3DXE	Protein Binding	date	Jul 24, 2008
title	Crystal Structure Of The Intracellular Domain Of Human App (T668a Mutant) In Complex With Fe65-Ptb2
authors	J.Radzimanowski, I.Sinning, K.Wild
compound		source
Molecule: Amyloid Beta A4 Protein-Binding Family B Member 1; Chain: A, C Fragment: Ptb2 Domain, Unp Residues 534-667 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Apbb1, Fe65, Rir Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3)Ril Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet21d
Molecule: Amyloid Beta A4 Protein Chain: B, D Fragment: App Intracellular Domain, Unp Residues 739-770 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: App, A4, Ad1 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3)Ril Expression_system_vector_type: Plasmid Expression_system_plasmid: Pettrx_1b
symmetry	Space Group: P 61	R_factor 0.206 R_Free 0.241
crystal cell	length a length b length c angle alpha angle beta angle gamma 115.377 115.377 75.523 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.00 Å
note	3DXE is a representative structure
Primary reference	Structure of the intracellular domain of the amyloid precursor protein in complex with Fe65-PTB2., Radzimanowski J, Simon B, Sattler M, Beyreuther K, Sinning I, Wild K, EMBO Rep. 2008 Nov;9(11):1134-40. Epub 2008 Oct 3. PMID:18833287

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (59 Kb) [Save to disk] Biological Unit Coordinates (3dxe.pdb1.gz) 28 Kb Biological Unit Coordinates (3dxe.pdb2.gz) 29 Kb CSU: Contacts of Structural Units for 3DXE Likely Quarternary Molecular Structure file(s) for 3DXE Structure Factors (361 Kb) Retrieve 3DXE in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3DXE from S2C, [Save to disk] Re-refined 3dxe structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3DXE 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 3DXE

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 3DXE, from MSDmotif at EBI Fold representative 3dxe from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3dxe_A] [3dxe_B] [3dxe_C] [3dxe_D] SWISS-PROT database: [P05067] [O00213] Belongs to the amyloid -protein peptide (app) family according to TCDB. Domain organization of [A4_HUMAN] [APBB1_HUMAN] by SWISSPFAM Domain found in 3DXE: [PTB ] by SMART Alignments of the sequence of 3DXE with the sequences similar proteins can be viewed for 3DXE's classification [A4_HUMAN] [APBB1_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] [APBB1_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 3DXE

Community annotation for 3DXE at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

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