4YN0: APP E2 domain

Crystal structure of APP E2 domain in complex with DR6 CRD domain. Determined by X-ray diffraction at 2.2 Å resolution. Released 15 Apr 2015.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Mus musculus
Chains: 2
Atoms: 3,068
Mol. weight: 48.43 kDa
Ligands: MG, NAG
Released: 15 Apr 2015

Explore 4YN0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4YN0 contains 15 α-helices and 22 β-strands across 2 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: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	53-57	5	1
β-strand	64-68	5	1
α-helix	69	1
β-strand	70	1	2
α-helix	71	1
β-strand	74-78	5	3
β-strand	87-90	4	3
α-helix	91-92	2
β-strand	95-96	2	4
β-strand	101	1	2
α-helix	106	1
β-strand	107-108	2	4
α-helix	109-114	6
β-strand	118-121	4	5
β-strand	124	1	6
β-strand	127	1	6
β-strand	130-132	3	5
α-helix	133-134	2
β-strand	137-140	4	7
β-strand	143-146	4	7
α-helix	147-149	3
β-strand	150	1	8
β-strand	154-158	5	9
β-strand	167-170	4	9
α-helix	171-172	2
β-strand	175-176	2	10
β-strand	181	1	8
β-strand	187-188	2	10
α-helix	189-190	2
α-helix	193-195	3
β-strand	198-201	4	11
β-strand	210-212	3	11

Chain B: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	307-344	38
α-helix	350-406	57
α-helix	412-443	32
α-helix	445-475	31
α-helix	477-506	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor receptor superfamily member 21	A	protein	190	Mus musculus	Q9EPU5 (AlphaFold model)
Amyloid beta A4 protein	B	protein	233	Mus musculus	P12023 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4YN0_1 Tumor necrosis factor receptor superfamily member 21 (chains A)
GSQPEQKTLSLPGTYRHVDRTTGQVLTCDKCPAGTYVSEHCTNMSLRVCSSCPAGTFTRH
ENGIERCHDCSQPCPWPMIERLPCAALTDRECICPPGMYQSNGTCAPHTVCPVGWGVRKK
GTENEDVRCKQCARGTFSDVPSSVMKCKAHTDCLGQNLEVVKPGTKETDNVCGMRLFFSS
TASGRGLVPR

Sequence of entity 2 (B), FASTA

>4YN0_2 Amyloid beta A4 protein (chains B)
GSSTPDAVDKYLETPGDENEHAHFQKAKERLEAKHRERMSQVMREWEEAERQAKNLPKAD
KKAVIQHFQEKVESLEQEAANERQQLVETHMARVEAMLNDRRRLALENYITALQAVPPRP
HHVFNMLKKYVRAEQKDRQHTLKHFEHVRMVDPKKAAQIRSQVMTHLRVIYERMNQSLSL
LYNVPAVAEEIQDEVDELLQKEQNYSDDVLANMISEPRISYGNDASGRGLVPR

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

The crystal structure of DR6 in complex with the amyloid precursor protein provides insight into death receptor activation. Xu, K., Olsen, O., Tzvetkova-Robev, D. et al. Genes Dev (2015) 29:785-790. DOI 10.1101/gad.257675.114 · PubMed

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