3IFL	Immune System	date	Jul 24, 2009
title	X-Ray Structure Of Amyloid Beta Peptide:Antibody (Abeta1- 7:12a11) 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 Diffraction	resolution	1.50 Å
Primary reference	Structural 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

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_H] [3ifl_L] [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: [IG_like] [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)

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