8Y3P: ASFV p72

ASFV p72 in complex with Fab C9. Determined by electron microscopy at 3.48 Å resolution. Released 4 Sept 2024.

Method: Electron microscopy
Resolution: 3.48 Å
Organisms: African swine fever virus, Sus scrofa
Chains: 9
Atoms: 17,028
Mol. weight: 312.42 kDa
Released: 4 Sept 2024

Explore 8Y3P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y3P contains 65 α-helices and 224 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: 19 helices, 49 β-strands

Element	Residues	Length	Sheet
β-strand	74-77	4	22
α-helix	78	1
β-strand	79	1	23
β-strand	89-93	5	23
β-strand	100-110	11	22
β-strand	113	1	24
α-helix	115-116	2
β-strand	117-118	2	25
α-helix	120-122	3
β-strand	126-128	3	26
β-strand	134-136	3	26
α-helix	138-139	2
β-strand	142	1	27
β-strand	149	1	27
β-strand	153-158	6	28
β-strand	164	1	28
β-strand	173-174	2	25
β-strand	176-177	2	29
α-helix	183-187	5
β-strand	188-195	8	23
β-strand	201-204	4	23
α-helix	205-214	10
α-helix	221-227	7
β-strand	234-237	4	9
β-strand	241	1	30
β-strand	246	1	9
β-strand	307	1	30
β-strand	308-314	7	9
β-strand	321	1	29
β-strand	324	1	24
α-helix	325-326	2
β-strand	327-333	7	22
α-helix	341-343	3
α-helix	344-345	2
β-strand	346	1	22
β-strand	355-361	7	23
α-helix	362-363	2
β-strand	370-371	2	29
β-strand	375-382	8	28
β-strand	387	1	31
β-strand	388-395	8	28
α-helix	402-406	5
β-strand	407-417	11	22
β-strand	436	1	32
α-helix	438-439	2
β-strand	440	1	33
β-strand	443-446	4	33
β-strand	454-455	2	34
β-strand	466-472	7	33
α-helix	473-475	3
β-strand	492-498	7	9
β-strand	502-503	2	28
β-strand	506	1	31
β-strand	518	1	31
β-strand	521-522	2	28
β-strand	528-534	7	9
β-strand	539-542	4	35
β-strand	550-554	5	35
α-helix	555-556	2
α-helix	557-561	5
α-helix	562-565	4
α-helix	568-570	3
α-helix	572-574	3
β-strand	580-582	3	33
β-strand	607-608	2	34
β-strand	609-610	2	35
β-strand	621-627	7	33
β-strand	631	1	32

Chain B: 17 helices, 47 β-strands

Element	Residues	Length	Sheet
β-strand	74-77	4	1
α-helix	78	1
β-strand	79	1	2
β-strand	89-93	5	2
β-strand	100-110	11	1
β-strand	113	1	3
α-helix	115-116	2
β-strand	117-118	2	4
α-helix	120-122	3
β-strand	126-128	3	5
β-strand	134-136	3	5
α-helix	138-139	2
β-strand	142	1	6
β-strand	149	1	6
β-strand	153-158	6	7
β-strand	164	1	7
β-strand	173-174	2	4
β-strand	176-177	2	8
α-helix	183-187	5
β-strand	188-195	8	2
β-strand	201-204	4	2
α-helix	205-214	10
α-helix	221-227	7
β-strand	234-241	8	9
β-strand	246	1	9
β-strand	307-314	8	9
β-strand	321	1	8
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
β-strand	355-361	7	2
α-helix	362-363	2
β-strand	370-371	2	8
β-strand	375-382	8	7
β-strand	387	1	10
β-strand	388-395	8	7
α-helix	402-406	5
β-strand	407-417	11	1
β-strand	436	1	11
α-helix	438-439	2
β-strand	440	1	12
β-strand	443-446	4	12
β-strand	454-455	2	13
β-strand	466-472	7	12
α-helix	473-475	3
β-strand	492-498	7	9
β-strand	502-503	2	7
β-strand	506	1	10
β-strand	518	1	10
β-strand	521-522	2	7
β-strand	528-534	7	9
β-strand	539-542	4	14
β-strand	550-554	5	14
α-helix	555-556	2
α-helix	557-561	5
α-helix	562-565	4
α-helix	572-574	3
β-strand	580-582	3	12
β-strand	607-608	2	13
β-strand	609-610	2	14
β-strand	621-627	7	12
β-strand	631	1	11

Chain C: 17 helices, 47 β-strands

Element	Residues	Length	Sheet
β-strand	74-77	4	43
α-helix	78	1
β-strand	79	1	44
β-strand	89-93	5	44
β-strand	100-110	11	43
β-strand	113	1	45
α-helix	115-116	2
β-strand	117-118	2	46
α-helix	119-122	4
β-strand	126-128	3	47
β-strand	134-136	3	47
α-helix	138-139	2
β-strand	142	1	48
β-strand	149	1	48
β-strand	153-158	6	49
β-strand	164	1	49
β-strand	173-174	2	46
β-strand	176-177	2	50
α-helix	183-187	5
β-strand	188-195	8	44
β-strand	201-204	4	44
α-helix	205-214	10
α-helix	221-227	7
β-strand	234-241	8	9
β-strand	245-246	2	9
β-strand	307-314	8	9
β-strand	321	1	50
β-strand	324	1	45
α-helix	325-326	2
β-strand	327-333	7	43
α-helix	344-345	2
β-strand	346	1	43
β-strand	355-361	7	44
α-helix	362-363	2
β-strand	370-371	2	50
β-strand	375-382	8	49
β-strand	387	1	51
β-strand	388-395	8	49
α-helix	402-405	4
β-strand	408-417	10	43
β-strand	436	1	52
α-helix	438-439	2
β-strand	440	1	53
β-strand	443-446	4	53
β-strand	454-455	2	54
β-strand	466-472	7	53
α-helix	473-475	3
β-strand	492-498	7	9
β-strand	502-503	2	49
β-strand	506	1	51
β-strand	518	1	51
β-strand	521-522	2	49
β-strand	528-534	7	9
β-strand	539-542	4	55
β-strand	550-554	5	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	53
β-strand	607-608	2	54
β-strand	609-610	2	55
β-strand	621-627	7	53
β-strand	631	1	52

Chain D: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	36
β-strand	6-7	2	37
β-strand	11-12	2	38
β-strand	18-23	6	37
β-strand	25	1	36
α-helix	29-31	3
β-strand	34-39	6	39
β-strand	45-51	7	39
β-strand	59-60	2	39
β-strand	65	1	37
β-strand	68-73	6	37
β-strand	78-83	6	37
α-helix	88-90	3
β-strand	92-100	9	39
β-strand	110-114	5	39
β-strand	118-120	3	39
β-strand	121-122	2	38

Chain E: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	56
β-strand	6-7	2	57
β-strand	11-12	2	58
β-strand	18-23	6	57
β-strand	25	1	56
α-helix	29-31	3
β-strand	34-39	6	59
β-strand	45-51	7	59
β-strand	60	1	59
β-strand	65	1	57
β-strand	68-73	6	57
β-strand	78-83	6	57
α-helix	88-90	3
β-strand	92-100	9	59
β-strand	110-114	5	59
β-strand	118-120	3	59
β-strand	121-122	2	58

Chains F, H and L: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	40
β-strand	8-11	4	41
β-strand	17-23	7	40
α-helix	30-32	3
β-strand	35-39	5	41
β-strand	46-49	4	41
β-strand	50	1	42
β-strand	54	1	42
β-strand	63-68	6	40
β-strand	71-76	6	40
α-helix	81-83	3
β-strand	86-93	8	41
β-strand	97-100	4	41
β-strand	104-108	5	41

Chain G: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	15
β-strand	6-7	2	16
β-strand	12	1	17
β-strand	18-23	6	16
β-strand	25	1	15
α-helix	29-31	3
β-strand	34-39	6	18
β-strand	45-51	7	18
β-strand	59-60	2	18
β-strand	65	1	16
β-strand	68-73	6	16
β-strand	78-83	6	16
α-helix	88-90	3
β-strand	92-100	9	18
β-strand	110-114	5	18
β-strand	118-120	3	18
β-strand	122	1	17

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 C9	D, E, G	protein	125	Sus scrofa
Light chain of C9	F, H, L	protein	109	Sus scrofa

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

>8Y3P_1 B646L (chains A, B, C)
MHHHHHHHHHHGSDYKDHDGDYKDHDIDYKDDDDKELENLYFQGAGSMASGGAFCLIAND
GKADKIILAQDLLNSRISNIKNVNKSYGKPDPEPTLSQIEETHLVHFNAHFKPYVPVGFE
YNKVRPHTGTPTLGNKLTFGIPQYGDFFHDMVGHHILGACHSSWQDAPIQGTSQMGAHGQ
LQTFPRNGYDWDNQTPLEGAVYTLVDPFGRPIVPGTKNAYRNLVYYCEYPGERLYENVRF
DVNGNSLDEYSSDVTTLVRKFCIPGDKMTGYKHLVGQEVSVEGTSGPLLCNIHDLHKPHQ
SKPILTDENDTQRTCSHTNPKFLSQHFPENSHNIQTAGKQDITPITDATYLDIRRNVHYS
CNGPQTPKYYQPPLALWIKLRFWFNENVNLAIPSVSIPFGERFITIKLASQKDLVNEFPG
LFVRQSRFIAGRPSRRNIRFKPWFIPGVINEISLTNNELYINNLFVTPEIHNLFVKRVRF
SLIRVHKTQVTHTNNNHHDEKLMSALKWPIEYMFIGLKPTWNISDQNPHQHRDWHKFGHV
VNAIMQPTHHAEISFQDRDTALPDACSSISDISPVTYPITLPIIKNISVTAHGINLIDKF
PSKFCSSYIPFHYGGNAIKTPDDPGAMMITFALKPREEYQPSGHINVSRAREFYISWDTD
YVGSITTADLVVSASAINFLLLQNGSAVLRYST

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

>8Y3P_2 Heavy chain of C9 (chains D, E, G)
EVKLVESGGGLVQPGGSLRLSCVGSGFTFSSYEINWVRQAPGKGLEWLAVVSKIGDRTYY
ADSVRGRLTISRDNSQNTAYLQMNSLRTEDTARYYCVRAWCASTCLPGDIMDLWGPGVGV
VVSSL

Sequence of entity 3 (F, H, L), FASTA

>8Y3P_3 Light chain of C9 (chains F, H, L)
QTVIQEPAMSVSPGGTVTLTCAWSSGSVTTSNYPSWFQQTPGQPPRQLIYNTNSRPTGVP
RRFSGKISGNKAALTITGAQAEDEADYFCGLYKRSANNIFGGGTHLTVL

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