4FRW: Human nectin-4 extracellular fragment D1-D2

Crystal structure of human nectin-4 extracellular fragment D1-D2. Determined by X-ray diffraction at 3.5 Å resolution. Released 22 Aug 2012.

Method: X-ray diffraction
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 6
Atoms: 9,257
Mol. weight: 140.8 kDa
Released: 22 Aug 2012

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

Secondary structure: helices and β-sheets

4FRW contains 36 α-helices and 132 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.

Chain A: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	34-35	2	1
β-strand	39-43	5	2
α-helix	47	1
β-strand	48-50	3	3
β-strand	53-54	2	1
β-strand	61-70	10	2
β-strand	76-83	8	2
β-strand	87-90	4	2
α-helix	92-94	3
β-strand	98-99	2	3
α-helix	100-101	2
α-helix	104	1
β-strand	109	1	1
β-strand	112-114	3	3
α-helix	119-121	3
β-strand	123-132	10	2
β-strand	135-146	12	2
β-strand	147	1	4
β-strand	152-155	4	5
α-helix	158	1
β-strand	159-160	2	6
β-strand	166-175	10	5
β-strand	176	1	4
α-helix	178-179	2
β-strand	180-185	6	7
β-strand	190-197	8	5
β-strand	202-210	9	5
α-helix	214-216	3
β-strand	220-226	7	7
β-strand	234-239	6	7
β-strand	242-243	2	6

Chain B: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	34-35	2	8
β-strand	39-43	5	9
α-helix	47	1
β-strand	48-50	3	10
β-strand	53-54	2	8
β-strand	61-71	11	9
β-strand	75-83	9	9
β-strand	87-90	4	9
β-strand	98-99	2	10
α-helix	100-102	3
β-strand	109	1	8
β-strand	112-114	3	10
α-helix	119-121	3
β-strand	123-132	10	9
β-strand	135-146	12	9
β-strand	147	1	11
β-strand	152-155	4	12
β-strand	159-160	2	13
β-strand	166-175	10	12
β-strand	176	1	11
β-strand	180-185	6	14
β-strand	190-197	8	12
β-strand	202-210	9	12
α-helix	214-216	3
β-strand	219-226	8	14
β-strand	234-240	7	14
β-strand	242-243	2	13

Chain C: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	34-35	2	15
β-strand	39-43	5	16
β-strand	48-50	3	17
β-strand	53-54	2	15
β-strand	61-69	9	16
β-strand	77-83	7	16
β-strand	87-90	4	16
α-helix	92-94	3
β-strand	98-99	2	17
α-helix	100-102	3
α-helix	104	1
β-strand	109	1	15
β-strand	112-114	3	17
α-helix	119-121	3
β-strand	123-132	10	16
β-strand	135-146	12	16
β-strand	147	1	18
β-strand	152-155	4	19
α-helix	158-159	2
β-strand	166-175	10	19
β-strand	176	1	18
α-helix	178-179	2
β-strand	180-185	6	20
β-strand	191-197	7	19
β-strand	202-210	9	19
β-strand	220-226	7	20
β-strand	234-239	6	20

Chain D: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	34-35	2	21
β-strand	39-43	5	22
α-helix	47	1
β-strand	48-50	3	23
β-strand	53-54	2	21
β-strand	61-69	9	22
β-strand	77-83	7	22
β-strand	87-90	4	22
β-strand	98-99	2	23
α-helix	100-101	2
α-helix	104	1
β-strand	109	1	21
β-strand	112-114	3	23
β-strand	123-132	10	22
β-strand	135-146	12	22
β-strand	147	1	24
β-strand	152-155	4	25
α-helix	156	1
α-helix	158	1
β-strand	159-160	2	26
β-strand	166-175	10	25
β-strand	176	1	24
α-helix	178-179	2
β-strand	180-185	6	27
β-strand	190-197	8	25
β-strand	202-210	9	25
α-helix	214-216	3
β-strand	220-226	7	27
β-strand	234-239	6	27
β-strand	242-243	2	26

Chain E: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	35	1	28
β-strand	39-43	5	29
α-helix	47	1
β-strand	48-49	2	30
β-strand	53	1	28
β-strand	64-70	7	29
β-strand	78-83	6	29
β-strand	98-99	2	30
α-helix	100-102	3
β-strand	109	1	28
β-strand	113-114	2	30
α-helix	119-121	3
β-strand	123-130	8	29
β-strand	139-146	8	29
β-strand	147	1	31
β-strand	152-155	4	32
α-helix	156	1
α-helix	158	1
β-strand	166-175	10	32
β-strand	176	1	31
α-helix	178-179	2
β-strand	180-185	6	33
β-strand	189-197	9	32
β-strand	202-210	9	32
β-strand	220-226	7	33
β-strand	234-239	6	33

Chain F: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	39-43	5	34
β-strand	48-50	3	35
β-strand	66-69	4	34
β-strand	77-81	5	34
β-strand	90	1	34
α-helix	92-94	3
β-strand	98-99	2	35
α-helix	110-111	2
β-strand	112-114	3	35
α-helix	119-121	3
β-strand	123-128	6	34
β-strand	140-146	7	34
β-strand	147	1	36
β-strand	152-155	4	37
β-strand	166-175	10	37
β-strand	176	1	36
α-helix	178-179	2
β-strand	180-181	2	38
β-strand	184	1	38
β-strand	191	1	39
β-strand	196-197	2	37
β-strand	202-207	6	37
β-strand	208	1	39
β-strand	209-210	2	37
α-helix	214-216	3
β-strand	219-226	8	38
β-strand	234-240	7	38

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Poliovirus receptor-related protein 4	A, B, C, D, E, F	protein	218	Homo sapiens	Q96NY8 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>4FRW_1 Poliovirus receptor-related protein 4 (chains A, B, C, D, E, F)
GELETSDVVTVVLGQDAKLPCFYRGDSGEQVGQVAWARVDAGEGAQELALLHSKYGLHVS
PAYEGRVEQPPPPRNPLDGSVLLRNAVQADEGEYECRVSTFPAGSFQARLRLRVLVPPLP
SLNPGPALEEGQGLTLAASCTAEGSPAPSVTWDTEVKGTTSSRSFKHSRSAAVTSEFHLV
PSRSMNGQPLTCVVSHPGLLQDQRITHILHVSHHHHHH

Primary citation

Nectin ectodomain structures reveal a canonical adhesive interface. Harrison, O.J., Vendome, J., Brasch, J. et al. Nat Struct Mol Biol (2012) 19:906-915. DOI 10.1038/nsmb.2366 · PubMed

Other PDB entries of the same protein (UniProt Q96NY8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4JJH 2.25 Å, Crystal structure of the D1 domain from human Nectin-4 extracellular fragment…
9UCL 2.43 Å, CryoEM structure of IgV domain of human Nectin-4 with Trimbody
4GJT 3.1 Å, complex structure of nectin-4 bound to MV-H
9KKJ 3.26 Å, Structure of Nectin-4 D1 domain in complex with the Fab fragment of 9MW2821 mAb

Browse structure collections

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