8Y3Q: ASFV p72

ASFV p72 in complex with Fab F11. Determined by electron microscopy at 2.98 Å resolution. Released 4 Sept 2024.

Method: Electron microscopy
Resolution: 2.98 Å
Organisms: African swine fever virus, Sus scrofa
Chains: 9
Atoms: 15,738
Mol. weight: 310.35 kDa
Released: 4 Sept 2024

Explore 8Y3Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y3Q contains 59 α-helices and 196 β-strands across 9 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: 16 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	72-77	6	1
β-strand	79	1	2
β-strand	89-93	5	2
β-strand	100-110	11	1
β-strand	113	1	3
β-strand	115	1	4
β-strand	118	1	5
β-strand	126-128	3	6
α-helix	130-132	3
β-strand	134-136	3	6
β-strand	142	1	7
β-strand	149	1	7
β-strand	153-158	6	8
β-strand	164	1	8
β-strand	173	1	5
β-strand	176-179	4	9
α-helix	183-186	4
β-strand	188-195	8	2
β-strand	201-204	4	2
α-helix	207-214	8
α-helix	221-227	7
β-strand	234-237	4	10
β-strand	241-246	6	11
β-strand	304-309	6	11
β-strand	310-314	5	10
β-strand	321	1	9
β-strand	324	1	3
α-helix	325-326	2
β-strand	327-333	7	1
α-helix	344-345	2
β-strand	346	1	1
α-helix	352-354	3
β-strand	355-361	7	2
α-helix	362-363	2
α-helix	364-366	3
β-strand	368-371	4	9
β-strand	375-382	8	8
β-strand	387-395	9	8
β-strand	402	1	4
α-helix	403-405	3
β-strand	407-417	11	1
β-strand	465-472	8	12
α-helix	473-475	3
α-helix	483-486	4
β-strand	492-498	7	13
β-strand	501-506	6	8
β-strand	518-523	6	8
β-strand	528-534	7	13
β-strand	539-543	5	14
β-strand	553-554	2	14
α-helix	555-556	2
α-helix	557-561	5
α-helix	562-565	4
α-helix	572-573	2
β-strand	579-582	4	12
β-strand	607-611	5	14
β-strand	618-625	8	12

Chain B: 19 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	72-77	6	36
β-strand	79	1	37
β-strand	89-93	5	37
β-strand	100-101	2	36
β-strand	104-110	7	36
β-strand	113	1	38
β-strand	117-118	2	39
α-helix	119-121	3
β-strand	126-128	3	40
α-helix	130-132	3
β-strand	134-136	3	40
α-helix	138-139	2
β-strand	142	1	41
β-strand	149	1	41
β-strand	153-158	6	42
β-strand	164	1	42
β-strand	173-174	2	39
β-strand	176-179	4	43
α-helix	183-186	4
β-strand	188-195	8	37
β-strand	201-204	4	37
α-helix	207-214	8
α-helix	221-227	7
β-strand	234-237	4	11
β-strand	241-246	6	13
β-strand	304-309	6	13
β-strand	310-314	5	11
β-strand	321	1	43
β-strand	324	1	38
α-helix	325-326	2
β-strand	327-333	7	36
α-helix	336-338	3
α-helix	344-345	2
β-strand	346	1	36
α-helix	352-354	3
β-strand	355-361	7	37
α-helix	362-363	2
α-helix	364-366	3
β-strand	368-371	4	43
β-strand	375-382	8	42
β-strand	387-395	9	42
α-helix	402-405	4
β-strand	407-417	11	36
β-strand	465-472	8	44
α-helix	473-475	3
α-helix	483-486	4
β-strand	492-498	7	10
β-strand	502-506	5	42
β-strand	518-522	5	42
β-strand	528-534	7	10
β-strand	539-543	5	45
β-strand	550-554	5	45
α-helix	555-556	2
α-helix	557-561	5
α-helix	562-565	4
α-helix	572-573	2
β-strand	579-582	4	44
β-strand	607-611	5	45
β-strand	618-625	8	44

Chain C: 15 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	72-77	6	46
β-strand	79	1	47
β-strand	89-92	4	47
β-strand	100-110	11	46
β-strand	113	1	48
β-strand	117-118	2	49
β-strand	126-128	3	50
α-helix	130-132	3
β-strand	134-136	3	50
β-strand	142	1	51
β-strand	149	1	51
β-strand	153-158	6	52
β-strand	164	1	52
β-strand	173-174	2	49
β-strand	176-179	4	53
α-helix	183-186	4
β-strand	188-195	8	47
β-strand	201-204	4	47
α-helix	207-214	8
α-helix	221-227	7
β-strand	234-237	4	13
β-strand	241-246	6	10
β-strand	304-309	6	10
β-strand	310-314	5	13
β-strand	321	1	53
β-strand	324	1	48
β-strand	327-333	7	46
α-helix	336-338	3
α-helix	344-345	2
β-strand	346	1	46
α-helix	352-354	3
β-strand	355-361	7	47
α-helix	362-363	2
α-helix	364-366	3
β-strand	368-371	4	53
β-strand	375-382	8	52
β-strand	387-395	9	52
α-helix	403-405	3
β-strand	407-417	11	46
β-strand	465-472	8	54
α-helix	483-486	4
β-strand	492-498	7	11
β-strand	501-506	6	52
β-strand	518-523	6	52
β-strand	528-534	7	11
β-strand	539-543	5	55
β-strand	553-554	2	55
α-helix	555-556	2
α-helix	557-561	5
α-helix	562-565	4
α-helix	572-574	3
β-strand	579-582	4	54
β-strand	607-611	5	55
β-strand	618-625	8	54

Chain D: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	15
β-strand	11-12	2	16
β-strand	17-24	8	15
α-helix	29-31	3
β-strand	34-39	6	17
β-strand	45-51	7	17
β-strand	54	1	18
β-strand	56	1	18
β-strand	60-62	3	17
β-strand	70-75	6	15
β-strand	80-86	7	15
α-helix	90-92	3
β-strand	94-100	7	17
β-strand	113-114	2	17
β-strand	118-120	3	17
β-strand	121-122	2	16

Chain E: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	19
β-strand	11-12	2	20
β-strand	17-24	8	19
α-helix	29-31	3
β-strand	35-39	5	21
β-strand	45-51	7	21
β-strand	54	1	22
β-strand	56	1	22
β-strand	60-62	3	21
β-strand	70-75	6	19
β-strand	80-86	7	19
α-helix	90-92	3
β-strand	94-98	5	21
β-strand	99-100	2	23
β-strand	113-114	2	23
β-strand	118-120	3	21
β-strand	121-122	2	20

Chain F: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	24
β-strand	11-12	2	25
β-strand	17-24	8	24
α-helix	29-31	3
β-strand	34-39	6	26
β-strand	45-51	7	26
β-strand	54	1	27
β-strand	56	1	27
β-strand	60-62	3	26
β-strand	70-75	6	24
β-strand	80-86	7	24
α-helix	90-92	3
β-strand	94-98	5	26
β-strand	118-120	3	26
β-strand	121-122	2	25

Chain G: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	28
β-strand	9-12	4	29
β-strand	17-24	8	28
α-helix	31-33	3
β-strand	36-40	5	29
β-strand	47-51	5	29
β-strand	55	1	29
β-strand	64-69	6	28
β-strand	72-78	7	28
β-strand	86-91	6	29
β-strand	94	1	30
β-strand	98	1	30
β-strand	105-109	5	29

Chain H: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	31
β-strand	9-12	4	32
β-strand	17-24	8	31
α-helix	31-33	3
β-strand	36-40	5	32
β-strand	47-51	5	32
β-strand	55	1	32
β-strand	64-69	6	31
β-strand	72-78	7	31
β-strand	87-91	5	32
β-strand	94	1	33
β-strand	98	1	33
β-strand	105-109	5	32

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
B646L	A, B, C	protein	693	African swine fever virus	P22776 (AlphaFold model)
Heavy chain of F11	D, E, F	protein	122	Sus scrofa
Light chain of F11	G, H, I	protein	110	Sus scrofa

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

>8Y3Q_1 B646L (chains A, B, C)
MHHHHHHHHHHGSDYKDHDGDYKDHDIDYKDDDDKELENLYFQGAGSMASGGAFCLIAND
GKADKIILAQDLLNSRISNIKNVNKSYGKPDPEPTLSQIEETHLVHFNAHFKPYVPVGFE
YNKVRPHTGTPTLGNKLTFGIPQYGDFFHDMVGHHILGACHSSWQDAPIQGTSQMGAHGQ
LQTFPRNGYDWDNQTPLEGAVYTLVDPFGRPIVPGTKNAYRNLVYYCEYPGERLYENVRF
DVNGNSLDEYSSDVTTLVRKFCIPGDKMTGYKHLVGQEVSVEGTSGPLLCNIHDLHKPHQ
SKPILTDENDTQRTCSHTNPKFLSQHFPENSHNIQTAGKQDITPITDATYLDIRRNVHYS
CNGPQTPKYYQPPLALWIKLRFWFNENVNLAIPSVSIPFGERFITIKLASQKDLVNEFPG
LFVRQSRFIAGRPSRRNIRFKPWFIPGVINEISLTNNELYINNLFVTPEIHNLFVKRVRF
SLIRVHKTQVTHTNNNHHDEKLMSALKWPIEYMFIGLKPTWNISDQNPHQHRDWHKFGHV
VNAIMQPTHHAEISFQDRDTALPDACSSISDISPVTYPITLPIIKNISVTAHGINLIDKF
PSKFCSSYIPFHYGGNAIKTPDDPGAMMITFALKPREEYQPSGHINVSRAREFYISWDTD
YVGSITTADLVVSASAINFLLLQNGSAVLRYST

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

>8Y3Q_2 Heavy chain of F11 (chains D, E, F)
EKLVESGGGLVKPGGSLKLSCVGSGSTFSSDAVSWVRQAPGKGLEWLAGIDGDGYGVSTY
YADSVKGRFTISRDNSQKTAYLQMNSLRTDDTARYYCAECPMVLLAKCSMEFWGPGVEVV
VS

Sequence of entity 3 (G, H, I), FASTA

>8Y3Q_3 Light chain of F11 (chains G, H, I)
LQTVIQEPAMSVSLGGTVTLTCAFSSGSVTSSNYPGWFQQTPGQPPRLLIYQTNSRPTGV
PSRFSGAISGNRAALTITGAQAEDEADYFCGLWKSGTDLPFGGGTHLTVL

Primary citation

p72 antigenic mapping reveals a potential supersite of vulnerability for African swine fever virus. Yu, Q., Liang, D., Fu, W. et al. Cell Discov (2024) 10:80-80. DOI 10.1038/s41421-024-00692-x · PubMed

Other PDB entries of the same protein (UniProt P22776 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7EMD 1.7 Å, Mooring Stone-Like Arg114 Pulls Diverse Bulged Peptides: First Insight into African…
6KU9 2.67 Å, Structure of the African swine fever virus major capsid protein p72
8Y3O 2.75 Å, ASFV p72 in complex with Fab B1
8Y3P 3.48 Å, ASFV p72 in complex with Fab C9
8Y3R 3.48 Å, ASFV p72 in complex with Fab H3
6L2T 4.1 Å, African swine fever virus major capsid protein p72
8ZL9 4.36 Å, ASFV p72 in complex with Fab G6

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