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- PDB-9nxs: Crystal structure of the post-reactive state of porcine OAS1 in c... -

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Basic information

Entry
Database: PDB / ID: 9nxs
TitleCrystal structure of the post-reactive state of porcine OAS1 in complex with dsRNA and products 25A2 and PPi bound to the catalytic center.
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 / Innate immunity / bimetallic nucleotidyltransferases / TRANSFERASE / TRANSFERASE-RNA complex
Function / homology
Function and homology information


2'-5' oligoadenylate synthase / 2'-5'-oligoadenylate synthetase activity / regulation of ribonuclease activity / interleukin-27-mediated signaling pathway / negative regulation of viral genome replication / type I interferon-mediated signaling pathway / antiviral innate immune response / double-stranded RNA binding / defense response to virus / endoplasmic reticulum ...2'-5' oligoadenylate synthase / 2'-5'-oligoadenylate synthetase activity / regulation of ribonuclease activity / interleukin-27-mediated signaling pathway / negative regulation of viral genome replication / type I interferon-mediated signaling pathway / antiviral innate immune response / double-stranded RNA binding / defense response to virus / endoplasmic reticulum / mitochondrion / extracellular region / nucleoplasm / ATP binding / membrane / metal ion binding / cytoplasm / cytosol
Similarity search - Function
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 / Nucleotidyltransferase domain / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
Chem-25L / : / PYROPHOSPHATE 2- / 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: 1.8 Å
AuthorsKats, P. / Zhou, X. / Wiebe, J. / Zeymer, O. / Baruch, P. / Taft, M.H. / Reinke, P.Y.A. / Guenther, S. / Meents, A. / Hartmann, R. ...Kats, P. / Zhou, X. / Wiebe, J. / Zeymer, O. / Baruch, P. / Taft, M.H. / Reinke, P.Y.A. / Guenther, S. / Meents, A. / Hartmann, R. / Manstein, D.J. / Fedorov, R.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)The Cluster of Excellence RESIST (Resolving Infection Susceptibility; EXC 2155), Project ID: 39087428 Germany
German Research Foundation (DFG)MA1081/28-1 Germany
CitationJournal: Acs Omega / Year: 2026
Title: The Enzymatic Mechanism of OAS: How Metal Ions and Quantum Effects Help Activate Innate Immunity.
Authors: Kats, P. / Zhou, X. / Wiebe, J. / Zeymer, O. / Baruch, P. / Taft, M.H. / Reinke, P.Y.A. / Gunther, S. / Meents, A. / Hartmann, R. / Manstein, D.J. / Fedorov, R.
History
DepositionMar 26, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.1May 20, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8488
Polymers53,3663
Non-polymers1,4835
Water11,566642
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-51 kcal/mol
Surface area20350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.070, 72.070, 207.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#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

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RNA chain , 2 types, 2 molecules BC

#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)

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Non-polymers , 6 types, 647 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-25L / [[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] phosphono hydrogen phosphate / 2'-5'-oligoadenylate trimer


Mass: 1165.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H40N15O25P5 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 642 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.52 Å3/Da / Density % sol: 51.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 100 mM Tris HCl pH 7.6, 33% (v/v) PEG200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03323 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 14, 2024
RadiationMonochromator: double crystal monochromator Si-111 and Si-113 reflection
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03323 Å / Relative weight: 1
ReflectionResolution: 1.8→45.77 Å / Num. obs: 51650 / % possible obs: 99.8 % / Redundancy: 52.88 % / Biso Wilson estimate: 39.191 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.102 / Rsym value: 0.023 / Net I/σ(I): 22.59
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 53.66 % / Rmerge(I) obs: 0.885 / Mean I/σ(I) obs: 2.61 / Num. unique obs: 7571 / CC1/2: 0.872 / Rsym value: 0.424 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→45.77 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / Cross valid method: FREE R-VALUE / ESU R: 0.133 / ESU R Free: 0.121
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2213 2611 5.065 %
Rwork0.1956 48937 -
all0.197 --
obs-51548 99.772 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 45.285 Å2
Baniso -1Baniso -2Baniso -3
1-2.031 Å2-0 Å2-0 Å2
2--2.031 Å2-0 Å2
3----4.063 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2835 799 68 642 4344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0123891
X-RAY DIFFRACTIONr_bond_other_d0.0310.0153212
X-RAY DIFFRACTIONr_angle_refined_deg2.0171.6995435
X-RAY DIFFRACTIONr_angle_other_deg2.1491.5957444
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5935352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.44120.877171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57715533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.7421529
X-RAY DIFFRACTIONr_chiral_restr0.1530.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023760
X-RAY DIFFRACTIONr_gen_planes_other0.0210.02871
X-RAY DIFFRACTIONr_nbd_refined0.2270.2751
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2290.23084
X-RAY DIFFRACTIONr_nbtor_refined0.1980.21757
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21669
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2220.2220
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0470.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2390.221
X-RAY DIFFRACTIONr_nbd_other0.2620.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2780.216
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1720.21
X-RAY DIFFRACTIONr_mcbond_it2.8414.1951399
X-RAY DIFFRACTIONr_mcbond_other2.8374.1871398
X-RAY DIFFRACTIONr_mcangle_it4.6936.2821748
X-RAY DIFFRACTIONr_mcangle_other4.6936.2931749
X-RAY DIFFRACTIONr_scbond_it3.6284.6142492
X-RAY DIFFRACTIONr_scbond_other3.6284.6132493
X-RAY DIFFRACTIONr_scangle_it5.6896.8133685
X-RAY DIFFRACTIONr_scangle_other5.6886.8133686
X-RAY DIFFRACTIONr_lrange_it8.04347.9644611
X-RAY DIFFRACTIONr_lrange_other7.88646.9324521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.3991850.3393572X-RAY DIFFRACTION99.761
1.847-1.8970.3111840.3113459X-RAY DIFFRACTION99.7263
1.897-1.9520.3241860.2743340X-RAY DIFFRACTION99.7736
1.952-2.0120.2941780.2493270X-RAY DIFFRACTION99.4233
2.012-2.0780.2741970.243147X-RAY DIFFRACTION99.8805
2.078-2.1510.2091380.2263104X-RAY DIFFRACTION100
2.151-2.2320.2451580.2142990X-RAY DIFFRACTION99.9682
2.232-2.3230.2641580.2352876X-RAY DIFFRACTION99.3451
2.323-2.4260.2231400.2042752X-RAY DIFFRACTION100
2.426-2.5450.2171440.1882641X-RAY DIFFRACTION100
2.545-2.6820.191360.1882554X-RAY DIFFRACTION100
2.682-2.8450.2321220.1982376X-RAY DIFFRACTION99.6013
2.845-3.0410.2261270.1872259X-RAY DIFFRACTION99.9163
3.041-3.2840.209910.182157X-RAY DIFFRACTION100
3.284-3.5960.1911190.1811936X-RAY DIFFRACTION100
3.596-4.0190.193940.1691789X-RAY DIFFRACTION100
4.019-4.6380.176770.1531608X-RAY DIFFRACTION100
4.638-5.6740.224750.1721341X-RAY DIFFRACTION98.0609
5.674-7.9970.22640.2091099X-RAY DIFFRACTION100
7.997-45.770.222380.204667X-RAY DIFFRACTION99.1561

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