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- PDB-1efn: HIV-1 NEF PROTEIN IN COMPLEX WITH R96I MUTANT FYN SH3 DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1efn
TitleHIV-1 NEF PROTEIN IN COMPLEX WITH R96I MUTANT FYN SH3 DOMAIN
Components
  • FYN TYROSINE KINASE
  • HIV-1 NEF PROTEIN
KeywordsCOMPLEX (SH3 DOMAIN/VIRAL ENHANCER) / COMPLEX (SH3 DOMAIN-VIRAL ENHANCER) / PROTO-ONCOGENE / TRANSFERASE / TYROSINE-PROTEIN KINASE / PHOSPHORYLATION / AIDS / MYRISTYLATION / GTP-BINDING / ATP-BINDING / SH3 DOMAIN / SH2 DOMAIN / PPII HELIX / PXXP MOTIF / COMPLEX (SH3 DOMAIN-VIRAL ENHANCER) complex
Function / homology
Function and homology information


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 apoptosis / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / perinuclear endoplasmic reticulum / 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 apoptosis / 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 / Activated NTRK2 signals through FYN / heart process / cellular response to L-glutamate / 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 / G protein-coupled glutamate receptor signaling pathway / Platelet Adhesion to exposed collagen / CD28 co-stimulation / 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 / Nef and signal transduction / type 5 metabotropic glutamate receptor binding / Nephrin family interactions / DCC mediated attractive signaling / dendrite morphogenesis / EPH-Ephrin signaling / 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 / leukocyte migration / phospholipase activator activity / Fc-gamma receptor signaling pathway involved in phagocytosis / EPHA-mediated growth cone collapse / cellular response to platelet-derived growth factor stimulus / Dectin-2 family / host cell Golgi membrane / MHC class I protein binding / stimulatory C-type lectin receptor signaling pathway / PECAM1 interactions / CD28 dependent PI3K/Akt signaling / phospholipase binding / response to amyloid-beta / glial cell projection / Sema3A PAK dependent Axon repulsion / cellular response to glycine / FCGR activation / alpha-tubulin binding / EPH-ephrin mediated repulsion of cells / positive regulation of protein targeting to membrane / 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 / negative regulation of inflammatory response to antigenic stimulus / extrinsic component of cytoplasmic side of plasma membrane / Signaling by ERBB2 / negative regulation of protein ubiquitination / GPVI-mediated activation cascade / cellular response to transforming growth factor beta stimulus / cell surface receptor protein tyrosine kinase signaling pathway / viral life cycle / T cell costimulation / EPHB-mediated forward signaling / ephrin receptor binding / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / 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 / actin filament / Regulation of signaling by CBL / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / axon guidance / non-specific protein-tyrosine kinase / neuron migration / non-membrane spanning protein tyrosine kinase activity / Schaffer collateral - CA1 synapse
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 / SH3 domain ...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 / SH3 type barrels. / SH2 domain / Src homology 3 domains / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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
TRIMETHYL LEAD ION / Protein Nef / Tyrosine-protein kinase Fyn
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsLee, C.-H. / Kuriyan, J.
Citation
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.
#1: 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.
#2: Journal: Embo J. / Year: 1995
Title: A Single Amino Acid in the SH3 Domain of HCK Determines its High Affinity and Specificity in Binding to HIV-1 Nef Protein
Authors: Lee, C.H. / Leung, B. / Lemmon, M.A. / Zheng, J. / Cowburn, D. / Kuriyan, J. / Saksela, K.
History
DepositionJun 29, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FYN TYROSINE KINASE
B: HIV-1 NEF PROTEIN
C: FYN TYROSINE KINASE
D: HIV-1 NEF PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4276
Polymers48,9224
Non-polymers5052
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.800, 107.800, 229.100
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 FYN TYROSINE KINASE / SRC-HOMOLOGY 3 DOMAIN


Mass: 6652.169 Da / Num. of mol.: 2 / Fragment: SH3 DOMAIN, RESIDUES 85-141 / Mutation: R96I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIV-1 NEF / Plasmid: PET3A / Species (production host): Escherichia coli / Gene (production host): FYN TYROSINE KINASE / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06241, EC: 2.7.1.112
#2: Protein HIV-1 NEF PROTEIN


Mass: 17809.047 Da / Num. of mol.: 2 / Fragment: CONSERVED CORE DOMAIN OF NEF, RESIDUES 71-203 / Mutation: T71R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: NL4-3 / Gene: HIV-1 NEF / Plasmid: PGEX-2T(TEV) / Gene (production host): SYSTEM_GENE: HIV-1 NEF / Production host: Escherichia coli (E. coli) / Strain (production host): K12 PR745 / References: UniProt: P03406
#3: Chemical ChemComp-PBM / TRIMETHYL LEAD ION


Mass: 252.304 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H9Pb
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.92 Å3/Da / Density % sol: 68.2 %
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 Mammonium salfate1reservoir
2100 mMTris1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.92
DetectorDetector: CCD / Date: Jan 6, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionNum. obs: 26464 / % possible obs: 94.2 % / Observed criterion σ(I): -3 / Redundancy: 9 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.068
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å / Num. measured all: 565661
Reflection shell
*PLUS
% possible obs: 84.9 % / Rmerge(I) obs: 0.358

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.5→6 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.282 -10 %RANDOM
Rwork0.215 ---
obs0.215 20684 80.1 %-
Displacement parametersBiso mean: 33.55 Å2
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2635 0 8 99 2742
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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

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