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- PDB-3sdl: Crystal structure of human ISG15 in complex with NS1 N-terminal r... -

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Basic information

Entry
Database: PDB / ID: 3sdl
TitleCrystal structure of human ISG15 in complex with NS1 N-terminal region from influenza B virus, Northeast Structural Genomics Consortium Target IDs HX6481, HR2873, and OR2
Components
  • Non-structural protein 1
  • Ubiquitin-like protein ISG15
KeywordsViral Protein/antiviral Protein / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG / protein complex / Viral Protein-antiviral 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
Non-structural protein 1 / Ubiquitin-like protein ISG15
Similarity search - Component
Biological speciesInfluenza B virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsGuan, R. / Ma, L.-C. / Krug, R.M. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural basis for the sequence-specific recognition of human ISG15 by the NS1 protein of influenza B virus.
Authors: Guan, R. / Ma, L.C. / Leonard, P.G. / Amer, B.R. / Sridharan, H. / Zhao, C. / Krug, R.M. / Montelione, G.T.
History
DepositionJun 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2011Group: Database references
Revision 1.2Aug 31, 2011Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 13, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 29, 2023Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)62,4074
Polymers62,4074
Non-polymers00
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7300 Å2
ΔGint-53 kcal/mol
Surface area24600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.009, 56.142, 74.020
Angle α, β, γ (deg.)70.59, 84.24, 83.91
Int Tables number1
Space group name H-MP1
DetailsThe NS1B-NTR dimer interacts with two ISG15 molecules to form a heterotetramer.

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Components

#1: Protein Non-structural protein 1 / NS1 / NS1B


Mass: 13123.993 Da / Num. of mol.: 2 / Fragment: G1P2-binding region, residues 1-103
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza B virus / Strain: B/LEE/1940 / Gene: NS / Production host: Escherichia coli (E. coli) / References: UniProt: P03502
#2: 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: 18079.658 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: G1P2, ISG15, UCRP / Production host: Escherichia coli (E. coli) / References: UniProt: P05161
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.5
Details: 15% PEG3350, 1% dioxane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, EVAPORATION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9798 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 12, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. all: 24402 / Num. obs: 24402 / % possible obs: 93.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.062
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 3.5 / Num. unique all: 2492 / % possible all: 96.4

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z2M, 1XEQ

1z2m

1xeq


Resolution: 2.29→36.715 Å / SU ML: 0.33 / σ(F): 0.07 / Phase error: 29.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 1080 4.74 %RANDOM
Rwork0.2222 ---
obs0.224 22769 86.14 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.114 Å2 / ksol: 0.343 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.3941 Å2-1.3122 Å2-1.9815 Å2
2---10.2593 Å29.3659 Å2
3----0.1349 Å2
Refinement stepCycle: LAST / Resolution: 2.29→36.715 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3870 0 0 142 4012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033944
X-RAY DIFFRACTIONf_angle_d0.6485321
X-RAY DIFFRACTIONf_dihedral_angle_d12.7991515
X-RAY DIFFRACTIONf_chiral_restr0.045603
X-RAY DIFFRACTIONf_plane_restr0.003692
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2903-2.39450.3471060.28712408X-RAY DIFFRACTION76
2.3945-2.52080.31881400.29062760X-RAY DIFFRACTION89
2.5208-2.67870.42951260.35072543X-RAY DIFFRACTION80
2.6787-2.88540.29231490.29462712X-RAY DIFFRACTION87
2.8854-3.17560.28161420.24573066X-RAY DIFFRACTION97
3.1756-3.63480.2851290.2332761X-RAY DIFFRACTION87
3.6348-4.57810.21141340.18822612X-RAY DIFFRACTION83
4.5781-36.71950.22641540.1792827X-RAY DIFFRACTION90
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)
11.94460.60920.76844.6328-1.55864.2551-0.0010.1575-0.1996-0.3670.247-0.49210.58490.02830.00040.22320.07560.05910.405-0.01530.32721.0574-42.297762.335
23.86422.3161-0.0433.5991-1.71634.2981-0.1418-0.3280.31140.72510.1116-0.174-0.84450.0079-0.00050.35750.0627-0.05710.4408-0.08440.33660.5968-29.221870.2377
30.62540.6680.90841.10211.74565.1340.1980.083-0.04620.0172-0.06020.021-0.1654-0.3267-0.00020.34440.0040.03510.25230.02440.3646-7.9361-43.448292.4296
40.2653-0.4957-0.06133.56011.20456.21680.0405-0.0711-0.0925-0.4040.06920.4913-0.0277-0.28260.00610.3242-0.0583-0.07350.33370.04080.4097-9.7492-26.432140.535
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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