8Y3O: ASFV p72

ASFV p72 in complex with Fab B1. Determined by electron microscopy at 2.75 Å resolution. Released 4 Sept 2024.

Method: Electron microscopy
Resolution: 2.75 Å
Organisms: African swine fever virus, Sus scrofa
Chains: 9
Atoms: 17,058
Mol. weight: 312.6 kDa
Released: 4 Sept 2024

Explore 8Y3O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y3O contains 76 α-helices and 212 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: 21 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	72-75	4	19
β-strand	79	1	20
β-strand	89-93	5	20
β-strand	100	1	19
β-strand	104-110	7	19
α-helix	111-112	2
β-strand	113	1	21
β-strand	115	1	22
α-helix	116	1
β-strand	117-118	2	23
α-helix	119-122	4
β-strand	126-127	2	24
α-helix	130-132	3
β-strand	135-136	2	24
α-helix	138-139	2
β-strand	153-158	6	25
β-strand	164	1	25
β-strand	173-174	2	23
β-strand	176-179	4	26
α-helix	180	1
α-helix	183-187	5
β-strand	188-195	8	20
β-strand	201-204	4	20
α-helix	205-213	9
α-helix	222-227	6
β-strand	234-246	13	9
β-strand	305-314	10	9
β-strand	321	1	26
β-strand	324	1	21
α-helix	325-326	2
β-strand	327-332	6	19
α-helix	341-343	3
α-helix	344-345	2
β-strand	346	1	19
β-strand	355-361	7	20
α-helix	362-363	2
α-helix	364-366	3
β-strand	368-371	4	26
β-strand	375-382	8	25
β-strand	387-395	9	25
β-strand	402	1	22
α-helix	403-405	3
β-strand	407-417	11	19
β-strand	436-439	4	27
β-strand	444-446	3	28
β-strand	451-453	3	29
β-strand	463	1	27
β-strand	466-472	7	28
α-helix	483-486	4
β-strand	492-498	7	9
β-strand	501-506	6	25
β-strand	518-523	6	25
β-strand	528-534	7	9
β-strand	537-543	7	29
β-strand	553-554	2	29
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	28
β-strand	607-612	6	29
β-strand	621-625	5	28
α-helix	627	1
β-strand	628-631	4	27

Chain B: 21 helices, 46 β-strands

Element	Residues	Length	Sheet
β-strand	72-75	4	37
β-strand	79	1	38
β-strand	89-93	5	38
β-strand	100	1	37
β-strand	104-110	7	37
α-helix	111-112	2
β-strand	113	1	39
β-strand	115	1	40
α-helix	116	1
β-strand	117-118	2	41
α-helix	119-122	4
β-strand	126-127	2	42
α-helix	130-132	3
β-strand	135-136	2	42
α-helix	138-139	2
β-strand	153-158	6	43
β-strand	164	1	43
β-strand	173-174	2	41
β-strand	176-179	4	44
α-helix	180	1
α-helix	183-187	5
β-strand	188-195	8	38
β-strand	201-204	4	38
α-helix	205-214	10
α-helix	222-227	6
α-helix	233	1
β-strand	234-237	4	9
β-strand	241-243	3	45
β-strand	244-246	3	9
β-strand	305-307	3	45
β-strand	308-314	7	9
β-strand	321	1	44
β-strand	324	1	39
α-helix	325-326	2
β-strand	327-332	6	37
α-helix	341-343	3
α-helix	344-345	2
β-strand	346	1	37
β-strand	355-361	7	38
α-helix	362-363	2
α-helix	364-366	3
β-strand	368-371	4	44
β-strand	375-382	8	43
β-strand	387-395	9	43
β-strand	402	1	40
α-helix	403-405	3
β-strand	408-417	10	37
β-strand	436-439	4	46
β-strand	444-446	3	47
β-strand	451-453	3	48
β-strand	463	1	46
β-strand	466-472	7	47
α-helix	483-486	4
β-strand	492-498	7	9
β-strand	501-506	6	43
β-strand	518-523	6	43
β-strand	528-534	7	9
β-strand	537-543	7	48
β-strand	553-554	2	48
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	47
β-strand	607-612	6	48
β-strand	621-625	5	47
β-strand	628-631	4	46

Chain C: 22 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	72-75	4	1
β-strand	79	1	2
β-strand	89-93	5	2
β-strand	100	1	1
β-strand	104-110	7	1
α-helix	111-112	2
β-strand	113	1	3
β-strand	115	1	4
α-helix	116	1
β-strand	117-118	2	5
α-helix	119-122	4
β-strand	126-127	2	6
α-helix	130-132	3
α-helix	133-134	2
β-strand	135-136	2	6
α-helix	138-139	2
β-strand	153-158	6	7
β-strand	164	1	7
β-strand	173-174	2	5
β-strand	176-179	4	8
α-helix	180	1
α-helix	183-187	5
β-strand	188-195	8	2
β-strand	201-204	4	2
α-helix	205-214	10
α-helix	222-227	6
β-strand	234-246	13	9
β-strand	305-314	10	9
β-strand	321	1	8
β-strand	324	1	3
α-helix	325-326	2
β-strand	327-332	6	1
α-helix	341-343	3
α-helix	344-345	2
β-strand	346	1	1
β-strand	355-361	7	2
α-helix	362-363	2
α-helix	364-366	3
β-strand	368-371	4	8
β-strand	375-382	8	7
β-strand	387-395	9	7
β-strand	402	1	4
α-helix	403-405	3
β-strand	408-417	10	1
β-strand	436-439	4	10
β-strand	444-446	3	11
β-strand	451-453	3	12
β-strand	463	1	10
β-strand	466-472	7	11
α-helix	473-475	3
α-helix	483-486	4
β-strand	492-498	7	9
β-strand	501-506	6	7
β-strand	518-523	6	7
β-strand	528-534	7	9
β-strand	537-543	7	12
β-strand	553-554	2	12
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	11
β-strand	607-612	6	12
β-strand	621-625	5	11
β-strand	628-631	4	10

Chain D: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	13
β-strand	10	1	14
α-helix	13-14	2
β-strand	19-24	6	13
β-strand	30-31	2	15
β-strand	34-35	2	15
β-strand	37-42	6	14
β-strand	49-53	5	14
β-strand	57-58	2	14
β-strand	66	1	13
β-strand	71	1	13
β-strand	74-79	6	13
β-strand	88-94	7	14
α-helix	100	1
β-strand	102	1	14
β-strand	106-108	3	14

Chain E: 2 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	30
β-strand	10	1	31
β-strand	13	1	32
α-helix	14	1
β-strand	19-24	6	30
β-strand	30-31	2	33
β-strand	34-35	2	33
β-strand	37-42	6	31
β-strand	49-53	5	31
β-strand	57-58	2	31
β-strand	66	1	30
β-strand	71	1	30
β-strand	74-79	6	30
β-strand	88-94	7	31
α-helix	100	1
β-strand	102	1	31
β-strand	106-108	3	31
β-strand	110	1	32

Chain F: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	49
β-strand	10	1	50
α-helix	13-14	2
β-strand	19-24	6	49
β-strand	30-31	2	51
β-strand	34-35	2	51
β-strand	37-42	6	50
β-strand	49-53	5	50
β-strand	57-58	2	50
β-strand	66	1	49
β-strand	71	1	49
β-strand	74-79	6	49
β-strand	88-94	7	50
α-helix	100	1
β-strand	102	1	50
β-strand	106-108	3	50

Chains G, H and I: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	34
β-strand	11-12	2	35
β-strand	17-25	9	34
α-helix	29-31	3
β-strand	34-39	6	36
β-strand	45-51	7	36
β-strand	60-62	3	36
β-strand	70-75	6	34
β-strand	80-86	7	34
α-helix	90-92	3
β-strand	94-100	7	36
β-strand	113	1	36
β-strand	118-120	3	36
β-strand	121-122	2	35

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
B646L	A, B, C	protein	693	African swine fever virus	P22776 (AlphaFold model)
Light chain of B1	D, E, F	protein	111	Sus scrofa
Heavy chain of B1	G, H, I	protein	123	Sus scrofa

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

>8Y3O_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

>8Y3O_2 Light chain of B1 (chains D, E, F)
DIVLTQTPRSLSVSPGEPASISCRSSQSLEEYGKNWLSWYQQKPGQSPRLLIYQATNRAS
WVPERFSGSGSGTDFTLKISRVEAEDVGVYYCFQDLQPPNGFGAGTKLELK

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

>8Y3O_3 Heavy chain of B1 (chains G, H, I)
EVKLVESGGGLVQPGGSLKLSCVGSGSTFSSDAVSWVRQAPGKGLEWLAGIDGDGGGGST
YYADSVKGRFTISRDNSQKTAYLQMNSLRTDDTARYYCAECPMVLLAKCSMEFWGPGVEV
VVS

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
8Y3Q 2.98 Å, ASFV p72 in complex with Fab F11
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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