8Y3R: ASFV p72

ASFV p72 in complex with Fab H3. 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: 15,735
Mol. weight: 311.38 kDa
Released: 4 Sept 2024

Explore 8Y3R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y3R contains 56 α-helices and 203 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: 17 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	77	1	1
β-strand	89-92	4	2
β-strand	100-101	2	3
β-strand	105-109	5	4
β-strand	115	1	5
β-strand	117-118	2	6
α-helix	120-122	3
β-strand	128	1	7
β-strand	134	1	7
α-helix	138-139	2
β-strand	142	1	8
β-strand	149	1	8
β-strand	154-158	5	9
β-strand	164	1	9
β-strand	173-174	2	6
β-strand	176-179	4	10
α-helix	180	1
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	11
β-strand	305-314	10	11
β-strand	321	1	10
α-helix	324-327	4
β-strand	328-332	5	4
α-helix	341-343	3
α-helix	344-346	3
β-strand	355-361	7	2
α-helix	362-363	2
α-helix	364-367	4
β-strand	368-371	4	10
β-strand	375-379	5	9
β-strand	382	1	12
β-strand	387-390	4	12
β-strand	391-392	2	9
β-strand	395	1	9
α-helix	401	1
β-strand	402	1	5
α-helix	403-404	2
β-strand	408	1	4
β-strand	412	1	1
β-strand	416-417	2	3
β-strand	466-472	7	13
α-helix	473-475	3
α-helix	483-486	4
β-strand	493-498	6	11
β-strand	501-503	3	12
β-strand	506	1	12
β-strand	518-523	6	12
β-strand	528-533	6	11
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
β-strand	579-582	4	13
β-strand	609-610	2	14
β-strand	619-624	6	13

Chains B and F: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	15
β-strand	11	1	16
β-strand	18-25	8	15
β-strand	34-39	6	17
β-strand	45-51	7	17
β-strand	58-60	3	17
β-strand	68-73	6	15
β-strand	78-83	6	15
α-helix	88-90	3
β-strand	92-97	6	17
β-strand	102	1	18
β-strand	104	1	18
β-strand	114	1	17
β-strand	118-120	3	17
β-strand	121	1	16

Chain C: 16 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	89-92	4	21
β-strand	100-101	2	22
β-strand	105-109	5	23
β-strand	115	1	24
β-strand	117-118	2	25
α-helix	120-122	3
β-strand	128	1	26
β-strand	134	1	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	176-179	4	29
α-helix	180	1
β-strand	188-195	8	21
β-strand	201-204	4	21
α-helix	205-214	10
α-helix	222-227	6
β-strand	234-246	13	11
β-strand	305-314	10	11
β-strand	321	1	29
α-helix	324-327	4
β-strand	328-332	5	23
α-helix	341-343	3
α-helix	344-346	3
β-strand	355-361	7	21
α-helix	362-363	2
α-helix	364-367	4
β-strand	368-371	4	29
β-strand	375-380	6	28
β-strand	382	1	30
β-strand	387	1	31
β-strand	388	1	30
β-strand	390	1	32
β-strand	391-392	2	28
β-strand	395	1	28
β-strand	402	1	24
α-helix	403-404	2
β-strand	408	1	23
β-strand	412	1	23
β-strand	416-417	2	22
β-strand	466-472	7	33
α-helix	473-475	3
α-helix	483-486	4
β-strand	493-498	6	11
β-strand	501-503	3	32
β-strand	506	1	31
β-strand	518	1	31
β-strand	521-523	3	32
β-strand	528-533	6	11
β-strand	539-542	4	34
β-strand	550-554	5	34
α-helix	555-556	2
α-helix	557-561	5
α-helix	562-565	4
β-strand	579-582	4	33
β-strand	609-610	2	34
β-strand	619-624	6	33

Chain D: 17 helices, 45 β-strands

Element	Residues	Length	Sheet
β-strand	77	1	40
β-strand	89-92	4	41
β-strand	100-101	2	42
β-strand	105-109	5	43
β-strand	115	1	44
β-strand	117-118	2	45
α-helix	120-122	3
β-strand	128	1	46
β-strand	134	1	46
α-helix	138-139	2
β-strand	142	1	47
β-strand	149	1	47
β-strand	154-158	5	48
β-strand	164	1	48
β-strand	173-174	2	45
β-strand	176-179	4	49
α-helix	180	1
β-strand	188-195	8	41
β-strand	201-204	4	41
α-helix	205-214	10
α-helix	222-227	6
β-strand	234-246	13	11
β-strand	305-314	10	11
β-strand	321	1	49
α-helix	324-327	4
β-strand	328-332	5	43
α-helix	341-343	3
α-helix	344-346	3
β-strand	355-361	7	41
α-helix	362-363	2
α-helix	364-367	4
β-strand	368-371	4	49
β-strand	375-379	5	48
β-strand	382	1	50
β-strand	387	1	51
β-strand	388	1	50
β-strand	390	1	52
β-strand	391-392	2	48
β-strand	395	1	48
α-helix	401	1
β-strand	402	1	44
α-helix	403-404	2
β-strand	408	1	43
β-strand	412	1	40
β-strand	416-417	2	42
β-strand	466-472	7	53
α-helix	473-475	3
α-helix	483-486	4
β-strand	493-498	6	11
β-strand	501-503	3	52
β-strand	506	1	51
β-strand	518	1	51
β-strand	521-523	3	52
β-strand	528-533	6	11
β-strand	540-542	3	54
β-strand	550-553	4	54
α-helix	555-556	2
α-helix	557-561	5
α-helix	562-565	4
β-strand	580-582	3	53
β-strand	609-610	2	54
β-strand	619-624	6	53

Chain E: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	35
β-strand	11	1	36
β-strand	18-25	8	35
β-strand	34-39	6	37
β-strand	45-51	7	37
β-strand	58-60	3	37
β-strand	68-73	6	35
β-strand	78-83	6	35
α-helix	88-90	3
β-strand	92-97	6	37
β-strand	102	1	38
β-strand	104	1	38
β-strand	118-120	3	37
β-strand	121	1	36

Chains G and L: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	39
β-strand	9-12	4	37
β-strand	17-24	8	39
α-helix	31-33	3
β-strand	36-40	5	37
β-strand	47-50	4	37
β-strand	64	1	39
β-strand	67-69	3	39
β-strand	72-78	7	39
β-strand	87-94	8	37
β-strand	98-109	12	37

Chain H: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	59
β-strand	11-12	2	60
β-strand	17-24	8	59
α-helix	31-33	3
β-strand	36-40	5	57
β-strand	47-50	4	57
β-strand	64	1	59
β-strand	67-69	3	59
β-strand	72-78	7	59
β-strand	87-94	8	57
β-strand	98-106	9	57
β-strand	108-109	2	60

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
B646L	A, C, D	protein	693	African swine fever virus	P22776 (AlphaFold model)
Heavy chain of H3	B, E, F	protein	122	Sus scrofa
Light chain of H3	G, H, L	protein	108	Sus scrofa

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

>8Y3R_1 B646L (chains A, C, D)
MHHHHHHHHHHGSDYKDHDGDYKDHDIDYKDDDDKELENLYFQGAGSMASGGAFCLIAND
GKADKIILAQDLLNSRISNIKNVNKSYGKPDPEPTLSQIEETHLVHFNAHFKPYVPVGFE
YNKVRPHTGTPTLGNKLTFGIPQYGDFFHDMVGHHILGACHSSWQDAPIQGTSQMGAHGQ
LQTFPRNGYDWDNQTPLEGAVYTLVDPFGRPIVPGTKNAYRNLVYYCEYPGERLYENVRF
DVNGNSLDEYSSDVTTLVRKFCIPGDKMTGYKHLVGQEVSVEGTSGPLLCNIHDLHKPHQ
SKPILTDENDTQRTCSHTNPKFLSQHFPENSHNIQTAGKQDITPITDATYLDIRRNVHYS
CNGPQTPKYYQPPLALWIKLRFWFNENVNLAIPSVSIPFGERFITIKLASQKDLVNEFPG
LFVRQSRFIAGRPSRRNIRFKPWFIPGVINEISLTNNELYINNLFVTPEIHNLFVKRVRF
SLIRVHKTQVTHTNNNHHDEKLMSALKWPIEYMFIGLKPTWNISDQNPHQHRDWHKFGHV
VNAIMQPTHHAEISFQDRDTALPDACSSISDISPVTYPITLPIIKNISVTAHGINLIDKF
PSKFCSSYIPFHYGGNAIKTPDDPGAMMITFALKPREEYQPSGHINVSRAREFYISWDTD
YVGSITTADLVVSASAINFLLLQNGSAVLRYST

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

>8Y3R_2 Heavy chain of H3 (chains B, E, F)
QEKLVESGGGLVQPGGSLILSCVGSGFTFITYEINWVRQAPGKGLEWLAVVSKIGDRTYY
AHSVRGRLTISRDNSQNTAYLQMNSLRTEDTARYYCVRAWCATTCLPGDIMDLWGPGVGV
IV

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

>8Y3R_3 Light chain of H3 (chains G, H, L)
TVIHEPAMSLSPGGTDTLTCAFSSGSITNNNYPSWFQQTPRQPPRLLIYNTNNRPTGVPS
RFSGAISGNKAALTITGAQANDEADYFCTLYISIADVIFGGGTHLTVL

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
8Y3P 3.48 Å, ASFV p72 in complex with Fab C9
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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