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- PDB-1avz: V-1 NEF PROTEIN IN COMPLEX WITH WILD TYPE FYN SH3 DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1avz
TitleV-1 NEF PROTEIN IN COMPLEX WITH WILD TYPE FYN SH3 DOMAIN
Components
  • FYN TYROSINE KINASE
  • NEGATIVE FACTOR
KeywordsCOMPLEX (MYRISTYLATION/TRANSFERASE) / COMPLEX (MYRISTYLATION-TRANSFERASE) / GTP-BINDING / HIV-1 / PHOSPHORYLATION / NEF / SH3 DOMAIN / FYN / TYROSINE KINASE / COMPLEX (MYRISTYLATION-TRANSFERASE) complex
Function / homology
Function and homology information


: / : / negative regulation of hydrogen peroxide biosynthetic process / response to singlet oxygen / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / Reelin signalling pathway / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / perinuclear endoplasmic reticulum / peptidase activator activity / NTRK2 activates RAC1 ...: / : / negative regulation of hydrogen peroxide biosynthetic process / response to singlet oxygen / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / Reelin signalling pathway / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / perinuclear endoplasmic reticulum / peptidase activator activity / NTRK2 activates RAC1 / growth factor receptor binding / symbiont-mediated suppression of host apoptosis / heart process / regulation of glutamate receptor signaling pathway / Activated NTRK2 signals through FYN / : / reelin-mediated signaling pathway / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / regulation of calcium ion import across plasma membrane / Co-stimulation by CD28 / Platelet Adhesion to exposed collagen / positive regulation of protein localization to membrane / cellular response to L-glutamate / G protein-coupled glutamate receptor signaling pathway / CRMPs in Sema3A signaling / activated T cell proliferation / FLT3 signaling through SRC family kinases / CD4 receptor binding / thioesterase binding / type 5 metabotropic glutamate receptor binding / Nef and signal transduction / negative regulation of dendritic spine maintenance / feeding behavior / Nephrin family interactions / natural killer cell activation / DCC mediated attractive signaling / EPH-Ephrin signaling / regulation of T cell activation / Ephrin signaling / dendritic spine maintenance / CD28 dependent Vav1 pathway / dendrite morphogenesis / Regulation of KIT signaling / leukocyte migration / phospholipase activator activity / tau-protein kinase activity / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / MHC class I protein binding / Fc-gamma receptor signaling pathway involved in phagocytosis / phospholipase binding / response to amyloid-beta / PECAM1 interactions / host cell Golgi membrane / CD28 dependent PI3K/Akt signaling / glial cell projection / FCGR activation / cellular response to glycine / ephrin receptor signaling pathway / Sema3A PAK dependent Axon repulsion / positive regulation of protein targeting to membrane / EPH-ephrin mediated repulsion of cells / alpha-tubulin binding / Role of LAT2/NTAL/LAB on calcium mobilization / vascular endothelial growth factor receptor signaling pathway / regulation of peptidyl-tyrosine phosphorylation / detection of mechanical stimulus involved in sensory perception of pain / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / forebrain development / cellular response to transforming growth factor beta stimulus / GPVI-mediated activation cascade / regulation of calcium-mediated signaling / cellular response to platelet-derived growth factor stimulus / T cell costimulation / Signaling by ERBB2 / ephrin receptor binding / viral life cycle / EPHB-mediated forward signaling / negative regulation of protein ubiquitination / CD209 (DC-SIGN) signaling / NCAM signaling for neurite out-growth / FCGR3A-mediated IL10 synthesis / negative regulation of angiogenesis / axon guidance / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / learning / actin filament / Cell surface interactions at the vascular wall / Regulation of signaling by CBL / FCGR3A-mediated phagocytosis / non-membrane spanning protein tyrosine kinase activity / negative regulation of inflammatory response to antigenic stimulus / non-specific protein-tyrosine kinase / G protein-coupled receptor binding / modulation of chemical synaptic transmission / neuron migration / protein catabolic process
Similarity search - Function
Nef Regulatory Factor / Nef Regulatory Factor / : / Fyn/Yrk, SH3 domain / HIV-1 Nef protein, anchor domain superfamily / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / SH3 Domains / : ...Nef Regulatory Factor / Nef Regulatory Factor / : / Fyn/Yrk, SH3 domain / HIV-1 Nef protein, anchor domain superfamily / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH3 type barrels. / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Protein Nef / Tyrosine-protein kinase Fyn
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsArold, S. / Franken, P. / Dumas, C.
Citation
Journal: Structure / Year: 1997
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: Journal: Cell(Cambridge,Mass.) / Year: 1996
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: Journal: Nat.Struct.Biol. / Year: 1996
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
DepositionSep 23, 1997Processing site: BNL
Revision 1.0Mar 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.type / _pdbx_database_status.process_site
Revision 1.4Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.5Aug 2, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEGATIVE FACTOR
B: NEGATIVE FACTOR
C: FYN TYROSINE KINASE


Theoretical massNumber of molelcules
Total (without water)41,6623
Polymers41,6623
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.200, 108.200, 223.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein NEGATIVE FACTOR / NEF / F-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.) Human immunodeficiency virus 1 / Genus: Lentivirus / Cell line: BL21 / Gene: HIV-1 NEF / Variant: LAI ISOLATE / Plasmid: PGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P03406
#2: Protein FYN TYROSINE KINASE / SH3 DOMAIN


Mass: 6524.066 Da / Num. of mol.: 1 / Fragment: SRC-HOMOLOGY 3 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Gene: FYN TYROSINE KINASE / Plasmid: PGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P06241, EC: 2.7.1.112

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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: 4.2 Å3/Da / Density % sol: 70 %
Crystal growpH: 8.9 / Details: pH 8.9
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown / Details: unpublished data

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM02 / Wavelength: 1.0373
DetectorType: PRINCETON 2K / Detector: CCD / Date: Oct 4, 1996 / Details: TWO BENT MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0373 Å / Relative weight: 1
ReflectionResolution: 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

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
XDSdata reduction
XSCALEdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1EFN AND 1SHF

1efn

1shf


Resolution: 3→30 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.27 -10 %RANDOM
Rwork0.22 ---
obs0.22 11662 75.6 %-
Displacement parametersBiso mean: 33 Å2
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2216 0 0 0 2216
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.21
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.21

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