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- PDB-4rwo: Crystal structure of the porcine OAS1 L149R mutant in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4rwo
TitleCrystal structure of the porcine OAS1 L149R mutant in complex with dsRNA and ApCpp in the AMP donor position
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 / Interferon-induced / 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 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
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / 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: 2.2 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_ref_seq_dif.details / _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
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')
A: 2'-5'-oligoadenylate synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9636
Polymers53,4103
Non-polymers5543
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-55 kcal/mol
Surface area20940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.100, 73.100, 208.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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RNA chain , 2 types, 2 molecules BC

#1: 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)
#2: 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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Protein , 1 types, 1 molecules A

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


Mass: 41322.363 Da / Num. of mol.: 1 / Mutation: L149R
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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Non-polymers , 3 types, 76 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.61 Å3/Da / Density % sol: 52.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris-HCl pH 8.0, 25% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0645 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 12, 2013
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0645 Å / Relative weight: 1
ReflectionResolution: 2.2→46.306 Å / Num. all: 29751 / Num. obs: 29636 / % possible obs: 99.6 % / 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: 2.2→46.306 Å / SU ML: 0.27 / σ(F): 1.36 / Phase error: 25.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2367 1495 5.06 %random
Rwork0.2024 ---
obs0.204 29537 99.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.68 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.306 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2820 799 33 73 3725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0173810
X-RAY DIFFRACTIONf_angle_d1.055334
X-RAY DIFFRACTIONf_dihedral_angle_d14.471563
X-RAY DIFFRACTIONf_chiral_restr0.083611
X-RAY DIFFRACTIONf_plane_restr0.01545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2710.35261440.30842473X-RAY DIFFRACTION100
2.271-2.35220.34351320.29212510X-RAY DIFFRACTION100
2.3522-2.44640.33591410.28772470X-RAY DIFFRACTION99
2.4464-2.55770.30761330.26552492X-RAY DIFFRACTION99
2.5577-2.69250.27261230.25612533X-RAY DIFFRACTION100
2.6925-2.86120.30411280.24912508X-RAY DIFFRACTION99
2.8612-3.08210.29051320.26182530X-RAY DIFFRACTION99
3.0821-3.39220.25991490.21342529X-RAY DIFFRACTION99
3.3922-3.88280.22821440.1862569X-RAY DIFFRACTION100
3.8828-4.89110.17971320.15992632X-RAY DIFFRACTION100
4.8911-46.31640.19381370.16812796X-RAY DIFFRACTION100

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