OAS1 in complex with dsRNA -

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Basic information

Entry
Database: PDB / ID: 4rwp
TitleCrystal structure of porcine OAS1 in complex with dsRNA
Components
  • 2'-5'-oligoadenylate synthase 1
  • 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 / Interferon-induced / dsRNA-activated / TRANSFERASE-RNA complex
Function / homology
Function and homology information


negative regulation of transformation of host cell by virus / 2'-5' oligoadenylate synthase / 2'-5'-oligoadenylate synthetase activity / regulation of ribonuclease activity / negative regulation of viral genome replication / double-stranded RNA binding / defense response to virus / innate immune response / endoplasmic reticulum / mitochondrion ...negative regulation of transformation of host cell by virus / 2'-5' oligoadenylate synthase / 2'-5'-oligoadenylate synthetase activity / regulation of ribonuclease activity / negative regulation of viral genome replication / double-stranded RNA binding / defense response to virus / innate immune response / endoplasmic reticulum / mitochondrion / extracellular region / nucleoplasm / ATP binding / membrane / metal ion binding / 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 synthases signature 2. / 2'-5'-oligoadenylate synthetase 1, domain 2, C-terminus / 2'-5'-oligoadenylate synthase N-terminal region profile. / 2-5OAS/ClassI-CCAase, nucleotidyltransferase domain / Poly(a)-polymerase, middle 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 synthases signature 2. / 2'-5'-oligoadenylate synthetase 1, domain 2, C-terminus / 2'-5'-oligoadenylate synthase N-terminal region profile. / 2-5OAS/ClassI-CCAase, nucleotidyltransferase domain / Poly(a)-polymerase, middle domain / Polymerase, nucleotidyl transferase 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 1
Similarity search - Component
Biological speciesSus scrofa (pig)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsLohoefener, J. / Steinke, N. / Kay-Fedorov, P. / Baruch, P. / Nikulin, A. / Tishchenko, S. / Manstein, D.J. / Fedorov, R.
CitationJournal: Structure / Year: 2015
Title: The Activation Mechanism of 2'-5'-Oligoadenylate Synthetase Gives New Insights Into OAS/cGAS Triggers of Innate Immunity.
Authors: Lohofener, J. / Steinke, N. / Kay-Fedorov, P. / Baruch, P. / Nikulin, A. / Tishchenko, S. / Manstein, D.J. / Fedorov, R.
History
DepositionDec 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 1
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)53,3663
Polymers53,3663
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-31 kcal/mol
Surface area20240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.668, 72.668, 189.532
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein 2'-5'-oligoadenylate synthase 1 / / (2-5')oligo(A) synthase 1 / 2-5A synthase 1 / p42 OAS


Mass: 41278.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: OAS1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q29599, 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 construct (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 construct (others)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.34 Å3/Da / Density % sol: 47.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM KCl, 100 mM HEPES pH 7.0, 15% PEG 5000 MME, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 22, 2013
RadiationMonochromator: Silicon 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.25→47.68 Å / Num. all: 25084 / Num. obs: 25074 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 37.79 Å2

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→47.68 Å / SU ML: 0.22 / σ(F): 1.36 / Phase error: 21.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.226 1273 5.09 %
Rwork0.194 --
obs0.195 24998 100 %
all-25084 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.79 Å2
Refinement stepCycle: LAST / Resolution: 2.25→47.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2808 764 0 98 3670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063726
X-RAY DIFFRACTIONf_angle_d0.8135208
X-RAY DIFFRACTIONf_dihedral_angle_d11.671522
X-RAY DIFFRACTIONf_chiral_restr0.064599
X-RAY DIFFRACTIONf_plane_restr0.004539
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.34010.26451470.23492589X-RAY DIFFRACTION100
2.3401-2.44660.26921260.23042574X-RAY DIFFRACTION100
2.4466-2.57560.28271360.22352594X-RAY DIFFRACTION100
2.5756-2.73690.27061280.21552576X-RAY DIFFRACTION100
2.7369-2.94820.27551500.21172608X-RAY DIFFRACTION100
2.9482-3.24480.22111370.1952618X-RAY DIFFRACTION100
3.2448-3.71420.22341710.18542610X-RAY DIFFRACTION100
3.7142-4.67890.17551320.16952698X-RAY DIFFRACTION100
4.6789-47.68860.21331460.18732858X-RAY DIFFRACTION100

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