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Yorodumi- PDB-4u5w: Crystal Structure of HIV-1 Nef-SF2 Core Domain in Complex with th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4u5w | ||||||||||||
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Title | Crystal Structure of HIV-1 Nef-SF2 Core Domain in Complex with the Src Family Kinase Hck SH3-SH2 Tandem Regulatory Domains | ||||||||||||
Components |
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Keywords | Viral protein/Transferase / Hck / SH3-SH2 regulatory domains / SH3 / SH2 / Src Family Kinase / SFK / HIV-1 / Nef / virus / protein-protein complex / Nef-Hck complex / viral protein-transferase complex | ||||||||||||
Function / homology | Function and homology information leukocyte degranulation / respiratory burst after phagocytosis / innate immune response-activating signaling pathway / leukocyte migration involved in immune response / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / regulation of podosome assembly / suppression by virus of host autophagy / regulation of phagocytosis / FLT3 signaling through SRC family kinases ...leukocyte degranulation / respiratory burst after phagocytosis / innate immune response-activating signaling pathway / leukocyte migration involved in immune response / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / regulation of podosome assembly / suppression by virus of host autophagy / regulation of phagocytosis / FLT3 signaling through SRC family kinases / Nef and signal transduction / regulation of DNA-binding transcription factor activity / activation of transmembrane receptor protein tyrosine kinase activity / positive regulation of actin filament polymerization / Fc-gamma receptor signaling pathway involved in phagocytosis / host cell Golgi membrane / mesoderm development / FCGR activation / type II interferon-mediated signaling pathway / Signaling by CSF3 (G-CSF) / lipopolysaccharide-mediated signaling pathway / transport vesicle / cell surface receptor protein tyrosine kinase signaling pathway / negative regulation of inflammatory response to antigenic stimulus / phosphotyrosine residue binding / FCGR3A-mediated IL10 synthesis / caveola / cell projection / integrin-mediated signaling pathway / Regulation of signaling by CBL / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / peptidyl-tyrosine phosphorylation / Inactivation of CSF3 (G-CSF) signaling / endocytosis involved in viral entry into host cell / cytoplasmic side of plasma membrane / cytokine-mediated signaling pathway / SH3 domain binding / virion component / Signaling by CSF1 (M-CSF) in myeloid cells / regulation of inflammatory response / regulation of cell shape / protein tyrosine kinase activity / protein autophosphorylation / cell differentiation / lysosome / cytoskeleton / cell adhesion / intracellular signal transduction / inflammatory response / protein phosphorylation / intracellular membrane-bounded organelle / innate immune response / focal adhesion / signaling receptor binding / virus-mediated perturbation of host defense response / positive regulation of cell population proliferation / lipid binding / negative regulation of apoptotic process / GTP binding / apoptotic process / host cell plasma membrane / Golgi apparatus / extracellular region / ATP binding / membrane / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | Human immunodeficiency virus type 1 Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||||||||
Authors | Alvarado, J.J. / Yeh, J.I. / Smithgall, T.E. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Interaction with the Src Homology (SH3-SH2) Region of the Src-family Kinase Hck Structures the HIV-1 Nef Dimer for Kinase Activation and Effector Recruitment. Authors: Alvarado, J.J. / Tarafdar, S. / Yeh, J.I. / Smithgall, T.E. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4u5w.cif.gz | 256.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u5w.ent.gz | 204.2 KB | Display | PDB format |
PDBx/mmJSON format | 4u5w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4u5w_validation.pdf.gz | 468.5 KB | Display | wwPDB validaton report |
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Full document | 4u5w_full_validation.pdf.gz | 472.7 KB | Display | |
Data in XML | 4u5w_validation.xml.gz | 29.1 KB | Display | |
Data in CIF | 4u5w_validation.cif.gz | 42.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u5/4u5w ftp://data.pdbj.org/pub/pdb/validation_reports/u5/4u5w | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17592.930 Da / Num. of mol.: 2 / Fragment: UNP residues 62-209 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: isolate ARV2/SF2 / Gene: nef / Plasmid: pET21b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: P03407 #2: Protein | Mass: 20742.232 Da / Num. of mol.: 2 / Fragment: SH3-SH2 domain, UNP residues 72-242 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HCK / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS References: UniProt: P08631, non-specific protein-tyrosine kinase #3: Chemical | #4: Chemical | ChemComp-IOD / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.22 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.09 M ADA, pH 6.5, 10.8% (v/v) 2-methyl-2,4-pentanediol, 100 mM NaI |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 14, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→50 Å / Num. obs: 64501 / % possible obs: 97.8 % / Redundancy: 4 % / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.86→1.89 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.768 / Mean I/σ(I) obs: 2.59 / % possible all: 96.4 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NHN, 3RBB Resolution: 1.86→26.377 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 21.29 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86→26.377 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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