3IFO Immune System date Jul 24, 2009
title X-Ray Structure Of Amyloid Beta Peptide:Antibody (Abeta1-7:1 Complex
authors W.I.Weis, H.Feinberg, G.S.Basi, D.Schenk
compound source
Molecule: 10d5 Fab Antibody Heavy Chain
Chain: H, A
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10090
Expression_system_cell_line: Cho Cells
Expression_system_tissue: Ovary
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Cet1018

Molecule: 10d5 Fab Antibody Light Chain
Chain: L, B
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10090
Expression_system_cell_line: Cho Cells
Expression_system_tissue: Ovary
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Cet1018

Molecule: Amyloid Beta A4 Protein
Chain: P, Q
Fragment: Residues 672-678
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 21 21 21
R_factor 0.162 R_Free 0.218
crystal
cell
length a length b length c angle alpha angle beta angle gamma
96.310 99.970 103.960 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.15 Å
Primary referenceStructural correlates of antibodies associated with acute reversal of A-beta related behavioral deficits in a mouse model of Alzheimer's disease., Basi GS, Feinberg H, Oshidari F, Anderson J, Barbour R, Baker J, Comery TA, Diep L, Gill D, Johnson-Wood K, Goel A, Grantcharova K, Lee M, Li J, Partridge A, Griswold-Prenner I, Piot N, Walker D, Widom A, Pangalos MN, Seubert P, Jacobsen JS, Schenk D, Weis WI, J Biol Chem. 2009 Nov 18. PMID:19923222
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (304 Kb) [Save to disk]
  • Biological Unit Coordinates (3ifo.pdb1.gz) 151 Kb
  • Biological Unit Coordinates (3ifo.pdb2.gz) 151 Kb
  • CSU: Contacts of Structural Units for 3IFO
  • Structure Factors (399 Kb)
  • Retrieve 3IFO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3IFO from S2C, [Save to disk]
  • Re-refined 3ifo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3IFO 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 3IFO
  • 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 3IFO, from MSDmotif at EBI
  • Fold representative 3ifo from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ifo_B] [3ifo_Q] [3ifo_H] [3ifo] [3ifo_P] [3ifo_L] [3ifo_A]
  • SWISS-PROT database: [P05067]
  • Belongs to the amyloid -protein peptide (app) family according to TCDB.
  • Domain organization of [A4_HUMAN] by SWISSPFAM
  • Domains found in 3IFO: [IGc1] [IGv ] by SMART
  • Alignments of the sequence of 3IFO with the sequences similar proteins can be viewed for 3IFO's classification [A4_HUMAN] 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 [A4_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3IFO
  • Community annotation for 3IFO at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science