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- PDB-6jh0: Crystal structure of cISG15/NS1B complex -

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Basic information

Entry
Database: PDB / ID: 6jh0
TitleCrystal structure of cISG15/NS1B complex
Components
  • ISG15 ubiquitin-like modifier
  • Non-structural protein 1
KeywordsANTIVIRAL PROTEIN / Complex / Antiviral
Function / homology
Function and homology information


ISG15 antiviral mechanism / Termination of translesion DNA synthesis / Negative regulators of DDX58/IFIH1 signaling / ISG15-protein conjugation / positive regulation of protein oligomerization / symbiont-mediated suppression of host PKR/eIFalpha signaling / protein localization to mitochondrion / response to type I interferon / protein serine/threonine kinase inhibitor activity / negative regulation of type I interferon-mediated signaling pathway ...ISG15 antiviral mechanism / Termination of translesion DNA synthesis / Negative regulators of DDX58/IFIH1 signaling / ISG15-protein conjugation / positive regulation of protein oligomerization / symbiont-mediated suppression of host PKR/eIFalpha signaling / protein localization to mitochondrion / response to type I interferon / protein serine/threonine kinase inhibitor activity / 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 / positive regulation of type II interferon production / protein tag activity / integrin binding / cytosolic small ribosomal subunit / symbiont-mediated suppression of host ISG15-protein conjugation / defense response to virus / host cell cytoplasm / defense response to bacterium / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Helix Hairpins / Ubiquitin domain profile. / Ubiquitin-like domain ...Influenza B non-structural protein (NS1) / Influenza non-structural protein (NS1) / S15/NS1, RNA-binding / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Helix Hairpins / Ubiquitin domain profile. / Ubiquitin-like domain / S15/NS1, RNA-binding / Ubiquitin-like domain superfamily / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ISG15 ubiquitin like modifier / Non-structural protein 1
Similarity search - Component
Biological speciesInfluenza B virus
Canis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.403 Å
AuthorsJiang, Y.N. / Wang, X.Q.
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 cISG15/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 / Category: chem_comp_atom / chem_comp_bond / database_2
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
C: Non-structural protein 1
A: Non-structural protein 1
D: ISG15 ubiquitin-like modifier
B: ISG15 ubiquitin-like modifier


Theoretical massNumber of molelcules
Total (without water)59,8054
Polymers59,8054
Non-polymers00
Water82946
1
C: Non-structural protein 1
B: ISG15 ubiquitin-like modifier


Theoretical massNumber of molelcules
Total (without water)29,9032
Polymers29,9032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-12 kcal/mol
Surface area14450 Å2
MethodPISA
2
A: Non-structural protein 1
D: ISG15 ubiquitin-like modifier


Theoretical massNumber of molelcules
Total (without water)29,9032
Polymers29,9032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-11 kcal/mol
Surface area14700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.298, 77.298, 217.582
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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 ISG15 ubiquitin-like modifier


Mass: 18020.875 Da / Num. of mol.: 2 / Mutation: C78S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: ISG15 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: E2R7R1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M magnesium chloride, 0.1 M MES, pH 6.7, 16 %(w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→36.419 Å / Num. obs: 26531 / % possible obs: 100 % / Redundancy: 11.5 % / Net I/σ(I): 20.7
Reflection shellResolution: 2.4→2.48 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.403→36.419 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2657 1271 4.79 %
Rwork0.2072 --
obs0.21 26531 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.403→36.419 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3905 0 0 46 3951
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083973
X-RAY DIFFRACTIONf_angle_d1.0455354
X-RAY DIFFRACTIONf_dihedral_angle_d18.3612442
X-RAY DIFFRACTIONf_chiral_restr0.058597
X-RAY DIFFRACTIONf_plane_restr0.006696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4027-2.49890.31511260.27372753X-RAY DIFFRACTION99
2.4989-2.61260.31591520.26772726X-RAY DIFFRACTION100
2.6126-2.75030.29041260.26212801X-RAY DIFFRACTION100
2.7503-2.92250.29821450.24612748X-RAY DIFFRACTION100
2.9225-3.14810.36921400.25622780X-RAY DIFFRACTION100
3.1481-3.46460.29981630.23472786X-RAY DIFFRACTION100
3.4646-3.96550.26111350.21112814X-RAY DIFFRACTION100
3.9655-4.9940.2211350.1622880X-RAY DIFFRACTION100
4.994-36.42320.23361490.18452972X-RAY DIFFRACTION98
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)
14.92770.6935-2.7523.0807-0.9434.59010.38390.8560.3005-0.3279-0.00570.0127-0.6863-0.5006-0.32380.59530.07950.14070.43660.0690.3888-19.474-27.2318-36.2655
28.15270.04120.87045.456-0.98677.0569-0.00630.2611-0.74790.28940.06490.78770.1491-0.2993-0.06510.3220.07740.11250.383-0.01760.574-40.274-43.1716-19.089
36.38315.2144-2.60944.6759-0.66095.12450.12880.0134-0.26160.4248-0.3977-0.5644-0.33830.77460.25290.4861-0.00680.02570.68130.11470.5708-53.4018-30.5437-42.7186
44.77730.3355-1.90443.7496-0.37544.73260.5091-0.57240.25810.5093-0.27920.1178-0.62450.173-0.20890.5254-0.04280.17240.3168-0.06920.4113-18.346-28.2191-19.6792
57.30270.26460.84437.1426-1.81176.312-0.0110.2088-1.0073-0.4682-0.1586-0.47560.62980.30450.17470.49320.020.09780.4166-0.08190.52832.0833-43.0725-38.1083
69.5115-0.61891.08234.32391.6515.5196-0.1824-0.693-0.08020.27420.0661-0.0708-0.1871-0.36090.07150.54280.09410.07220.53240.01250.46215.0285-32.247-13.2905
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B and resid 9:85
3X-RAY DIFFRACTION3chain B and resid 86:161
4X-RAY DIFFRACTION4chain C
5X-RAY DIFFRACTION5chain D and resid 9:85
6X-RAY DIFFRACTION6chain D and resid 86:161

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