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- PDB-6jh1: Crystal structure of bISG15/NS1B complex -

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Basic information

Entry
Database: PDB / ID: 6jh1
TitleCrystal structure of bISG15/NS1B complex
Components
  • Non-structural protein 1
  • Ubiquitin-like protein ISG15
KeywordsANTIVIRAL PROTEIN / Complex / Antivral
Function / homology
Function and homology information


ISG15 antiviral mechanism / positive regulation of protein oligomerization / ISG15-protein conjugation / Termination of translesion DNA synthesis / Negative regulators of DDX58/IFIH1 signaling / regulation of type II interferon production / symbiont-mediated suppression of host PKR/eIFalpha signaling / protein localization to mitochondrion / protein serine/threonine kinase inhibitor activity / response to type I interferon ...ISG15 antiviral mechanism / positive regulation of protein oligomerization / ISG15-protein conjugation / Termination of translesion DNA synthesis / Negative regulators of DDX58/IFIH1 signaling / regulation of type II interferon production / symbiont-mediated suppression of host PKR/eIFalpha signaling / protein localization to mitochondrion / protein serine/threonine kinase inhibitor activity / response to type I interferon / negative regulation of type I interferon-mediated signaling pathway / negative regulation of viral genome replication / positive regulation of interleukin-10 production / positive regulation of bone mineralization / negative regulation of protein ubiquitination / positive regulation of interferon-beta production / positive regulation of erythrocyte differentiation / integrin-mediated signaling pathway / modification-dependent protein catabolic process / protein tag activity / positive regulation of type II interferon production / integrin binding / symbiont-mediated suppression of host ISG15-protein conjugation / cytosolic small ribosomal subunit / defense response to virus / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / defense response to bacterium / virus-mediated perturbation of host defense response / ubiquitin protein ligase binding / host cell nucleus / RNA binding / extracellular region / nucleus / cytoplasm
Similarity search - Function
Influenza B non-structural protein (NS1) / Influenza non-structural protein (NS1) / S15/NS1, RNA-binding / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Helix Hairpins / Ubiquitin domain profile. / Ubiquitin-like domain / S15/NS1, RNA-binding ...Influenza B non-structural protein (NS1) / Influenza non-structural protein (NS1) / S15/NS1, RNA-binding / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Helix Hairpins / Ubiquitin domain profile. / Ubiquitin-like domain / S15/NS1, RNA-binding / Ubiquitin-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ubiquitin-like protein ISG15 / Non-structural protein 1
Similarity search - Component
Biological speciesInfluenza B virus
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsJiang, Y.N. / Wang, X.W.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31470751 China
National Natural Science Foundation of ChinaU1405228 China
CitationJournal: To Be Published
Title: Crystal structure of bISG15/NS1B complex
Authors: Jiang, Y.N. / Wang, X.Q.
History
DepositionFeb 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-structural protein 1
B: Non-structural protein 1
D: Ubiquitin-like protein ISG15
C: Ubiquitin-like protein ISG15


Theoretical massNumber of molelcules
Total (without water)58,3914
Polymers58,3914
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7860 Å2
ΔGint-50 kcal/mol
Surface area24580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.140, 80.050, 109.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Non-structural protein 1 / NS1 / NS1A


Mass: 11881.639 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza B virus (strain B/Lee/1940) / Strain: B/Lee/1940 / Gene: NS / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03502
#2: Protein Ubiquitin-like protein ISG15


Mass: 17314.027 Da / Num. of mol.: 2 / Mutation: C78S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: Isg15 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O02741

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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: 2.22 Å3/Da / Density % sol: 44.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES, pH 6.7 11 %(w/v) PEG 6000, 5 %(v/v) MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→35.932 Å / Num. obs: 10914 / % possible obs: 98 % / Redundancy: 5.2 % / Net I/σ(I): 15.9
Reflection shellResolution: 3→3.1 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→33.33 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2735 568 5.2 %
Rwork0.2186 --
obs0.2215 10761 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→33.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3795 0 0 0 3795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113852
X-RAY DIFFRACTIONf_angle_d1.4275176
X-RAY DIFFRACTIONf_dihedral_angle_d19.3462393
X-RAY DIFFRACTIONf_chiral_restr0.082575
X-RAY DIFFRACTIONf_plane_restr0.007676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.30190.34311270.28922552X-RAY DIFFRACTION100
3.3019-3.77920.34791530.25852528X-RAY DIFFRACTION100
3.7792-4.75970.25741360.20742581X-RAY DIFFRACTION100
4.7597-35.93420.24511520.19672685X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 29.7814 Å / Origin y: 1.1472 Å / Origin z: 27.1504 Å
111213212223313233
T0.5193 Å20.007 Å2-0.0254 Å2-0.4721 Å20.0059 Å2--0.5565 Å2
L1.8389 °20.1863 °2-0.8233 °2-1.2625 °20.0396 °2--2.9525 °2
S-0.0256 Å °-0.1247 Å °0.0528 Å °-0.0156 Å °0.01 Å °-0.0092 Å °0.0523 Å °0.1049 Å °0.0116 Å °
Refinement TLS groupSelection details: all

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