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- PDB-3r66: Crystal structure of human ISG15 in complex with NS1 N-terminal r... -

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Basic information

Entry
Database: PDB / ID: 3r66
TitleCrystal structure of human ISG15 in complex with NS1 N-terminal region from influenza virus B, 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 / innate immunity / ISG15 conjugation / 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: 2.3 Å
AuthorsGuan, R. / Ma, L.C. / Krug, R.M. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: The Structure of the complex of ISG15 and Influenza B virus NS1 Protein: implications for the mechanism of SN1-mediated inhibition of ISG15 conjugation
Authors: Guan, R. / Ma, L.C. / Leonard, P.G. / Brendan, A.R. / Sridharan, H. / Zhao, C. / Krug, R.M. / Montelione, G.T.
History
DepositionMar 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 12, 2014Group: Non-polymer description
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 24, 2018Group: Refinement description / Category: refine / Item: _refine.pdbx_starting_model
Revision 1.5Sep 13, 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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)62,4714
Polymers62,4714
Non-polymers00
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7270 Å2
ΔGint-58 kcal/mol
Surface area24730 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 4 molecules in the asymmetric unit form a tetramer. We are guessing the biological unit is probably a tetramer but we are not sure at present.

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Components

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


Mass: 13123.993 Da / Num. of mol.: 2 / Fragment: 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: 18111.658 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ISG15, G1P2, UCRP / Production host: Escherichia coli (E. coli) / References: UniProt: P05161
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 49.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG3350, 1% dioxane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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 / Net I/σ(I): 19
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
REFMAC5.6.0111refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XEQ, PDB ENTRY 1Z2M

1xeq

1z2m


Resolution: 2.3→69.64 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.916 / SU B: 18.301 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26467 1082 4.7 %RANDOM
Rwork0.21391 ---
all0.21631 24402 --
obs0.21631 21712 86.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.635 Å2
Baniso -1Baniso -2Baniso -3
1-2.11 Å20.17 Å2-0.58 Å2
2---3.38 Å21.69 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.3→69.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3868 0 0 135 4003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193941
X-RAY DIFFRACTIONr_bond_other_d0.0030.022753
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.9875317
X-RAY DIFFRACTIONr_angle_other_deg1.11236744
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0645492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53324.451173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68115736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8081528
X-RAY DIFFRACTIONr_chiral_restr0.0710.2605
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214319
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02745
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.29→2.35 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 52 -
Rwork0.254 1253 -
obs--66.62 %
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)
12.76140.2122-0.505810.2189-4.84335.767-0.15670.1966-0.5465-0.82040.1521-0.55120.91210.09030.00460.20540.03990.01640.3285-0.01980.24661.171-42.35762.142
24.16020.6790.94649.1817-4.52696.5885-0.14-0.14040.45031.22210.0157-0.3469-1.05340.04990.12430.26520.0422-0.0450.3134-0.03750.19661.069-29.21770.568
31.39340.94242.15712.86783.72829.38910.2093-0.03820.07650.1553-0.24090.2296-0.0637-0.60320.03170.18890.00470.04620.17360.07810.2826-7.965-43.21392.585
41.1442-0.8412-1.28874.26933.32418.61540.0537-0.0328-0.0048-0.3479-0.06010.4552-0.1708-0.35770.00630.1434-0.029-0.08370.15870.08040.2271-9.826-26.58440.412
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 9999
2X-RAY DIFFRACTION2B1 - 9999
3X-RAY DIFFRACTION3C1 - 9999
4X-RAY DIFFRACTION4D1 - 9999

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