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Open data
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Basic information
Entry | Database: PDB / ID: 1avz | ||||||
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Title | V-1 NEF PROTEIN IN COMPLEX WITH WILD TYPE FYN SH3 DOMAIN | ||||||
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![]() | COMPLEX (MYRISTYLATION/TRANSFERASE) / COMPLEX (MYRISTYLATION-TRANSFERASE) / GTP-BINDING / HIV-1 / PHOSPHORYLATION / NEF / SH3 DOMAIN / FYN / TYROSINE KINASE / COMPLEX (MYRISTYLATION-TRANSFERASE) complex | ||||||
Function / homology | ![]() perturbation by virus of host immune response / negative regulation of CD4 production / response to singlet oxygen / Reelin signalling pathway / negative regulation of hydrogen peroxide biosynthetic process / 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 / perinuclear endoplasmic reticulum / symbiont-mediated suppression of host apoptosis / peptidase activator activity ...perturbation by virus of host immune response / negative regulation of CD4 production / response to singlet oxygen / Reelin signalling pathway / negative regulation of hydrogen peroxide biosynthetic process / 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 / perinuclear endoplasmic reticulum / symbiont-mediated suppression of host apoptosis / peptidase activator activity / NTRK2 activates RAC1 / Activated NTRK2 signals through FYN / heart process / cellular response to L-glutamate / growth factor receptor binding / suppression by virus of host autophagy / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / Platelet Adhesion to exposed collagen / CD28 co-stimulation / G protein-coupled glutamate receptor signaling pathway / positive regulation of protein localization to membrane / activated T cell proliferation / CRMPs in Sema3A signaling / positive regulation of cysteine-type endopeptidase activity / FLT3 signaling through SRC family kinases / CD4 receptor binding / thioesterase binding / negative regulation of dendritic spine maintenance / feeding behavior / type 5 metabotropic glutamate receptor binding / Nef and signal transduction / Nephrin family interactions / DCC mediated attractive signaling / EPH-Ephrin signaling / dendrite morphogenesis / CD28 dependent Vav1 pathway / regulation of T cell activation / Ephrin signaling / dendritic spine maintenance / Regulation of KIT signaling / tau-protein kinase activity / CTLA4 inhibitory signaling / phospholipase activator activity / leukocyte migration / Fc-gamma receptor signaling pathway involved in phagocytosis / EPHA-mediated growth cone collapse / cellular response to platelet-derived growth factor stimulus / Dectin-2 family / MHC class I protein binding / stimulatory C-type lectin receptor signaling pathway / PECAM1 interactions / host cell Golgi membrane / CD28 dependent PI3K/Akt signaling / phospholipase binding / response to amyloid-beta / glial cell projection / Sema3A PAK dependent Axon repulsion / FCGR activation / cellular response to glycine / alpha-tubulin binding / positive regulation of protein targeting to membrane / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / Role of LAT2/NTAL/LAB on calcium mobilization / vascular endothelial growth factor receptor signaling pathway / detection of mechanical stimulus involved in sensory perception of pain / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of peptidyl-tyrosine phosphorylation / positive regulation of tyrosine phosphorylation of STAT protein / regulation of calcium-mediated signaling / forebrain development / Signaling by ERBB2 / cell surface receptor protein tyrosine kinase signaling pathway / negative regulation of inflammatory response to antigenic stimulus / GPVI-mediated activation cascade / negative regulation of protein ubiquitination / cellular response to transforming growth factor beta stimulus / viral life cycle / T cell costimulation / EPHB-mediated forward signaling / ephrin receptor binding / CD209 (DC-SIGN) signaling / NCAM signaling for neurite out-growth / FCGR3A-mediated IL10 synthesis / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / learning / virion component / axon guidance / actin filament / Regulation of signaling by CBL / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / non-specific protein-tyrosine kinase / neuron migration / non-membrane spanning protein tyrosine kinase activity / modulation of chemical synaptic transmission / tau protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Arold, S. / Franken, P. / Dumas, C. | ||||||
![]() | ![]() Title: The crystal structure of HIV-1 Nef protein bound to the Fyn kinase SH3 domain suggests a role for this complex in altered T cell receptor signaling. Authors: Arold, S. / Franken, P. / Strub, M.P. / Hoh, F. / Benichou, S. / Benarous, R. / Dumas, C. #1: ![]() Title: Crystal Structure of the Conserved Core of HIV-1 Nef Complexed with a Src Family SH3 Domain Authors: Lee, C.H. / Saksela, K. / Mirza, U.A. / Chait, B.T. / Kuriyan, J. #2: ![]() Title: The Solution Structure of HIV-1 Nef Reveals an Unexpected Fold and Permits Delineation of the Binding Surface for the SH3 Domain of HCK Tyrosine Protein Kinase Authors: Grzesiek, S. / Bax, A. / Clore, G.M. / Gronenborn, A.M. / Hu, J.S. / Kaufman, J. / Palmer, I. / Stahl, S.J. / Wingfield, P.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62 KB | Display | ![]() |
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PDB format | ![]() | 46.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1avvC ![]() 1efnS ![]() 1shfS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17568.723 Da / Num. of mol.: 2 / Fragment: CONSERVED CORE DOMAIN Mutation: N-TERMINAL RESIDUES GS (PART OF A THROMBIN CLEAVAGE SITE) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | | Mass: 6524.066 Da / Num. of mol.: 1 / Fragment: SRC-HOMOLOGY 3 DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.2 Å3/Da / Density % sol: 70 % |
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Crystal grow | pH: 8.9 / Details: pH 8.9 |
Crystal | *PLUS |
Crystal grow | *PLUS Method: unknown / Details: unpublished data |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PRINCETON 2K / Detector: CCD / Date: Oct 4, 1996 / Details: TWO BENT MIRRORS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0373 Å / Relative weight: 1 |
Reflection | Resolution: 3→25 Å / Num. obs: 14778 / % possible obs: 91 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.067 |
Reflection | *PLUS Num. measured all: 57175 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 1EFN AND 1SHF Resolution: 3→30 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 2
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Displacement parameters | Biso mean: 33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→30 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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