[English] 日本語
Yorodumi
- PDB-1efn: HIV-1 NEF PROTEIN IN COMPLEX WITH R96I MUTANT FYN SH3 DOMAIN -

+
Open data


ID or keywords:

Loading...

-
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


negative regulation of hydrogen peroxide biosynthetic process / response to singlet oxygen / negative regulation of glycoprotein biosynthetic process / 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 / NTRK2 activates RAC1 / regulation of glutamate receptor signaling pathway / heart process ...negative regulation of hydrogen peroxide biosynthetic process / response to singlet oxygen / negative regulation of glycoprotein biosynthetic process / 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 / NTRK2 activates RAC1 / regulation of glutamate receptor signaling pathway / heart process / symbiont-mediated suppression of host autophagy / Activated NTRK2 signals through FYN / symbiont-mediated suppression of host apoptosis / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / regulation of calcium ion import across plasma membrane / reelin-mediated signaling pathway / Platelet Adhesion to exposed collagen / CRMPs in Sema3A signaling / G protein-coupled glutamate receptor signaling pathway / FLT3 signaling through SRC family kinases / activated T cell proliferation / thioesterase binding / positive regulation of protein localization to membrane / type 5 metabotropic glutamate receptor binding / CD4 receptor binding / Nef and signal transduction / cellular response to L-glutamate / feeding behavior / Co-stimulation by CD28 / DCC mediated attractive signaling / Nephrin family interactions / EPH-Ephrin signaling / natural killer cell activation / negative regulation of dendritic spine maintenance / Ephrin signaling / regulation of T cell activation / CD28 dependent Vav1 pathway / dendritic spine maintenance / growth factor receptor binding / cellular response to peptide hormone stimulus / tau-protein kinase activity / peptidase activator activity / Regulation of KIT signaling / leukocyte migration / phospholipase activator activity / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / dendrite morphogenesis / peptide hormone receptor binding / CD8 receptor binding / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / forebrain development / PECAM1 interactions / response to amyloid-beta / MHC class I protein binding / host cell Golgi membrane / cellular response to glycine / FCGR activation / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / CD28 dependent PI3K/Akt signaling / glial cell projection / positive regulation of protein targeting to membrane / Role of LAT2/NTAL/LAB on calcium mobilization / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ephrin receptor signaling pathway / vascular endothelial growth factor receptor signaling pathway / detection of mechanical stimulus involved in sensory perception of pain / alpha-tubulin binding / cellular response to transforming growth factor beta stimulus / postsynaptic density, intracellular component / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / T cell receptor binding / phosphatidylinositol 3-kinase binding / phospholipase binding / GPVI-mediated activation cascade / ephrin receptor binding / T cell costimulation / cellular response to platelet-derived growth factor stimulus / viral life cycle / Signaling by ERBB2 / regulation of calcium-mediated signaling / negative regulation of protein ubiquitination / EPHB-mediated forward signaling / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / FCGR3A-mediated IL10 synthesis / axon guidance / cell surface receptor protein tyrosine kinase signaling pathway / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / peptidyl-tyrosine phosphorylation / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / negative regulation of angiogenesis / Cell surface interactions at the vascular wall / learning / non-membrane spanning protein tyrosine kinase activity / FCGR3A-mediated phagocytosis / actin filament
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 / 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 / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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

-
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

+
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