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- PDB-4xq7: The crystal structure of the OAS-like domain (OLD) of human OASL -

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Basic information

Entry
Database: PDB / ID: 4xq7
TitleThe crystal structure of the OAS-like domain (OLD) of human OASL
Components2'-5'-oligoadenylate synthase-like protein
KeywordsTRANSFERASE / OAS / oligoadenylate synthetase / oligoadenylate synthetase-like / OASL / 2'-5' oligoadenylate synthetase
Function / homology
Function and homology information


positive regulation of RIG-I signaling pathway / interleukin-27-mediated signaling pathway / OAS antiviral response / nuclear thyroid hormone receptor binding / negative regulation of viral genome replication / nucleotidyltransferase activity / response to virus / Interferon gamma signaling / Interferon alpha/beta signaling / double-stranded RNA binding ...positive regulation of RIG-I signaling pathway / interleukin-27-mediated signaling pathway / OAS antiviral response / nuclear thyroid hormone receptor binding / negative regulation of viral genome replication / nucleotidyltransferase activity / response to virus / Interferon gamma signaling / Interferon alpha/beta signaling / double-stranded RNA binding / defense response to virus / innate immune response / nucleolus / DNA binding / RNA binding / nucleoplasm / membrane / cytoplasm / cytosol
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 / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-5'-oligoadenylate synthase-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsIbsen, M.S. / Gad, H.H. / Andersen, L.L. / Hornung, V. / Julkunen, I. / Sarkar, S.N. / Hartmann, R.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Structural and functional analysis reveals that human OASL binds dsRNA to enhance RIG-I signaling.
Authors: Ibsen, M.S. / Gad, H.H. / Andersen, L.L. / Hornung, V. / Julkunen, I. / Sarkar, S.N. / Hartmann, R.
History
DepositionJan 19, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2Jun 10, 2015Group: Database references
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2'-5'-oligoadenylate synthase-like protein


Theoretical massNumber of molelcules
Total (without water)41,8081
Polymers41,8081
Non-polymers00
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.800, 57.620, 64.790
Angle α, β, γ (deg.)90.00, 99.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 2'-5'-oligoadenylate synthase-like protein / 2'-5'-OAS-related protein / 2'-5'-OAS-RP / 59 kDa 2'-5'-oligoadenylate synthase-like protein / ...2'-5'-OAS-related protein / 2'-5'-OAS-RP / 59 kDa 2'-5'-oligoadenylate synthase-like protein / Thyroid receptor-interacting protein 14 / TRIP-14 / p59 OASL / p59OASL


Mass: 41807.859 Da / Num. of mol.: 1 / Fragment: UNP residues 1-350
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OASL, TRIP14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15646
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100 mM Tris pH 7.5, 200 mM LiSO4 and 20% (w/v) polyethylene glycol (PEG) 3350.
PH range: 7-8

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.97907 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 1.6→35.51 Å / Num. obs: 52563 / % possible obs: 99.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.07312 / Net I/σ(I): 13.97
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.7549 / Mean I/σ(I) obs: 1.82 / Num. measured obs: 19682 / Num. unique all: 5258 / CC1/2: 0.636 / % possible all: 99.92

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1839)refinement
XDSdata reduction
Cootmodel building
PHASERphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1px5

1px5


Resolution: 1.6→35.505 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1926 1577 3 %
Rwork0.1671 --
obs0.1679 52556 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→35.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2749 0 0 402 3151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012817
X-RAY DIFFRACTIONf_angle_d1.2033827
X-RAY DIFFRACTIONf_dihedral_angle_d13.6031051
X-RAY DIFFRACTIONf_chiral_restr0.048423
X-RAY DIFFRACTIONf_plane_restr0.006488
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6001-1.65170.29891430.24924629X-RAY DIFFRACTION100
1.6517-1.71070.23911420.22434586X-RAY DIFFRACTION100
1.7107-1.77920.25341420.20494599X-RAY DIFFRACTION100
1.7792-1.86020.23051430.19044633X-RAY DIFFRACTION100
1.8602-1.95830.20641430.16664614X-RAY DIFFRACTION100
1.9583-2.08090.21241420.16094605X-RAY DIFFRACTION100
2.0809-2.24160.18261440.15584637X-RAY DIFFRACTION100
2.2416-2.46710.17711420.15184614X-RAY DIFFRACTION100
2.4671-2.8240.19031450.15534667X-RAY DIFFRACTION100
2.824-3.55740.16741440.16444654X-RAY DIFFRACTION100
3.5574-35.5140.17251470.15464741X-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)
13.1241-1.4326-3.15540.90821.65393.33910.1535-0.23780.256-0.12070.0194-0.1828-0.429-0.0422-0.15870.1599-0.02080.04290.0987-0.01690.151641.13356.609349.7977
22.22452.78940.74327.35552.78162.2516-0.0840.2483-0.0536-0.40480.0750.1276-0.02590.026-0.00260.08480.0218-0.0160.1098-0.00340.095838.810832.463426.8214
31.09060.0503-0.05861.35940.39670.75990.0357-0.0197-0.07120.002-0.0690.1130.0043-0.10680.01550.06930.00120.01030.0802-0.00080.083237.281428.823635.1727
44.0923.6291-0.11826.25091.30641.27540.01790.0174-0.34360.0318-0.1552-0.08030.1875-0.25530.12550.1054-0.01430.03110.1685-0.02340.115321.59730.987442.2104
53.2631-2.4811.26287.5606-3.53833.40830.1447-0.06130.0476-0.2393-0.1475-0.25140.28040.16340.00690.0970.00880.01730.0976-0.00850.049637.869743.28853.0606
61.64440.90910.10312.2210.93121.18360.0963-0.30220.08290.1878-0.1820.20070.0469-0.21570.06050.1077-0.00890.01630.1926-0.00420.092324.809542.678156.7046
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 60 )
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 170 )
4X-RAY DIFFRACTION4chain 'A' and (resid 171 through 203 )
5X-RAY DIFFRACTION5chain 'A' and (resid 204 through 232 )
6X-RAY DIFFRACTION6chain 'A' and (resid 233 through 348 )

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