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- PDB-5ul6: The molecular mechanisms by which NS1 of the 1918 Spanish influen... -

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Basic information

Entry
Database: PDB / ID: 5ul6
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 of nonstructural protein 1 of influenza a virus
KeywordsVIRAL PROTEIN / SH3 / CrkII / Nonstructural Protein 1 / Influenza A Virus
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 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / signaling adaptor activity / 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 / Downstream signal transduction / SH2 domain binding / 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 / positive regulation of JNK cascade / FCGR3A-mediated phagocytosis / 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)
Influenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsShen, Q. / Zeng, D. / Zhao, B. / Li, P. / Cho, J.H.
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: The Molecular Mechanisms Underlying the Hijack of Host Proteins by the 1918 Spanish Influenza Virus.
Authors: Shen, Q. / Zeng, D. / Zhao, B. / Bhatt, V.S. / Li, P. / Cho, J.H.
History
DepositionJan 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: 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 of nonstructural protein 1 of influenza a virus


Theoretical massNumber of molelcules
Total (without water)8,5662
Polymers8,5662
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-4 kcal/mol
Surface area5290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.650, 39.260, 29.030
Angle α, β, γ (deg.)90.00, 98.43, 90.00
Int Tables number4
Space group name H-MP1211

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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 of nonstructural protein 1 of influenza a virus


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


Mass: 18.015 Da / Num. of mol.: 129 / 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: 1.82 Å3/Da / Density % sol: 32.4 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2 M Ammonium sulfate, 0.1 M Sodium acetate trihydrate pH4.6, 30% w/v Polyethylene glycol monomethyl ether 2000

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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: Oct 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45 Å / Relative weight: 1
ReflectionResolution: 1.45→27.351 Å / Num. obs: 10105 / % possible obs: 91.9 % / Redundancy: 3.5 % / Net I/σ(I): 9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IH2

5ih2


Resolution: 1.45→27.351 Å / SU ML: 0.17 / Cross valid method: NONE / σ(F): 1.43 / Phase error: 22.56
RfactorNum. reflection% reflection
Rfree0.187 483 4.78 %
Rwork0.1672 --
obs0.1681 10105 91.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→27.351 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms607 0 0 129 736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005633
X-RAY DIFFRACTIONf_angle_d0.804854
X-RAY DIFFRACTIONf_dihedral_angle_d18.374258
X-RAY DIFFRACTIONf_chiral_restr0.08477
X-RAY DIFFRACTIONf_plane_restr0.005118
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.65980.24151490.17982901X-RAY DIFFRACTION84
1.6598-2.09110.17681450.18163303X-RAY DIFFRACTION94
2.0911-27.35610.1811890.15843418X-RAY DIFFRACTION97
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)
11.0077-1.1140.69023.71871.47675.061-0.15570.01520.00150.09010.0883-0.01360.08630.18790.04650.0519-0.0261-0.01740.05150.01090.091139.13687.587612.1522
23.66452.1543.29434.78064.48487.417-0.11930.1394-0.022-0.1620.07280.067-0.13490.16160.06870.0573-0.0089-0.0010.07450.03280.080338.14798.24973.0946
37.6691.10862.25732.79810.53044.6482-0.13270.05640.3026-0.0659-0.00720.63340.058-0.43730.12790.0647-0.0056-0.00430.1003-0.00740.175529.48229.240112.2163
41.60231.58850.12584.2822.33572.28360.0543-0.12260.05460.0362-0.18130.25340.042-0.12320.09930.0696-0.00420.00260.0729-0.00910.103430.30161.36858.5563
55.4428-5.55952.22219.07420.31844.3037-0.17020.3990.4464-0.4849-0.034-0.2086-1.05360.09960.16690.1659-0.0043-0.02070.09050.01450.13532.711417.29756.6832
61.0956-0.48181.11172.31110.33655.3130.0341-0.0359-0.01260.0195-0.01130.09640.1292-0.1201-0.05670.0506-0.02370.01260.0611-0.00380.100435.83095.219612.8545
72.3361.15281.92111.93161.08442.0062-0.0110.262-0.1447-0.17160.1178-0.0899-0.04470.0541-0.10810.1595-0.02290.01620.1304-0.01050.116637.1952-4.21074.6085
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 157 )
3X-RAY DIFFRACTION3chain 'A' and (resid 158 through 163 )
4X-RAY DIFFRACTION4chain 'A' and (resid 164 through 173 )
5X-RAY DIFFRACTION5chain 'A' and (resid 174 through 178 )
6X-RAY DIFFRACTION6chain 'A' and (resid 179 through 191 )
7X-RAY DIFFRACTION7chain 'M' and (resid 0 through 12 )

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