8XZ9: BA.2.86 Spike

BA.2.86 Spike in complex with bovine ACE2 (bound 2 ACE2). Determined by electron microscopy at 3.37 Å resolution. Released 13 Nov 2024.

Method: Electron microscopy
Resolution: 3.37 Å
Organisms: Bos taurus, Severe acute respiratory syndrome coronavirus 2
Chains: 5
Atoms: 35,083
Mol. weight: 517.86 kDa
Released: 13 Nov 2024

Explore 8XZ9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8XZ9 contains 145 α-helices and 249 β-strands across 5 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: 30 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	21-52	32
α-helix	56-80	25
α-helix	91-100	10
α-helix	104-107	4
α-helix	110-129	20
β-strand	131-133	3	1
β-strand	140-142	3	1
α-helix	147-153	7
α-helix	157-192	36
α-helix	198-203	6
α-helix	204-206	3
α-helix	218-250	33
α-helix	260	1
β-strand	261-262	2	2
α-helix	263-265	3
α-helix	293-299	7
α-helix	303-316	14
α-helix	319-323	5
α-helix	324-329	6
β-strand	349-351	3	3
β-strand	354-355	2	3
α-helix	365-383	19
α-helix	399-412	14
α-helix	414-420	7
α-helix	431-446	16
α-helix	448-464	17
α-helix	473-483	11
β-strand	486-487	2	2
α-helix	498-500	3
α-helix	512-531	20
α-helix	547-557	11
α-helix	560-562	3
α-helix	565-572	8
α-helix	581-586	6
α-helix	588-597	10
α-helix	598-600	3

Chain B: 27 helices, 82 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	4
β-strand	27-30	4	5
β-strand	37	1	6
β-strand	50-54	5	7
α-helix	56-57	2
β-strand	61-64	4	5
β-strand	67	1	4
β-strand	84-85	2	8
β-strand	91-92	2	9
β-strand	104-107	4	8
β-strand	115	1	10
β-strand	122-123	2	11
β-strand	125	1	11
β-strand	131	1	12
β-strand	132	1	10
β-strand	166	1	12
β-strand	191	1	13
β-strand	192-193	2	9
β-strand	194-197	4	14
β-strand	200-203	4	14
β-strand	204-205	2	15
β-strand	206	1	13
β-strand	223	1	6
β-strand	224-225	2	15
β-strand	229	1	14
β-strand	237-240	4	8
α-helix	242-245	4
β-strand	272-279	8	7
β-strand	285-290	6	7
α-helix	295-303	9
β-strand	311-316	6	16
β-strand	320	1	17
α-helix	321-322	2
β-strand	324-325	2	18
β-strand	356	1	19
α-helix	366-369	4
β-strand	376	1	19
β-strand	392	1	20
β-strand	396-402	7	19
α-helix	404-409	6
β-strand	412	1	21
α-helix	417-421	5
β-strand	425	1	21
β-strand	430-437	8	19
β-strand	448	1	22
α-helix	460-462	3
β-strand	485	1	23
β-strand	488	1	23
β-strand	497	1	22
β-strand	508-515	8	19
β-strand	524	1	20
β-strand	538-543	6	18
β-strand	546-551	6	18
β-strand	554	1	24
β-strand	565-566	2	25
β-strand	576	1	25
β-strand	577	1	26
β-strand	584	1	26
β-strand	585	1	24
β-strand	588	1	18
β-strand	594-599	6	16
β-strand	609-613	5	16
α-helix	617-626	10
β-strand	629	1	17
β-strand	642-643	2	16
β-strand	648-651	4	16
β-strand	654-660	7	27
β-strand	664-667	4	27
β-strand	670-676	7	27
β-strand	690-697	8	27
β-strand	702	1	28
β-strand	713-715	3	29
β-strand	718-728	11	30
β-strand	733-734	2	31
α-helix	738-742	5
α-helix	747-753	7
α-helix	754-756	3
α-helix	760-782	23
β-strand	790	1	32
β-strand	797	1	33
β-strand	800	1	33
α-helix	817-824	8
α-helix	849-855	7
β-strand	860-861	2	31
α-helix	862-863	2
α-helix	867-883	17
α-helix	887-890	4
α-helix	893-895	3
α-helix	898-909	12
α-helix	914-917	4
α-helix	920-940	21
α-helix	946-964	19
α-helix	965-967	3
α-helix	977-983	7
α-helix	986-1032	47
β-strand	1047-1056	10	30
β-strand	1059-1069	11	30
β-strand	1072-1074	3	29
β-strand	1077-1078	2	34
β-strand	1081-1082	2	35
β-strand	1087-1090	4	35
β-strand	1094-1097	4	34
β-strand	1102-1105	4	34
β-strand	1113	1	34
β-strand	1116	1	36
β-strand	1120-1122	3	35
β-strand	1133-1134	2	35
β-strand	1138	1	36
α-helix	1140-1143	4

Chain C: 29 helices, 78 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	37
β-strand	37	1	38
β-strand	42-43	2	25
β-strand	47	1	39
β-strand	50-55	6	39
α-helix	56-57	2
β-strand	61-65	5	37
β-strand	84-85	2	40
β-strand	90-96	7	37
β-strand	104-105	2	41
β-strand	116-118	3	41
β-strand	121	1	42
β-strand	126	1	42
β-strand	129-131	3	41
β-strand	188-195	8	37
β-strand	201-207	7	37
β-strand	223	1	38
β-strand	224-229	6	37
β-strand	237-238	2	40
β-strand	239-240	2	41
β-strand	264-269	6	37
β-strand	271-279	9	39
β-strand	285-290	6	39
α-helix	295-303	9
β-strand	311-316	6	43
β-strand	320	1	44
α-helix	321-322	2
β-strand	324-326	3	45
α-helix	330-332	3
β-strand	356-358	3	46
β-strand	362	1	47
α-helix	367-370	4
β-strand	374-376	3	46
β-strand	379	1	46
β-strand	392	1	48
β-strand	395-402	8	46
α-helix	404-409	6
β-strand	430-436	7	46
β-strand	452-454	3	49
α-helix	460-462	3
β-strand	473-474	2	50
β-strand	485	1	50
β-strand	488-489	2	50
β-strand	492-494	3	49
β-strand	508-515	8	46
β-strand	524	1	48
β-strand	525	1	47
β-strand	538-541	4	45
α-helix	543-545	3
β-strand	548-554	7	45
β-strand	575-577	3	45
β-strand	584-588	5	45
β-strand	594-599	6	43
β-strand	609-613	5	43
α-helix	617-626	10
β-strand	629	1	44
β-strand	642-646	5	43
β-strand	648-651	4	43
β-strand	654-655	2	51
β-strand	660	1	52
β-strand	664-665	2	51
β-strand	670-676	7	51
β-strand	690-696	7	51
β-strand	697	1	52
α-helix	698	1
β-strand	703-704	2	53
β-strand	713-715	3	54
β-strand	718-728	11	55
α-helix	732	1
β-strand	733-734	2	56
α-helix	738-742	5
α-helix	747-754	8
α-helix	761-782	22
β-strand	788	1	28
β-strand	797	1	57
β-strand	800	1	57
β-strand	808	1	58
β-strand	815	1	58
α-helix	817-825	9
α-helix	846-848	3
α-helix	849-856	8
β-strand	860-861	2	56
α-helix	862-863	2
α-helix	867-883	17
α-helix	887-890	4
α-helix	898-909	12
α-helix	913-918	6
α-helix	920-940	21
α-helix	946-964	19
α-helix	965-967	3
α-helix	977-983	7
α-helix	986-1028	43
α-helix	1029-1033	5
β-strand	1047-1050	4	55
β-strand	1053-1056	4	55
β-strand	1059-1069	11	55
β-strand	1072-1074	3	54
β-strand	1081-1082	2	59
β-strand	1087-1090	4	59
β-strand	1094-1097	4	60
β-strand	1102-1105	4	60
β-strand	1113-1114	2	60
β-strand	1116	1	61
β-strand	1120-1122	3	59
β-strand	1133-1134	2	59
β-strand	1138	1	61
α-helix	1140-1143	4

Chain D: 29 helices, 73 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	62
β-strand	37	1	63
β-strand	50-55	6	64
α-helix	56-57	2
β-strand	61-65	5	62
β-strand	84-85	2	65
β-strand	90-95	6	62
β-strand	104-107	4	65
β-strand	116-118	3	65
β-strand	121	1	66
β-strand	126	1	66
β-strand	128-131	4	65
β-strand	167-170	4	65
β-strand	189-195	7	62
β-strand	201-207	7	62
β-strand	223	1	63
β-strand	224-229	6	62
β-strand	237-240	4	65
β-strand	264-269	6	62
β-strand	271-279	9	64
β-strand	285-289	5	64
α-helix	295-303	9
β-strand	311-316	6	67
β-strand	319	1	68
β-strand	320	1	69
β-strand	324-325	2	70
α-helix	334	1
β-strand	335	1	71
α-helix	336	1
α-helix	338-342	5
β-strand	354-358	5	72
β-strand	361	1	73
β-strand	362	1	71
α-helix	366-371	6
β-strand	376	1	72
β-strand	379	1	72
β-strand	392	1	73
β-strand	395-402	8	72
α-helix	418-421	4
β-strand	431-437	7	72
β-strand	452-454	3	74
α-helix	460-462	3
β-strand	473-474	2	75
β-strand	485	1	75
β-strand	488-489	2	75
β-strand	492-494	3	74
β-strand	508-515	8	72
β-strand	524	1	73
β-strand	538-543	6	70
β-strand	546-554	9	70
β-strand	575-577	3	70
β-strand	584-588	5	70
α-helix	589-591	3
β-strand	592	1	68
β-strand	595-599	5	67
β-strand	609-612	4	67
α-helix	617-626	10
β-strand	629	1	69
β-strand	642-643	2	67
β-strand	650-651	2	67
β-strand	654-655	2	76
β-strand	664-665	2	76
β-strand	670-676	7	76
β-strand	690-696	7	76
α-helix	697-698	2
β-strand	704	1	32
β-strand	713-715	3	77
β-strand	718-728	11	78
β-strand	733-734	2	79
α-helix	738-742	5
α-helix	747-753	7
α-helix	754-756	3
α-helix	760-782	23
β-strand	789-790	2	53
α-helix	791-792	2
β-strand	797	1	80
β-strand	800	1	80
α-helix	817-824	8
α-helix	849-853	5
β-strand	860-861	2	79
α-helix	862-863	2
α-helix	867-884	18
α-helix	887-889	3
α-helix	898-907	10
α-helix	914-918	5
α-helix	924-940	17
α-helix	946-964	19
α-helix	965-967	3
α-helix	977-983	7
α-helix	986-1028	43
α-helix	1029-1033	5
β-strand	1047-1056	10	78
β-strand	1059-1069	11	78
β-strand	1072-1074	3	77
β-strand	1077	1	81
β-strand	1081-1082	2	82
β-strand	1087-1090	4	82
β-strand	1094-1097	4	81
β-strand	1102-1105	4	81
β-strand	1113	1	81
β-strand	1120-1122	3	82
β-strand	1133-1134	2	82

Chain E: 30 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	21-51	31
α-helix	56-80	25
α-helix	91-100	10
α-helix	104-107	4
α-helix	110-128	19
β-strand	131-133	3	83
β-strand	140-142	3	83
α-helix	147-153	7
α-helix	157-192	36
α-helix	198-203	6
β-strand	208	1	84
β-strand	216	1	84
α-helix	219-250	32
β-strand	259	1	85
α-helix	260	1
β-strand	261-262	2	86
α-helix	278-281	4
α-helix	293-299	7
α-helix	303-315	13
α-helix	319-323	5
α-helix	324-329	6
β-strand	351	1	87
β-strand	354	1	87
α-helix	365-372	8
α-helix	376-383	8
α-helix	399-412	14
α-helix	414-420	7
α-helix	431-445	15
α-helix	448-464	17
α-helix	473-479	7
α-helix	480-484	5
β-strand	486-487	2	86
α-helix	498-500	3
α-helix	503-506	4
α-helix	512-532	21
α-helix	547-559	13
α-helix	565-570	6
α-helix	581-586	6
α-helix	588-596	9
β-strand	606	1	85

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Processed angiotensin-converting enzyme 2	A, E	protein	596	Bos taurus	Q58DD0 (AlphaFold model)
Spike glycoprotein	B, C, D	protein	1120	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>8XZ9_1 Processed angiotensin-converting enzyme 2 (chains A, E)
STTEEQAKTFLEKFNHEAEDLSYQSSLASWNYNTNITDENVQKMNEARAKWSAFYEEQSR
MAKTYSLEEIQNLTLKRQLKALQHSGTSALSAEKSKRLNTILNKMSTIYSTGKVLDPNTQ
ECLALEPGLDDIMENSRDYNRRLWAWEGWRAEVGKQLRPLYEEYVVLENEMARANNYEDY
GDYWRGDYEVTGAGDYDYSRDQLMKDVERTFAEIKPLYEQLHAYVRAKLMHTYPSYISPT
GCLPAHLLGDMWGRFWTNLYSLTVPFEHKPSIDVTEKMENQSWDAERIFKEAEKFFVSIS
LPYMTQGFWDNSMLTEPGDGRKVVCHPTAWDLGKGDFRIKMCTKVTMDDFLTAHHEMGHI
QYDMAYAAQPYLLRNGANEGFHEAVGEIMSLSAATPHYLKALGLLAPDFHEDNETEINFL
LKQALTIVGTLPFTYMLEKWRWMVFKGEIPKQQWMEKWWEMKREIVGVVEPLPHDETYCD
PACLFHVAEDYSFIRYYTRTIYQFQFHEALCKTAKHEGALFKCDISNSTEAGQRLLQMLR
LGKSEPWTLALENIVGIKTMDVKPLLNYFEPLFTWLKEQNRNSFVGWSTEWTPYSD

Sequence of entity 2 (B, C, D), FASTA

>8XZ9_2 Spike glycoprotein (chains B, C, D)
TTTQSYTNSFTRGVYYPDKVFRSSVLHLTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNP
VLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVFIKVCEFQFCNDPFLG
VYYHKNNKSWMESEFGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFK
IYSKHTPIIGRDFPQGFSALEPLVDLPIGINITRFQTLLALNRSYLTPGDSSSGWTAGAA
DYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPT
ESIVRFPNVTNLCPFHEVFNATRFASVYAWNRTRISNCVADYSVLYNFAPFFAFKCYGVS
PTKLNDLCFTNVYADSFVIKGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDS
KHSGNYDYWYRLFRKSKLKPFERDISTEIYQAGNKPCKGKGPNCYFPLQSYGFRPTYGVG
HQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTKSNKKFLPFQQ
FGRDIVDTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVSVAI
HADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTNSPRRA
RSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICG
DSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQ
ILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPL
LTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIA
NQFNSAIGKIQDSLFSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRL
DPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCG
KGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFV
TQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQLE

Primary citation

BA.2.86 Spike in complex with bovine ACE2. Yue, C., Liu, P. To be published.

Other PDB entries of the same protein (UniProt Q58DD0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9E0I 2.4 Å, Structure of the HKU5-19s RBD bound to the Bos taurus ACE2 receptor
8HFX 2.98 Å, Cryo-EM structure of SARS-CoV-2 Omicron BA.1 spike protein in complex with white-tailed…
8HFY 3.21 Å, SARS-CoV-2 Omicron BA.1 spike protein receptor-binding domain in complex with…
8HG0 3.51 Å, Cryo-EM structure of SARS-CoV-2 prototype spike protein receptor-binding domain in…
9KOW 3.98 Å, Crystal structure of RaTG13 RBD complexed with cattle ACE2

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