3DXD: Intracellular domain of human APP

Crystal structure of the intracellular domain of human APP (T668E mutant) in complex with Fe65-PTB2. Determined by X-ray diffraction at 2.2 Å resolution. Released 16 Sept 2008.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,569
Mol. weight: 39.17 kDa
Released: 16 Sept 2008

Explore 3DXD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3DXD contains 12 α-helices and 16 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	541-542	2
β-strand	543-553	11	1
α-helix	559-571	13
β-strand	579-585	7	1
β-strand	589-594	6	1
β-strand	600-605	6	1
α-helix	606-608	3
β-strand	609-614	6	1
β-strand	620-628	9	1
β-strand	631-638	8	1
α-helix	644-665	22

Chain B: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	669-679	11
β-strand	682-683	2	1
α-helix	685-691	7

Chain C: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	544-553	10	2
α-helix	559-571	13
α-helix	575-577	3
β-strand	579-585	7	2
β-strand	589-594	6	2
β-strand	600-605	6	2
α-helix	606-608	3
β-strand	609-614	6	2
β-strand	620-628	9	2
β-strand	631-640	10	2
α-helix	644-663	20

Chain D: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	669-679	11
β-strand	682-683	2	2
α-helix	685-689	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Amyloid beta A4 protein-binding family B member 1	A, C	protein	140	Homo sapiens	O00213 (AlphaFold model)
Amyloid beta A4 protein	B, D	protein	35	Homo sapiens	P05067 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3DXD_1 Amyloid beta A4 protein-binding family B member 1 (chains A, C)
APKNELVQKFQVYYLGNVPVAKPVGVDVINGALESVLSSSSREQWTPSHVSVAPATLTIL
HQQTEAVLGECRVRFLSFLAVGRDVHTFAFIMAAGPASFCCHMFWCEPNAASLSEAVQAA
CMLRYQKCLDARSQHHHHHH

Sequence of entity 2 (B, D), FASTA

>3DXD_2 Amyloid beta A4 protein (chains B, D)
GAMDAAVEPEERHLSKMQQNGYENPTYKFFEQMQN

Primary citation

Structure of the intracellular domain of the amyloid precursor protein in complex with Fe65-PTB2. Radzimanowski, J., Simon, B., Sattler, M. et al. EMBO Rep (2008) 9:1134-1140. DOI 10.1038/embor.2008.188 · PubMed

Other PDB entries of the same protein (UniProt O00213 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2HO2 1.33 Å, Structure of human FE65-WW domain in complex with hMena peptide.
2OEI 1.35 Å, Crystal structure of human FE65-WW domain in complex with human Mena peptide
3DXE 2.0 Å, Crystal structure of the intracellular domain of human APP (T668A mutant) in complex…
3DXC 2.1 Å, Crystal structure of the intracellular domain of human APP in complex with Fe65-PTB2
3D8D 2.2 Å, Crystal structure of the human Fe65-PTB1 domain
2IDH 2.28 Å, Crystal Structure of human FE65 WW domain
5NQH 2.6 Å, Structure of the human Fe65-PTB2 homodimer
3D8F 2.7 Å, Crystal structure of the human Fe65-PTB1 domain with bound phosphate (trigonal crystal…
3D8E 2.8 Å, Crystal structure of the human Fe65-PTB1 domain (trigonal crystal form)
2E45 Solution structure of Fe65 WW domain

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