4AFI Endocytosis date Jan 19, 2012
title Complex Between Vamp7 Longin Domain And Fragment Of Delta-Ad Ap3
authors H.M.Kent, P.R.Evans, J.P.Luzio, A.A.Peden, D.J.Owen
compound source
Molecule: Ap-3 Complex Subunit Delta-1, Vesicle-Associated Protein 7;
Chain: A, B
Fragment: Delta-Adaptin Hinge, Residues 680-729, Vamp7 Long Residues 1-120;
Synonym: Ap-3 Complex Subunit Delta, Adapter-Related Protei Subunit Delta-1, Delta-Adaptin, Vamp-7, Synaptobrevin-Lik 1;
Engineered: Yes
Organism_scientific: Homo Sapiens, Mus Musculus
Organism_common: Human, House Mouse
Organism_taxid: 9606, 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Rosetta2 Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex4t2
symmetry Space Group: P 43 21 2
R_factor 0.231 R_Free 0.253
crystal
cell
length a length b length c angle alpha angle beta angle gamma
63.555 63.555 217.915 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand PR enzyme
Primary referenceStructural basis of the intracellular sorting of the SNARE VAMP7 by the AP3 adaptor complex., Kent HM, Evans PR, Schafer IB, Gray SR, Sanderson CM, Luzio JP, Peden AA, Owen DJ, Dev Cell. 2012 May 15;22(5):979-88. Epub 2012 Apr 19. PMID:22521722
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (55 Kb) [Save to disk]
  • Biological Unit Coordinates (4afi.pdb1.gz) 50 Kb
  • LPC: Ligand-Protein Contacts for 4AFI
  • CSU: Contacts of Structural Units for 4AFI
  • Structure Factors (601 Kb)
  • Retrieve 4AFI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4AFI from S2C, [Save to disk]
  • Re-refined 4afi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4AFI in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 4AFI
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4AFI, from MSDmotif at EBI
  • Fold representative 4afi from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4afi_B] [4afi] [4afi_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4AFI: [BLVR] [Longin ] by SMART
  • Other resources with information on 4AFI
  • Community annotation for 4AFI at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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