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- PDB-6atv: The molecular mechanisms by which NS1 of the 1918 Spanish influen... -

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Basic information

Entry
Database: PDB / ID: 6atv
TitleThe molecular mechanisms by which NS1 of the 1918 Spanish influenza A virus hijack host protein-protein interactions
Components
  • Adapter molecule crk
  • proline-rich motif in IAV-NS1
Keywordsprotein binding/viral protein / SH3 / CrkII / Nonstructural Protein 1 / Influenza A Virus / VIRAL PROTEIN / protein binding-viral protein complex
Function / homology
Function and homology information


response to hepatocyte growth factor / regulation of intracellular signal transduction / cellular response to endothelin / helper T cell diapedesis / cerebellar neuron development / response to cholecystokinin / postsynaptic specialization assembly / protein phosphorylated amino acid binding / regulation of T cell migration / symbiont-mediated suppression of host mRNA processing ...response to hepatocyte growth factor / regulation of intracellular signal transduction / cellular response to endothelin / helper T cell diapedesis / cerebellar neuron development / response to cholecystokinin / postsynaptic specialization assembly / protein phosphorylated amino acid binding / regulation of T cell migration / symbiont-mediated suppression of host mRNA processing / reelin-mediated signaling pathway / regulation of dendrite development / positive regulation of skeletal muscle acetylcholine-gated channel clustering / symbiont-mediated suppression of host PKR/eIFalpha signaling / negative regulation of natural killer cell mediated cytotoxicity / response to yeast / negative regulation of wound healing / regulation of protein binding / negative regulation of cell motility / ARMS-mediated activation / protein serine/threonine kinase inhibitor activity / protein localization to membrane / MET receptor recycling / MET activates RAP1 and RAC1 / cellular response to insulin-like growth factor stimulus / establishment of cell polarity / regulation of GTPase activity / p130Cas linkage to MAPK signaling for integrins / positive regulation of smooth muscle cell migration / dendrite development / positive regulation of Rac protein signal transduction / regulation of cell adhesion mediated by integrin / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / cellular response to nitric oxide / regulation of signal transduction / ephrin receptor signaling pathway / signaling adaptor activity / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of substrate adhesion-dependent cell spreading / cellular response to transforming growth factor beta stimulus / cytoskeletal protein binding / ephrin receptor binding / phosphotyrosine residue binding / SH2 domain binding / Downstream signal transduction / protein tyrosine kinase binding / cell chemotaxis / cellular response to nerve growth factor stimulus / Regulation of signaling by CBL / hippocampus development / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / positive regulation of JNK cascade / insulin-like growth factor receptor binding / neuron migration / response to hydrogen peroxide / neuromuscular junction / lipid metabolic process / receptor tyrosine kinase binding / cerebral cortex development / Regulation of actin dynamics for phagocytic cup formation / kinase binding / VEGFA-VEGFR2 Pathway / SH3 domain binding / : / signaling receptor complex adaptor activity / cell migration / actin cytoskeleton / regulation of cell shape / actin cytoskeleton organization / scaffold protein binding / positive regulation of cell growth / cell population proliferation / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response / ubiquitin protein ligase binding / host cell nucleus / regulation of transcription by RNA polymerase II / signal transduction / protein-containing complex / RNA binding / extracellular exosome / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
CRK, N-terminal SH3 domain / CRK, C-terminal SH3 domain / Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) / Variant SH3 domain / SH3 Domains / SH3 domain / SH2 domain ...CRK, N-terminal SH3 domain / CRK, C-terminal SH3 domain / Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) / Variant SH3 domain / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH3 type barrels. / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / S15/NS1, RNA-binding / Roll / Mainly Beta
Similarity search - Domain/homology
Adapter molecule crk / Non-structural protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Orthomyxoviridae (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.751 Å
AuthorsShen, Q. / Zeng, D. / Zhao, B. / Li, P. / Cho, J.H.
CitationJournal: Biophys. J. / Year: 2018
Title: Molecular Mechanisms of Tight Binding through Fuzzy Interactions.
Authors: Shen, Q. / Shi, J. / Zeng, D. / Zhao, B. / Li, P. / Hwang, W. / Cho, J.H.
History
DepositionAug 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
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
A: Adapter molecule crk
M: proline-rich motif in IAV-NS1


Theoretical massNumber of molelcules
Total (without water)8,5662
Polymers8,5662
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR titration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-4 kcal/mol
Surface area5100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.840, 39.840, 171.951
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Adapter molecule crk / Proto-oncogene c-Crk / p38


Mass: 6971.731 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRK / Production host: Escherichia coli (E. coli) / References: UniProt: P46108
#2: Protein/peptide proline-rich motif in IAV-NS1


Mass: 1593.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Orthomyxoviridae (virus) / References: UniProt: Q99AU3*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.3 Å3/Da / Density % sol: 46.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate (pH 4.6), 30% PEG 2000, and 0.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.45 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Dec 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45 Å / Relative weight: 1
ReflectionResolution: 1.751→34.5 Å / Num. obs: 8437 / % possible obs: 94.62 % / Redundancy: 12 % / Net I/σ(I): 16.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UL6

5ul6


Resolution: 1.751→34.5 Å / SU ML: 0.17 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 23.47
RfactorNum. reflection% reflection
Rfree0.2053 456 5.4 %
Rwork0.1845 --
obs0.1857 8437 94.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.751→34.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms607 0 0 114 721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006624
X-RAY DIFFRACTIONf_angle_d0.781840
X-RAY DIFFRACTIONf_dihedral_angle_d15.167386
X-RAY DIFFRACTIONf_chiral_restr0.0576
X-RAY DIFFRACTIONf_plane_restr0.007115
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.751-2.0040.2411270.19172272X-RAY DIFFRACTION84
2.004-2.52470.20571500.18142754X-RAY DIFFRACTION100
2.5247-34.50.19821790.18432955X-RAY DIFFRACTION100
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)
15.48812.1627-1.26037.13090.95375.99630.2295-0.2071-0.03610.2363-0.4421-0.0434-0.190.10870.11810.01780.0229-0.00440.0921-0.02080.0605-6.79517.666-1.9791
25.1547-0.5876-4.13234.2808-2.56895.6824-0.06330.397-0.1678-0.62850.1227-0.2960.0964-0.0237-0.01970.1568-0.0048-0.0090.1894-0.02260.155-4.159116.8652-17.7083
34.1332-0.5075-0.52251.98081.20136.6498-0.03360.0439-0.1161-0.02260.08740.05560.0161-0.1544-0.02760.0088-0.0149-0.00470.0717-0.01290.0865-9.204414.7319-5.6133
46.0010.3371-3.60442.2888-1.02172.7888-0.01190.2041-0.1341-0.0798-0.11510.11460.0835-0.03190.07960.0960.0045-0.00730.0716-0.03060.0894-0.53929.9189-7.4481
54.48382.2089-2.66722.70330.54093.9345-0.06260.0947-0.0993-0.0421-0.03090.0877-0.0758-0.01450.07240.06360.0438-0.01090.04470.00440.1217-7.582814.1829-3.709
64.48070.26960.29361.3848-0.68015.2031-0.05840.013-0.3116-0.07210.053-0.08150.29990.00950.00220.07210.00590.00230.09260.02030.15644.673616.7401-8.5803
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 134 through 144 )
2X-RAY DIFFRACTION2chain 'A' and (resid 145 through 149 )
3X-RAY DIFFRACTION3chain 'A' and (resid 150 through 163 )
4X-RAY DIFFRACTION4chain 'A' and (resid 164 through 173 )
5X-RAY DIFFRACTION5chain 'A' and (resid 174 through 191 )
6X-RAY DIFFRACTION6chain 'M' and (resid 0 through 12 )

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