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- PDB-4rwq: Crystal structure of the apo-state of porcine OAS1 -

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Basic information

Entry
Database: PDB / ID: 4rwq
TitleCrystal structure of the apo-state of porcine OAS1
Components2'-5'-oligoadenylate synthase 1
KeywordsTRANSFERASE / Interferon-induced / dsRNA-activated
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
2'-5'-oligoadenylate synthase 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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: 2'-5'-oligoadenylate synthase 1


Theoretical massNumber of molelcules
Total (without water)82,5572
Polymers82,5572
Non-polymers00
Water181
1
A: 2'-5'-oligoadenylate synthase 1


Theoretical massNumber of molelcules
Total (without water)41,2781
Polymers41,2781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 2'-5'-oligoadenylate synthase 1


Theoretical massNumber of molelcules
Total (without water)41,2781
Polymers41,2781
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.840, 145.080, 80.140
Angle α, β, γ (deg.)90.00, 106.40, 90.00
Int Tables number5
Space group name H-MC121

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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.: 2
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.7 Å3/Da / Density % sol: 54.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M (NH4)2SO4, 0.1 M Sodium acetate pH 5.5, 10% PEG 2000 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: 3.1→46 Å / Num. all: 15926 / Num. obs: 15919 / % possible obs: 100 % / Observed criterion σ(I): -3

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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: 3.1→45.498 Å / SU ML: 0.44 / σ(F): 1.37 / Phase error: 29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2604 793 4.99 %random
Rwork0.2097 ---
obs0.2121 15906 99.91 %-
all-15926 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.3 Å2
Refinement stepCycle: LAST / Resolution: 3.1→45.498 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5616 0 0 1 5617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035746
X-RAY DIFFRACTIONf_angle_d0.667764
X-RAY DIFFRACTIONf_dihedral_angle_d12.4952190
X-RAY DIFFRACTIONf_chiral_restr0.04838
X-RAY DIFFRACTIONf_plane_restr0.0041006
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.29420.3421390.28222501X-RAY DIFFRACTION100
3.2942-3.54850.32741390.25972507X-RAY DIFFRACTION100
3.5485-3.90540.31541350.2322474X-RAY DIFFRACTION100
3.9054-4.47010.25321240.20462546X-RAY DIFFRACTION100
4.4701-5.63010.2491360.19892524X-RAY DIFFRACTION100
5.6301-45.50330.20771200.18072561X-RAY DIFFRACTION100
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)
12.17442.101-3.57122.2258-3.19066.5789-0.4156-0.92330.8171-0.0647-0.3577-0.5021-1.37172.03150.00021.0362-0.5237-0.22741.40180.31171.0913-11.96821.045216.9723
26.21212.91171.18113.05011.77164.273-0.1306-0.85590.4348-0.1326-0.13120.2735-0.2387-0.42060.07290.4740.13270.01890.5139-0.08980.5448-34.18116.95138.4206
32.44410.7957-3.64348.8749-0.83075.5946-0.25750.23850.4173-0.20960.582-0.3493-0.07840.0074-0.23360.79550.05550.04420.7142-0.11430.7975-33.990217.783340.1201
43.42590.38310.40394.05761.2544.56760.0203-0.21510.46050.2382-0.1814-0.2362-0.19930.10690.18810.5115-0.00190.05440.38070.09020.485-33.87111.929826.8039
53.15281.0686-0.16054.50720.52472.583-0.38790.95170.5726-0.56970.01120.0536-0.84180.55530.24770.9653-0.3176-0.18510.89890.40540.7051-27.71839.69079.5795
65.42351.13880.55392.03760.03761.00910.3579-1.726-0.69350.14250.07950.29810.2683-0.3465-0.18260.8463-0.1599-0.17111.25320.4650.8872-18.665-34.684229.5217
73.4528-1.08941.36635.2977-1.43744.3790.003-0.1609-0.52490.32570.4241-0.3278-0.0587-0.6038-0.00250.4954-0.0788-0.06331.06650.01410.5392-7.691-27.261813.3395
82.9362-2.07950.56833.6116-1.45843.45380.04170.1826-0.161-0.106-0.222-0.57470.19950.77770.090.5541-0.0724-0.0130.82490.04850.6746-8.1763-29.077513.3992
95.32941.8458-1.0283.6457-1.96254.26360.2720.1375-1.28990.09320.07050.02030.3885-0.472-0.30920.5578-0.0931-0.08520.52980.08990.7725-32.9877-29.642115.0201
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 111 )
3X-RAY DIFFRACTION3chain 'A' and (resid 112 through 132 )
4X-RAY DIFFRACTION4chain 'A' and (resid 133 through 201 )
5X-RAY DIFFRACTION5chain 'A' and (resid 202 through 346 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 43 )
7X-RAY DIFFRACTION7chain 'B' and (resid 44 through 93 )
8X-RAY DIFFRACTION8chain 'B' and (resid 94 through 185 )
9X-RAY DIFFRACTION9chain 'B' and (resid 186 through 346 )

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