2Y3J Protein Fibril date Dec 21, 2010
title Structure Of Segment Aiiglm From The Amyloid-Beta Peptide (A Residues 30-35)
authors J.P.Colletier, A.Laganowsky, M.R.Sawaya, D.Eisenberg
compound source
Molecule: Amyloid Beta A4 Protein
Chain: A, B, C, D, E, F, G, H
Fragment: Residues 701-706
Synonym: Amyloid Beta Peptide, Abpp, Appi, App, Alzheimer D Amyloid Protein, Cerebral Vascular Amyloid Peptide, Cvap, Protease Nexin-II, Pn-II
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Brain
Cell: Neuron
symmetry Space Group: P 1
R_factor 0.22194 R_Free 0.26710
crystal
cell
length a length b length c angle alpha angle beta angle gamma
9.560 15.640 45.230 89.87 90.02 89.91
method X-Ray Diffractionresolution 1.99 Å
subcellular loc. Membrane localization by OPM: Secreted
out side
in side
Primary referenceMolecular basis for amyloid-{beta} polymorphism., Colletier JP, Laganowsky A, Landau M, Zhao M, Soriaga AB, Goldschmidt L, Flot D, Cascio D, Sawaya MR, Eisenberg D, Proc Natl Acad Sci U S A. 2011 Oct 11;108(41):16938-43. Epub 2011 Sep 23. PMID:21949245
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (12 Kb) [Save to disk]
  • Biological Unit Coordinates (2y3j.pdb1.gz) 4 Kb
  • Biological Unit Coordinates (2y3j.pdb2.gz) 4 Kb
  • CSU: Contacts of Structural Units for 2Y3J
  • Structure Factors (11 Kb)
  • Retrieve 2Y3J in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2Y3J from S2C, [Save to disk]
  • Re-refined 2y3j structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2Y3J 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 2Y3J
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2Y3J, from MSDmotif at EBI
  • Fold representative 2y3j from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2y3j_C] [2y3j_H] [2y3j_B] [2y3j_E] [2y3j_D] [2y3j_G] [2y3j] [2y3j_A] [2y3j_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Alignments of the sequence of 2Y3J with the sequences similar proteins can be viewed for 2Y3J'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 2Y3J
  • Community annotation for 2Y3J at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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