3IFL 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: 12a11 Fab Antibody Light Chain
Chain: L
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_cell_line: Cho Cells
Expression_system_tissue: Ovary
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Cet1018

Molecule: 12a11 Fab Antibody Heavy Chain
Chain: H
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
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
Fragment: Residues 672-678
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 1 21 1
R_factor 0.178 R_Free 0.206
crystal
cell
length a length b length c angle alpha angle beta angle gamma
42.970 85.980 57.450 90.00 94.67 90.00
method X-Ray Diffractionresolution 1.50 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] (87 Kb) [Save to disk]
  • Biological Unit Coordinates (3ifl.pdb1.gz) 83 Kb
  • CSU: Contacts of Structural Units for 3IFL
  • Structure Factors (2857 Kb)
  • Retrieve 3IFL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3IFL from S2C, [Save to disk]
  • Re-refined 3ifl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3IFL 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 3IFL
  • 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 3IFL, from MSDmotif at EBI
  • Fold representative 3ifl from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ifl_L] [3ifl_H] [3ifl] [3ifl_P]
  • 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 3IFL: [IGc1] [IGv ] by SMART
  • Alignments of the sequence of 3IFL with the sequences similar proteins can be viewed for 3IFL'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 3IFL
  • Community annotation for 3IFL 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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