5CIR: Death receptor 4

Name: PDB 5CIR: Crystal structure of death receptor 4 (DR4; TNFFRSF10A) bound to TRAIL (TNFSF10)
Published: 2017-01-18
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: apoptosis

Crystal structure of death receptor 4 (DR4; TNFFRSF10A) bound to TRAIL (TNFSF10). Determined by X-ray diffraction at 3.0 Å resolution. Released 18 Jan 2017.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 6
Atoms: 5,611
Mol. weight: 94.3 kDa
Ligands: ZN
Released: 18 Jan 2017

Explore 5CIR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5CIR contains 22 α-helices and 87 β-strands across 6 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.

Chains A, B and D: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	123-128	6	1
β-strand	149-150	2	2
β-strand	154-155	2	1
β-strand	163-165	3	1
β-strand	167-170	4	2
β-strand	173-176	4	2
β-strand	180-193	14	1
β-strand	205-213	9	2
β-strand	220-228	9	2
β-strand	237-250	14	1
β-strand	255-260	6	2
α-helix	263-265	3
β-strand	266-267	2	1
β-strand	274-279	6	1

Chain E: 7 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	132	1	4
α-helix	133	1
β-strand	136-138	3	5
β-strand	145-147	3	5
α-helix	148-149	2
β-strand	153-154	2	6
β-strand	159	1	4
α-helix	164	1
β-strand	165-166	2	6
α-helix	167-168	2
β-strand	174-178	5	7
β-strand	181	1	8
β-strand	184	1	8
β-strand	187-190	4	7
α-helix	191	1
β-strand	194-195	2	9
β-strand	205-206	2	9
α-helix	207-208	2
α-helix	211-212	2
β-strand	217-219	3	10
β-strand	222	1	11
β-strand	225	1	11
β-strand	228-229	2	10

Chain F: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	132	1	12
α-helix	133	1
β-strand	136-138	3	13
β-strand	145-147	3	13
α-helix	148-149	2
β-strand	153-154	2	14
β-strand	159	1	12
α-helix	164	1
β-strand	165-166	2	14
α-helix	167-168	2
β-strand	174-178	5	15
β-strand	181	1	16
β-strand	184	1	16
β-strand	187-190	4	15
α-helix	191	1
β-strand	194-195	2	17
β-strand	205-206	2	17
α-helix	207-208	2
β-strand	217-219	3	18
β-strand	222	1	19
β-strand	225	1	19
β-strand	228-229	2	18

Chain G: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	132	1	20
α-helix	133	1
β-strand	136-138	3	21
β-strand	145-147	3	21
α-helix	148-149	2
β-strand	153-154	2	22
β-strand	159	1	20
α-helix	164	1
β-strand	165-166	2	22
α-helix	167-171	5
β-strand	174-178	5	23
β-strand	181	1	24
β-strand	184	1	24
β-strand	187-190	4	23
α-helix	191	1
β-strand	194-195	2	25
β-strand	205-206	2	25
α-helix	207-208	2
β-strand	219	1	26
β-strand	222	1	27
β-strand	225	1	27
β-strand	228	1	26

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor ligand superfamily member 10	A, B, D	protein	169	Homo sapiens	P50591 (AlphaFold model)
Tumor necrosis factor receptor superfamily member 10A	E, F, G	protein	108	Homo sapiens	O00220 (AlphaFold model)

Sequence of entity 1 (A, B, D), FASTA

>5CIR_1 Tumor necrosis factor ligand superfamily member 10 (chains A, B, D)
MVRERGPQRVAAHITGTRGRSNTLSSPNSKNEKALGRKINSWESSRSGHSFLSNLHLRNG
ELVIHEKGFYYIYSQTYFRFQEEIKENTKNDKQMVQYIYKYTSYPDPILLMKSARNSCWS
KDAEYGLYSIYQGGIFELKENDRIFVSVTNEHLIDMDHEASFFGAFLVG

Sequence of entity 2 (E, F, G), FASTA

>5CIR_2 Tumor necrosis factor receptor superfamily member 10A (chains E, F, G)
HSPLGELCPPGSHRSERPGACNRCTEGVGYTNASNNLFACLPCTACKSDEEERSPCTTTR
NTACQCKPGTFRNDNSAEMCRKCSTGCPRGMVKVKDCTPWSDIECVHK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Water and common crystallization additives (CL) are not listed.

Primary citation

The structure of the death receptor 4-TNF-related apoptosis-inducing ligand (DR4-TRAIL) complex. Ramamurthy, V., Yamniuk, A.P., Lawrence, E.J. et al. Acta Crystallogr F Struct Biol Commun (2015) 71:1273-1281. DOI 10.1107/S2053230X15016416 · PubMed

Other PDB entries of the same protein (UniProt P50591 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1DG6 1.3 Å, Crystal structure of APO2L/TRAIL
1D4V 2.2 Å, Crystal structure of trail-DR5 complex
1DU3 2.2 Å, Crystal structure of TRAIL-SDR5
1D0G 2.4 Å, Crystal structure of death receptor 5 (DR5) bound to APO2L/TRAIL
1D2Q 2.8 Å, Crystal structure of human trail
4N90 3.3 Å, Crystal structure of ternary complex of TRAIL, DR5, and Fab fragment from a DR5 agonist…

Browse structure collections

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