3L81 Transport Protein date Dec 29, 2009
title Crystal Structure Of Adaptor Protein Complex 4 (Ap-4) Mu4 Su Terminal Domain, In Complex With A Sorting Peptide From The Precursor Protein (App)
authors G.A.Mardones, A.L.Rojas, P.V.Burgos, L.L.P.Dasilva, Y.Prabhu, J.S.Bonifacino, J.H.Hurley
compound source
Molecule: Ap-4 Complex Subunit Mu-1
Chain: A
Fragment: C-Terminus, Residues 160-453
Synonym: Adapter-Related Protein Complex 4 Mu-1 Subunit, Ap Complex Mu Subunit, Mu Subunit Of Ap-4, Mu4-Adaptin, Mu4, M Related Protein 2, Mu-Arp2;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ap4m1, Muarp2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgst-Parallel-1

Molecule: Amyloid Beta A4 Protein
Chain: B
Fragment: C-Terminus, Residues 761-767
Synonym: Alzheimer Disease Amyloid Protein, Abpp, Appi, App Cerebral Vascular Amyloid Peptide, Cvap, Protease Nexin-II, App, Soluble App-Alpha, S-App-Alpha, Soluble App-Beta, S-Ap C99, Beta-Amyloid Protein 42, Beta-App42, Beta-Amyloid Prot Beta-App40, C83, P3(42), P3(40), C80, Gamma-Secretase C-Ter Fragment 59, Gamma-Ctf(59), Amyloid Intracellular Domain 59 Aid(59), Gamma-Secretase C-Terminal Fragment 57, Gamma-Ctf( Amyloid Intracellular Domain 57, Aicd-57, Aid(57), Gamma-Se Terminal Fragment 50, Gamma-Ctf(50), Amyloid Intracellular Aicd-50, Aid(50), C31;
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.207 R_Free 0.252
crystal
cell
length a length b length c angle alpha angle beta angle gamma
46.672 56.910 60.664 90.00 106.53 90.00
method X-Ray Diffractionresolution 1.60 Å
ligand GOL enzyme
Primary referenceSorting of the Alzheimer's disease amyloid precursor protein mediated by the AP-4 complex., Burgos PV, Mardones GA, Rojas AL, daSilva LL, Prabhu Y, Hurley JH, Bonifacino JS, Dev Cell. 2010 Mar 16;18(3):425-36. PMID:20230749
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (50 Kb) [Save to disk]
  • Biological Unit Coordinates (3l81.pdb1.gz) 46 Kb
  • LPC: Ligand-Protein Contacts for 3L81
  • CSU: Contacts of Structural Units for 3L81
  • Structure Factors (1395 Kb)
  • Retrieve 3L81 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3L81 from S2C, [Save to disk]
  • Re-refined 3l81 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3L81 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 3L81
  • 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 3L81, from MSDmotif at EBI
  • Fold representative 3l81 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3l81_A] [3l81] [3l81_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Alignments of the sequence of 3L81 with the sequences similar proteins can be viewed for 3L81's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3L81
  • Community annotation for 3L81 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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