8ZHM: SARS-CoV-2 spike trimer

SARS-CoV-2 spike trimer (6P) in complex with three H18 and three R1-32 Fabs. Determined by electron microscopy at 3.39 Å resolution. Released 21 Aug 2024.

Method: Electron microscopy
Resolution: 3.39 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, Enterobacteria phage T6, synthetic construct
Chains: 15
Atoms: 45,273
Mol. weight: 729.73 kDa
Ligands: NAG
Released: 21 Aug 2024

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

Secondary structure: helices and β-sheets

8ZHM contains 110 α-helices and 492 β-strands across 15 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: 22 helices, 72 β-strands

Element	Residues	Length	Sheet
β-strand	27-30	4	1
β-strand	37	1	2
β-strand	42-43	2	3
β-strand	48-55	8	4
α-helix	56-57	2
β-strand	61-66	6	1
β-strand	84-85	2	5
β-strand	90-94	5	1
β-strand	101-107	7	5
β-strand	116-121	6	5
β-strand	126-131	6	5
β-strand	135-145	11	6
β-strand	152-160	9	6
β-strand	169-171	3	5
β-strand	188-197	10	1
β-strand	200-209	10	1
β-strand	223	1	2
β-strand	224-230	7	1
β-strand	237-242	6	5
β-strand	243-246	4	6
β-strand	259	1	6
β-strand	264-269	6	1
β-strand	271-279	9	4
β-strand	285-290	6	4
α-helix	295-302	8
β-strand	311-313	3	7
β-strand	317	1	8
β-strand	325-326	2	9
α-helix	339-341	3
β-strand	354-358	5	10
β-strand	376-379	4	10
β-strand	391	1	11
β-strand	394-402	9	10
α-helix	404-409	6
β-strand	432-437	6	10
β-strand	448	1	12
β-strand	452-454	3	13
β-strand	466-467	2	14
α-helix	471-472	2
β-strand	473-474	2	15
β-strand	488-489	2	15
β-strand	492-494	3	13
β-strand	497	1	12
β-strand	508-516	9	10
β-strand	525	1	11
β-strand	539-542	4	9
β-strand	547-550	4	9
β-strand	551	1	16
β-strand	554	1	17
β-strand	575-578	4	17
β-strand	583-586	4	17
β-strand	588	1	16
β-strand	594	1	8
β-strand	595-599	5	7
β-strand	609-612	4	7
β-strand	642-643	2	7
β-strand	649-651	3	7
β-strand	654-655	2	18
β-strand	664-667	4	18
β-strand	670-675	6	18
β-strand	691-696	6	18
α-helix	697-698	2
β-strand	701-704	4	19
β-strand	711-715	5	20
β-strand	718-727	10	21
β-strand	733-735	3	22
α-helix	738-741	4
α-helix	747-753	7
α-helix	754-756	3
α-helix	757-781	25
β-strand	787-790	4	23
α-helix	791-792	2
α-helix	817-825	9
β-strand	859-861	3	22
α-helix	862-863	2
α-helix	867-884	18
α-helix	888-890	3
α-helix	898-908	11
α-helix	914-917	4
α-helix	920-938	19
α-helix	946-965	20
α-helix	977-983	7
α-helix	990-1028	39
α-helix	1029-1033	5
β-strand	1047-1056	10	21
β-strand	1059-1069	11	21
β-strand	1072-1077	6	20
β-strand	1081-1082	2	24
β-strand	1086-1090	5	24
β-strand	1093-1097	5	20
β-strand	1102-1106	5	20
β-strand	1113	1	20
β-strand	1120-1125	6	24
β-strand	1133-1134	2	24

Chain B: 23 helices, 65 β-strands

Element	Residues	Length	Sheet
β-strand	27-30	4	25
β-strand	50-55	6	26
α-helix	56-57	2
β-strand	61-66	6	25
β-strand	84-85	2	27
β-strand	90-94	5	25
β-strand	101-107	7	27
β-strand	116	1	28
β-strand	118-121	4	27
β-strand	126-128	3	27
β-strand	131	1	28
β-strand	140-145	6	29
β-strand	152-158	7	29
β-strand	170	1	27
β-strand	188-197	10	25
β-strand	200-209	10	25
β-strand	224-229	6	25
β-strand	237-242	6	27
β-strand	243-246	4	29
β-strand	259	1	29
β-strand	264-269	6	25
β-strand	271-279	9	26
β-strand	285-290	6	26
α-helix	295-302	8
β-strand	311-317	7	30
β-strand	324-326	3	31
α-helix	340-343	4
β-strand	354-358	5	32
β-strand	376-379	4	32
α-helix	384-386	3
β-strand	395-402	8	32
α-helix	424-426	3
β-strand	432-437	6	32
β-strand	448	1	33
β-strand	452-454	3	34
β-strand	466-467	2	35
α-helix	471-472	2
β-strand	473-474	2	36
β-strand	488-489	2	36
β-strand	492-494	3	34
β-strand	497	1	33
β-strand	508-515	8	32
β-strand	539-542	4	31
β-strand	547-550	4	31
β-strand	551	1	37
β-strand	554	1	38
α-helix	558-560	3
β-strand	565-566	2	39
β-strand	575-578	4	38
β-strand	583-586	4	38
β-strand	588	1	37
β-strand	594-599	6	30
β-strand	609-612	4	30
β-strand	642-645	4	30
β-strand	648-651	4	30
β-strand	654-655	2	40
β-strand	664-667	4	40
β-strand	670-675	6	40
β-strand	691-696	6	40
α-helix	697-698	2
β-strand	701-704	4	41
β-strand	711-727	17	42
β-strand	733-736	4	43
α-helix	738-741	4
α-helix	747-752	6
α-helix	753-756	4
α-helix	757-781	25
β-strand	787-790	4	19
α-helix	791-792	2
α-helix	817-825	9
β-strand	858-861	4	43
α-helix	862-863	2
α-helix	867-883	17
α-helix	898-908	11
α-helix	914-918	5
α-helix	920-938	19
α-helix	947-965	19
α-helix	977-983	7
α-helix	990-1028	39
α-helix	1029-1033	5
β-strand	1050-1056	7	42
β-strand	1059-1077	19	42
β-strand	1081-1082	2	44
β-strand	1087-1090	4	44
β-strand	1094-1097	4	42
β-strand	1102-1105	4	42
β-strand	1120-1122	3	44
β-strand	1133-1134	2	44

Chain C: 25 helices, 72 β-strands

Element	Residues	Length	Sheet
β-strand	27-30	4	45
β-strand	37	1	46
β-strand	42-43	2	39
β-strand	48-55	8	47
α-helix	56-57	2
β-strand	61-66	6	45
β-strand	84-85	2	48
β-strand	90-94	5	45
β-strand	101-107	7	48
β-strand	117-121	5	48
β-strand	126-130	5	48
β-strand	135-145	11	49
β-strand	152-160	9	49
β-strand	168-171	4	48
β-strand	188-197	10	45
β-strand	200-209	10	45
β-strand	223	1	46
β-strand	224-229	6	45
β-strand	237-242	6	48
β-strand	243-246	4	49
β-strand	259	1	49
β-strand	264-269	6	45
β-strand	271-279	9	47
β-strand	285-290	6	47
α-helix	295-302	8
β-strand	311-317	7	50
β-strand	325-326	2	51
α-helix	335-337	3
α-helix	339-341	3
β-strand	354-358	5	52
β-strand	376-379	4	52
α-helix	384-386	3
β-strand	392	1	53
β-strand	395-402	8	52
β-strand	432-437	6	52
α-helix	439-442	4
β-strand	448	1	54
β-strand	452-454	3	55
β-strand	466-467	2	56
α-helix	471-472	2
β-strand	473-474	2	57
β-strand	488-489	2	57
β-strand	492-494	3	55
β-strand	497	1	54
β-strand	508-515	8	52
β-strand	524	1	53
β-strand	539-542	4	51
β-strand	547-550	4	51
β-strand	551	1	58
β-strand	554	1	3
α-helix	558-560	3
β-strand	565-566	2	3
β-strand	575-578	4	3
β-strand	583-586	4	3
β-strand	588	1	58
β-strand	594-599	6	50
β-strand	609-612	4	50
β-strand	642-643	2	50
β-strand	649-651	3	50
β-strand	654-655	2	59
β-strand	664-667	4	59
β-strand	670-675	6	59
β-strand	691-696	6	59
α-helix	697-698	2
β-strand	701-704	4	23
β-strand	711-712	2	60
β-strand	715	1	61
β-strand	718-727	10	62
β-strand	733-735	3	63
α-helix	738-741	4
α-helix	747-751	5
α-helix	752-756	5
α-helix	757-781	25
β-strand	787-790	4	41
α-helix	791-792	2
α-helix	817-825	9
β-strand	859-861	3	63
α-helix	862-863	2
α-helix	867-883	17
α-helix	888-890	3
α-helix	898-908	11
α-helix	913-915	3
α-helix	920-939	20
α-helix	947-965	19
α-helix	977-983	7
α-helix	990-1028	39
α-helix	1029-1033	5
β-strand	1047-1056	10	62
β-strand	1059-1069	11	62
β-strand	1072	1	61
β-strand	1075-1078	4	60
β-strand	1081-1082	2	64
β-strand	1086-1090	5	64
β-strand	1093-1097	5	60
β-strand	1102-1106	5	60
β-strand	1120-1125	6	64
β-strand	1133-1134	2	64

Chain D: 5 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	101
β-strand	9-11	3	102
β-strand	17-24	8	101
α-helix	29-31	3
β-strand	35-39	5	102
β-strand	46-49	4	102
β-strand	50	1	103
β-strand	54	1	103
β-strand	57	1	104
β-strand	59	1	104
β-strand	64-68	5	101
β-strand	73-79	7	101
β-strand	88-93	6	102
β-strand	100-101	2	102
β-strand	102	1	101
β-strand	105-108	4	102
α-helix	119-121	3
β-strand	122	1	105
β-strand	125-129	5	106
α-helix	130-132	3
α-helix	133-137	5
β-strand	141-150	10	106
β-strand	151	1	105
β-strand	156-161	6	107
β-strand	164-166	3	107
β-strand	170-172	3	106
β-strand	176-177	2	106
β-strand	183-191	9	106
α-helix	193-198	6
β-strand	202-208	7	107
β-strand	211-217	7	107

Chain E: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	108
β-strand	11-12	2	109
β-strand	17-25	9	108
α-helix	31-33	3
β-strand	36-41	6	110
β-strand	48-53	6	110
β-strand	59-61	3	110
β-strand	69-74	6	108
β-strand	79-85	7	108
α-helix	89-91	3
β-strand	94-99	6	110
β-strand	109-110	2	110
α-helix	111-113	3
β-strand	114-115	2	110
β-strand	117-118	2	109
β-strand	124	1	111
β-strand	127-131	5	112
β-strand	138	1	112
β-strand	142-152	11	112
β-strand	153	1	111
β-strand	158-161	4	113
β-strand	166	1	113
β-strand	170-172	3	112
β-strand	176-177	2	112
β-strand	183-192	10	112
α-helix	193-195	3
β-strand	201-207	7	113
β-strand	212-218	7	113

Chain F: 4 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	114
β-strand	9-11	3	115
β-strand	17-24	8	114
β-strand	35-39	5	115
β-strand	46-49	4	115
β-strand	50	1	116
β-strand	54	1	116
α-helix	55-56	2
β-strand	57	1	117
β-strand	59	1	117
β-strand	64-68	5	114
β-strand	73-79	7	114
β-strand	88-93	6	115
β-strand	100-101	2	115
β-strand	105-108	4	115
β-strand	122	1	118
β-strand	125-129	5	119
α-helix	130-132	3
α-helix	133-137	5
β-strand	141-150	10	119
β-strand	151	1	118
β-strand	156-161	6	120
β-strand	164-166	3	120
β-strand	170-172	3	119
β-strand	176-177	2	119
β-strand	183-191	9	119
α-helix	193-198	6
β-strand	202-208	7	120
β-strand	211-217	7	120

Chain G: 1 helix, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	77
β-strand	10-12	3	78
β-strand	17	1	79
β-strand	20-25	6	77
β-strand	34-39	6	78
β-strand	45-52	8	78
β-strand	57-60	4	78
β-strand	69-73	5	77
β-strand	78-82	5	77
β-strand	84	1	79
β-strand	92-99	8	78
β-strand	103-104	2	56
β-strand	111-113	3	78
β-strand	118-122	5	78
β-strand	131-135	5	80
β-strand	146-156	11	80
β-strand	162-165	4	81
β-strand	187-196	10	80
α-helix	197-199	3
β-strand	206-210	5	81
β-strand	211	1	82
β-strand	216	1	82
β-strand	219-221	3	81

Chain H: 2 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	65
β-strand	10-12	3	66
β-strand	18-25	8	65
β-strand	34-39	6	66
β-strand	45-52	8	66
β-strand	57-60	4	66
β-strand	68-73	6	65
β-strand	78-83	6	65
β-strand	92-99	8	66
β-strand	103-104	2	14
β-strand	111-113	3	66
β-strand	118-122	5	66
β-strand	131-135	5	67
β-strand	146-156	11	67
β-strand	162-165	4	68
α-helix	166-168	3
β-strand	174-176	3	67
β-strand	187-196	10	67
α-helix	197-199	3
β-strand	206-210	5	68
β-strand	211	1	69
β-strand	216	1	69
β-strand	219-221	3	68

7 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
Spike glycoprotein,Fibritin,Expression Tag	A, B, C	protein	1278	Severe acute respiratory syndrome coronavirus 2, Enterobacteria phage T6, synthetic construct	A0A346FJN8, P0DTC2 (AlphaFold model)
Heavy chain of R1-32 Fab	G, H, N	protein	228	Homo sapiens
Light chain of R1-32 Fab	I, L, O	protein	214	Homo sapiens
Light chain of H18 Fab	D, F, K	protein	243	Homo sapiens
Heavy chain of H18 Fab	E, J, M	protein	243	Homo sapiens

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

>8ZHM_1 Spike glycoprotein,Fibritin,Expression Tag (chains A, B, C)
VSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHV
SGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKV
CEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLR
EFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLT
PGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEK
GIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYN
SASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFT
GCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYF
PLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTG
VLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAV
LYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGI
CASYQTQTNSPGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVS
MTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYK
TPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLI
CAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIG
VTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNTLVKQLSSNF
GAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMS
ECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFP
REGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKE
ELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGS
GYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHSAWSHPQFEKGGG
SGGGGSGGSAWSHPQFEK

Sequence of entity 2 (G, H, N), FASTA

>8ZHM_2 Heavy chain of R1-32 Fab (chains G, H, N)
EVQLVESGAEVKKPGSSVKVSCKASGGTFSSYAISWVRQAPGQGLEWMGGIIPILGIANY
AQKFQGRVTITADKSTSTAYMELSSLRSEDTAVYYCARENGYSGYGAAANFDLWGRGTLV
TVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAV
LQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD

Sequence of entity 3 (I, L, O), FASTA

>8ZHM_3 Light chain of R1-32 Fab (chains I, L, O)
QSVLTQPPSVSGAPGQRVTISCTGSSSNIGAGYDVHWYQQLPGTAPKLLIYGNSNRPSGV
PDRFSGSKSGTSASLAITGLQAEDEADYYCQSYDSSLSGSVFGGGTKLTVLGQPKAAPSV
TLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAAS
SYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT

Sequence of entity 4 (D, F, K), FASTA

>8ZHM_4 Light chain of H18 Fab (chains D, F, K)
MGWSCIILFLVATATGVHSANFMLTQPHSVSESPGKTVTISCTGSSGSIASNYVQWYQQR
PGSAPTTVIYEDNQRPSGVPDRFSGSIDSSSNSASLTISGLKTEDEADYYCQSYDSSNVV
FGGGTKLTVLGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWK
ADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT
ECS

Sequence of entity 5 (E, J, M), FASTA

>8ZHM_5 Heavy chain of H18 Fab (chains E, J, M)
MGWSLILLFLVAVATRVLSQVQLQESGPGLVKPSETLSLTCTVSGGSVSSGGYFWSWIRQ
PPGKGLEWIGCIYYSGSTNYNPSLKSRVTISVDTSKDQFSLKLSSVTAADTAVYYCARQL
WLRGRFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSW
NSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK
SCD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	33

Primary citation

Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein and potentially drive the genesis of Omicron variants. Yan, Q., Gao, X., Liu, B. et al. Nat Commun (2024) 15:7585-7585. DOI 10.1038/s41467-024-51770-3 · PubMed

Other PDB entries of the same protein (UniProt A0A346FJN8), best resolution first:

9VWE 2.06 Å, Cryo-EM structure of RSV pre-F (strain A2) in complex with Fabs 1A2 and 2D10
8ZQ6 2.77 Å, preF6P of RSV glycoprotein
8ZQ7 2.77 Å, Crystal structure of prefusion RSV F protein
9UE3 2.78 Å, The structure of FIPV spike glycoprotein
8WLU 2.87 Å, Cryo-EM structure of bat RsSHC014 spike glycoprotein
8ZPY 2.92 Å, Crystal structure of prefusion F of RSV
9VWF 3.14 Å, Cryo-EM structure of RSV pre-F (strain A2) in complex with Fab 3G12
8ZHE 3.16 Å, SARS-CoV-2 spike trimer (6P) in complex with three R1-26 Fabs
8ZHD 3.41 Å, SARS-CoV-2 spike trimer (6P) in complex with two R1-26 Fabs
8ZHG 3.51 Å, SARS-CoV-2 spike trimer (6P) in complex with R1-26 Fab, focused refinement of RBD-Fab…
8WLY 3.96 Å, Cryo-EM structure of bat WIV1 spike glycoprotein
8ZHL 3.96 Å, SARS-CoV-2 spike trimer (6P) in complex with two H18 and two R1-32 Fabs

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