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- PDB-4ig8: Structural basis for cytosolic double-stranded RNA surveillance b... -

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Basic information

Entry
Database: PDB / ID: 4ig8
TitleStructural basis for cytosolic double-stranded RNA surveillance by human OAS1
Components
  • 2'-5'-oligoadenylate synthase 1
  • RNA (5'-R(*GP*CP*AP*UP*AP*AP*AP*GP*GP*UP*CP*AP*AP*AP*AP*GP*CP*C)-3')
  • RNA (5'-R(*GP*GP*CP*UP*UP*UP*UP*GP*AP*CP*CP*UP*UP*UP*AP*UP*GP*C)-3')
KeywordsTRANSFERASE/RNA / Nucleotidyl transferase / Innate immune system Double-stranded dsRNA sensor RNA polymerase / Nucleotidyl transferase 2-5A synthetase / RNase L activator / Double-stranded RNA / Cytosol / TRANSFERASE-RNA complex
Function / homology
Function and homology information


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 / cellular response to interferon-alpha / interleukin-27-mediated signaling pathway / positive regulation of cellular respiration / toll-like receptor 3 signaling pathway / OAS antiviral response ...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 / cellular response to interferon-alpha / interleukin-27-mediated signaling pathway / positive regulation of cellular respiration / toll-like receptor 3 signaling pathway / OAS antiviral response / surfactant homeostasis / positive regulation of monocyte chemotactic protein-1 production / toll-like receptor 4 signaling pathway / negative regulation of type I interferon-mediated signaling pathway / negative regulation of viral genome replication / type I interferon-mediated signaling pathway / protein complex oligomerization / cellular response to interferon-beta / antiviral innate immune response / positive regulation of interferon-beta production / response to virus / cellular response to virus / glucose metabolic process / Interferon gamma signaling / positive regulation of tumor necrosis factor production / double-stranded RNA binding / Interferon alpha/beta signaling / glucose homeostasis / defense response to virus / ribosome / defense response to bacterium / endoplasmic reticulum / mitochondrion / extracellular region / nucleoplasm / ATP binding / membrane / nucleus / 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
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / RNA / RNA (> 10) / 2'-5'-oligoadenylate synthase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDonovan, J. / Korennykh, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural basis for cytosolic double-stranded RNA surveillance by human oligoadenylate synthetase 1.
Authors: Donovan, J. / Dufner, M. / Korennykh, A.
History
DepositionDec 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Feb 13, 2013Group: Database references
Revision 1.3Feb 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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
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*C)-3')
C: RNA (5'-R(*GP*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)52,1426
Polymers51,6023
Non-polymers5403
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-58 kcal/mol
Surface area20200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.200, 93.200, 98.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 / E18/E16 / p46/p42 OAS


Mass: 40135.199 Da / Num. of mol.: 1 / Fragment: UNP residues 1-347
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OAS1, OIAS / Production host: Escherichia coli (E. coli)
References: UniProt: P00973, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases

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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*C)-3')


Mass: 5664.332 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: RNA chain RNA (5'-R(*GP*CP*AP*UP*AP*AP*AP*GP*GP*UP*CP*AP*AP*AP*AP*GP*CP*C)-3')


Mass: 5802.571 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 53 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 3.17 Å3/Da / Density % sol: 61.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.4
Details: 10 mM HEPES (pH 7.4), 350 mM NaCl, and 5 mM MgCl2, VAPOR DIFFUSION, temperature 293K

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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
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: 2.3→67.7 Å / Num. all: 18616 / Num. obs: 18604

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→67.7 Å / SU ML: 0.31 / σ(F): 1.99 / Phase error: 34.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2827 930 5.01 %Random
Rwork0.2285 ---
all0.2311 18604 --
obs0.2311 18574 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→67.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2741 758 32 50 3581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033685
X-RAY DIFFRACTIONf_angle_d0.7765158
X-RAY DIFFRACTIONf_dihedral_angle_d20.0142173
X-RAY DIFFRACTIONf_chiral_restr0.055589
X-RAY DIFFRACTIONf_plane_restr0.003525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.84240.39751310.35482481X-RAY DIFFRACTION100
2.8424-3.02050.36151300.31192467X-RAY DIFFRACTION100
3.0205-3.25370.34791310.28382476X-RAY DIFFRACTION100
3.2537-3.58110.28451320.23862511X-RAY DIFFRACTION100
3.5811-4.09920.26971320.20312504X-RAY DIFFRACTION100
4.0992-5.16430.2171350.18952550X-RAY DIFFRACTION100
5.1643-67.75220.26551390.20082655X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 16.657 Å / Origin y: 3.0935 Å / Origin z: 18.812 Å
111213212223313233
T0.5229 Å20.0376 Å2-0.0169 Å2-0.5251 Å20.0352 Å2--0.4814 Å2
L1.71 °20.7769 °2-0.1935 °2-3.6646 °20.5968 °2--4.0818 °2
S0.1554 Å °-0.0735 Å °0.0088 Å °0.051 Å °-0.2072 Å °-0.0809 Å °-0.0229 Å °0.6187 Å °0.0454 Å °
Refinement TLS groupSelection details: all

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