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- PDB-3rt3: Complex of influenza virus protein with host anti-viral factor -

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Basic information

Entry
Database: PDB / ID: 3rt3
TitleComplex of influenza virus protein with host anti-viral factor
Components
  • Non-structural protein 1
  • Ubiquitin-like protein ISG15
KeywordsANTIVIRAL PROTEIN/VIRAL PROTEIN / ubiquitin-like domain / ISGylation / ANTIVIRAL PROTEIN-VIRAL PROTEIN complex
Function / homology
Function and homology information


ISG15-protein conjugation / positive regulation of protein oligomerization / symbiont-mediated suppression of host PKR/eIFalpha signaling / regulation of type II interferon production / NS1 Mediated Effects on Host Pathways / protein localization to mitochondrion / response to type I interferon / protein serine/threonine kinase inhibitor activity / Modulation of host responses by IFN-stimulated genes / negative regulation of type I interferon-mediated signaling pathway ...ISG15-protein conjugation / positive regulation of protein oligomerization / symbiont-mediated suppression of host PKR/eIFalpha signaling / regulation of type II interferon production / NS1 Mediated Effects on Host Pathways / protein localization to mitochondrion / response to type I interferon / protein serine/threonine kinase inhibitor activity / Modulation of host responses by IFN-stimulated genes / negative regulation of type I interferon-mediated signaling pathway / negative regulation of viral genome replication / RSV-host interactions / 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 / Negative regulators of DDX58/IFIH1 signaling / Termination of translesion DNA synthesis / PKR-mediated signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / response to virus / modification-dependent protein catabolic process / ISG15 antiviral mechanism / positive regulation of type II interferon production / protein tag activity / Interferon alpha/beta signaling / integrin binding / 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 / innate immune response / ubiquitin protein ligase binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / RNA binding / extracellular region / nucleoplasm / nucleus / cytosol / 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 domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Helix Hairpins ...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 domain / 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
SUCCINIC ACID / Non-structural protein 1 / Ubiquitin-like protein ISG15
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.006 Å
AuthorsWang, X.Q. / Li, L.
CitationJournal: To be Published
Title: Crystal structure of human ISG15 in complex with influenza B virus NS1B
Authors: Li, L. / Wang, X.Q.
History
DepositionMay 3, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _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: Ubiquitin-like protein ISG15
C: Non-structural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3094
Polymers30,0722
Non-polymers2362
Water1,53185
1
B: Ubiquitin-like protein ISG15
C: Non-structural protein 1
hetero molecules

B: Ubiquitin-like protein ISG15
C: Non-structural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6178
Polymers60,1454
Non-polymers4724
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area7490 Å2
ΔGint-48 kcal/mol
Surface area24540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.674, 39.147, 74.704
Angle α, β, γ (deg.)90.00, 90.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ubiquitin-like protein ISG15 / Interferon-induced 15 kDa protein / Interferon-induced 17 kDa protein / IP17 / Ubiquitin cross- ...Interferon-induced 15 kDa protein / Interferon-induced 17 kDa protein / IP17 / Ubiquitin cross-reactive protein / hUCRP


Mass: 17361.881 Da / Num. of mol.: 1 / Mutation: C78S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ISG15, G1P2, UCRP / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P05161
#2: Protein Non-structural protein 1 / NS1 / NS1B


Mass: 12710.521 Da / Num. of mol.: 1
Fragment: N-terminal G1P2-binding domain, UNP residues 1-103
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza B virus / Strain: B/Lee/1940 / Gene: NS / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / References: UniProt: P03502
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 8000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2010
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 18345 / Num. obs: 16786 / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 2→2.05 Å / % possible all: 86.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: dev_596)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1Z2M, 1XEQ

1z2m

1xeq


Resolution: 2.006→46.835 Å / FOM work R set: 0.828 / SU ML: 0.27 / σ(F): 0 / Phase error: 24.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2434 852 5.22 %random
Rwork0.1892 ---
all0.1921 18345 --
obs0.1921 16316 88.36 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.364 Å2 / ksol: 0.334 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.4126 Å20 Å21.3034 Å2
2--4.1132 Å2-0 Å2
3---0.2993 Å2
Refinement stepCycle: LAST / Resolution: 2.006→46.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1943 0 16 85 2044
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072000
X-RAY DIFFRACTIONf_angle_d1.0452695
X-RAY DIFFRACTIONf_dihedral_angle_d14.973768
X-RAY DIFFRACTIONf_chiral_restr0.07300
X-RAY DIFFRACTIONf_plane_restr0.004351
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0058-2.13140.28941430.2079220477
2.1314-2.2960.30011470.1897242884
2.296-2.5270.27151100.1994247285
2.527-2.89270.24081380.2128246285
2.8927-3.64420.26161550.1939290799
3.6442-46.84820.211590.1752299199
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)
12.6247-0.0438-1.69850.77210.15991.5915-0.07050.0579-0.2625-0.17-0.05470.07680.0636-0.14150.08540.20090.0013-0.01160.1689-0.04310.2029.1526-5.814812.2236
21.89210.303-0.69881.40271.1013.6475-0.0327-0.1820.0852-0.0427-0.0697-0.2097-0.24430.69790.04910.1628-0.0691-0.0020.23250.02170.1647.95919.35738.2909
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain B
2X-RAY DIFFRACTION2chain C

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