[English] 日本語
Yorodumi
- PDB-1avz: V-1 NEF PROTEIN IN COMPLEX WITH WILD TYPE FYN SH3 DOMAIN -

+
Open data


ID or keywords:

Loading...

-
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


perturbation by virus of host immune response / negative regulation of CD4 production / symbiont-mediated suppression of host T-cell mediated immune response / 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 / NTRK2 activates RAC1 ...perturbation by virus of host immune response / negative regulation of CD4 production / symbiont-mediated suppression of host T-cell mediated immune response / 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 / NTRK2 activates RAC1 / peptidase activator activity / growth factor receptor binding / Activated NTRK2 signals through FYN / heart process / cellular response to L-glutamate / suppression by virus of host autophagy / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / 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 / thioesterase binding / FLT3 signaling through SRC family kinases / CD4 receptor binding / feeding behavior / Nef and signal transduction / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / Nephrin family interactions / DCC mediated attractive signaling / dendrite morphogenesis / EPH-Ephrin signaling / CD28 dependent Vav1 pathway / Ephrin signaling / regulation of T cell activation / dendritic spine maintenance / Regulation of KIT signaling / CTLA4 inhibitory signaling / tau-protein kinase activity / 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 / cellular response to glycine / Dectin-2 family / host cell Golgi membrane / stimulatory C-type lectin receptor signaling pathway / PECAM1 interactions / glial cell projection / phospholipase binding / CD28 dependent PI3K/Akt signaling / response to amyloid-beta / Sema3A PAK dependent Axon repulsion / MHC class I protein binding / positive regulation of protein targeting to membrane / alpha-tubulin binding / FCGR activation / 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 / forebrain development / regulation of peptidyl-tyrosine phosphorylation / regulation of calcium-mediated signaling / positive regulation of tyrosine phosphorylation of STAT protein / negative regulation of inflammatory response to antigenic stimulus / negative regulation of protein ubiquitination / Signaling by ERBB2 / viral life cycle / GPVI-mediated activation cascade / cellular response to transforming growth factor beta stimulus / EPHB-mediated forward signaling / T cell costimulation / extrinsic component of cytoplasmic side of plasma membrane / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / ephrin receptor binding / 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 / protein catabolic process / neuron migration / non-membrane spanning protein tyrosine kinase activity / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission
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 / SH2 domain / SH3 type barrels. / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more