4GJT: Complex structure of nectin-4

complex structure of nectin-4 bound to MV-H. Determined by X-ray diffraction at 3.1 Å resolution. Released 10 Oct 2012.

Method: X-ray diffraction
Resolution: 3.1 Å
Organisms: Measles virus, Homo sapiens
Chains: 3
Atoms: 5,020
Mol. weight: 79.87 kDa
Ligands: NAG
Released: 10 Oct 2012

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

Secondary structure: helices and β-sheets

4GJT contains 12 α-helices and 62 β-strands across 3 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: 7 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	157-159	3
α-helix	162-165	4
β-strand	194-198	5	1
β-strand	203	1	2
α-helix	206-211	6
β-strand	215-224	10	2
β-strand	227-237	11	2
β-strand	249-261	13	2
β-strand	269-279	11	2
β-strand	287-291	5	3
β-strand	296-300	5	3
β-strand	305-307	3	3
β-strand	318-324	7	3
β-strand	333-338	6	3
β-strand	339	1	4
β-strand	346-350	5	3
β-strand	355-359	5	3
β-strand	362-371	10	3
α-helix	374-384	11
α-helix	400-403	4
β-strand	408-416	9	3
β-strand	425	1	4
β-strand	426-430	5	3
β-strand	442-445	4	5
β-strand	451-456	6	5
α-helix	457-458	2
β-strand	459	1	6
β-strand	463	1	6
β-strand	466-471	6	5
β-strand	477	1	5
β-strand	482	1	5
β-strand	484-486	3	7
β-strand	495-497	3	7
β-strand	499	1	6
β-strand	508-511	4	8
β-strand	515-517	3	8
α-helix	518	1
β-strand	523-530	8	8
β-strand	537-543	7	8
β-strand	548-551	4	8
β-strand	563-565	3	1
β-strand	568-573	6	1
β-strand	576-585	10	1
β-strand	594-604	11	1

Chain B: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	9
β-strand	8-10	3	10
β-strand	16-19	4	11
β-strand	22-23	2	9
β-strand	31-38	8	10
α-helix	45-46	2
β-strand	47-51	5	10
β-strand	59	1	10
α-helix	61-63	3
β-strand	67-68	2	11
α-helix	69-71	3
β-strand	78	1	9
β-strand	81-84	4	11
β-strand	93-100	8	10
β-strand	105-113	9	10

Chain C: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	12
β-strand	8	1	13
β-strand	17-19	3	14
β-strand	22	1	15
β-strand	23-24	2	12
β-strand	30-38	9	13
β-strand	46-52	7	13
β-strand	56-59	4	13
β-strand	67-68	2	14
α-helix	74-75	2
β-strand	78	1	15
β-strand	81-83	3	14
α-helix	88-90	3
β-strand	93-101	9	13
β-strand	104-111	8	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin glycoprotein	A	protein	473	Measles virus	Q786F2 (AlphaFold model)
Poliovirus receptor-related protein 4	B, C	protein	123	Homo sapiens	Q96NY8 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4GJT_1 Hemagglutinin glycoprotein (chains A)
ADGIQHHHHHHDVAAEELMNALVNSTLLEARATNQFLAVSKGNCSGPTTIRGQFSNMSLS
LLDLYLSRGYNVSSIVTMTSQGMYGGTYLVGKPNLSSKGSELSQLSMHRVFEVGVIRNPG
LGAPVFHMTNYFEQPVSNDFSNCMVALGELKFAALCHREDSITIPYQGSGKGVSFQLVKL
GVWKSPTDMRSWVPLSTDDPVIDRLYLSSHRGVIADNQAKWAVPTTRTDDKLRMETCFQQ
ACKGKNQALCENPEWAPLKDNRIPSYGVLSVNLSLTVELKIKIASGFGPLITHGSGMDLY
KTNHNNVYWLTIPPMKNLALGVINTLEWIPRFKVSPNLFTVPIKEAGEDCHAPTYLPAEV
DGDVKLSSNLVILPGQDLQYVLATYDTSRVEHAVVYYVYSPSRSFSYFYPFRLPIKGVPI
ELQVECFTWDKKLWCRHFCVLADSESGGHITHSGMVGMGVSCTVTREDGTNRR

Sequence of entity 2 (B, C), FASTA

>4GJT_2 Poliovirus receptor-related protein 4 (chains B, C)
MGELETSDVVTVVLGQDAKLPCFYRGDSGEQVGQVAWARVDAGEGAQELALLHSKYGLHV
SPAYEGRVEQPPPPRNPLDGSVLLRNAVQADEGEYECRVSTFPAGSFQARLRLRVLEHHH
HHH

Ligands and cofactors

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

Primary citation

Structure of measles virus hemagglutinin bound to its epithelial receptor nectin-4. Zhang, X., Lu, G., Qi, J. et al. Nat Struct Mol Biol (2013) 20:67-72. DOI 10.1038/nsmb.2432 · PubMed

Other PDB entries of the same protein (UniProt Q786F2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9Q1Z 3.05 Å, Structure of the Measles virus Hemagglutinin ectodomain in complex with neutralizing…
9Q20 3.25 Å, Structure of the Measles virus Hemagglutinin ectodomain in complex with neutralizing…
9Q24 3.25 Å, Structure of the Measles virus Hemagglutinin ectodomain in complex with two neutralizing…

Browse structure collections

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