8ZHD: SARS-CoV-2 spike trimer

SARS-CoV-2 spike trimer (6P) in complex with two R1-26 Fabs. Determined by electron microscopy at 3.41 Å resolution. Released 21 Aug 2024.

Method: Electron microscopy
Resolution: 3.41 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, Enterobacteria phage T6, synthetic construct
Chains: 7
Atoms: 29,306
Mol. weight: 539.7 kDa
Ligands: NAG
Released: 21 Aug 2024

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

Secondary structure: helices and β-sheets

8ZHD contains 90 α-helices and 257 β-strands across 7 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: 29 helices, 69 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	140-145	6	6
β-strand	152-158	7	6
β-strand	166-171	6	5
β-strand	188-197	10	1
β-strand	200-209	10	1
α-helix	222	1
β-strand	223	1	2
α-helix	224	1
β-strand	225-227	3	1
β-strand	230	1	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	311-319	9	7
α-helix	320-322	3
β-strand	325-326	2	8
β-strand	328	1	9
α-helix	329-331	3
β-strand	354-358	5	10
β-strand	361-362	2	11
α-helix	366-370	5
β-strand	374-379	6	10
β-strand	394-403	10	10
α-helix	408-410	3
α-helix	417-421	5
β-strand	432-437	6	10
β-strand	452-454	3	12
α-helix	471-472	2
β-strand	473-474	2	13
β-strand	485	1	13
β-strand	488-489	2	13
β-strand	492-494	3	12
β-strand	507-516	10	10
α-helix	521-522	2
β-strand	524-525	2	11
β-strand	530	1	9
α-helix	531-533	3
β-strand	539-542	4	8
β-strand	547-550	4	8
β-strand	551-554	4	14
α-helix	555	1
β-strand	575-578	4	14
β-strand	583-588	6	14
β-strand	592-599	8	7
β-strand	609-612	4	7
β-strand	642-645	4	7
β-strand	648-651	4	7
β-strand	654-655	2	15
β-strand	664-667	4	15
β-strand	670-675	6	15
β-strand	691-696	6	15
α-helix	697-698	2
β-strand	701-703	3	16
β-strand	711-715	5	17
β-strand	718-727	10	18
β-strand	733-735	3	19
α-helix	738-741	4
α-helix	747-753	7
α-helix	757-777	21
α-helix	779-782	4
β-strand	787-788	2	20
α-helix	817-825	9
β-strand	859-861	3	19
α-helix	867-883	17
α-helix	888-890	3
α-helix	898-906	9
α-helix	914-917	4
α-helix	920-939	20
α-helix	946-966	21
α-helix	977-983	7
α-helix	986-1028	43
α-helix	1029-1033	5
β-strand	1047-1056	10	18
β-strand	1059-1069	11	18
β-strand	1072-1078	7	17
β-strand	1081-1082	2	21
β-strand	1087-1090	4	21
β-strand	1094-1097	4	17
β-strand	1102-1105	4	17
β-strand	1113	1	17
β-strand	1120-1122	3	21
β-strand	1133-1134	2	21
α-helix	1141-1145	5

Chain B: 29 helices, 69 β-strands

Element	Residues	Length	Sheet
β-strand	27-30	4	22
β-strand	37	1	23
β-strand	50-55	6	24
α-helix	56-57	2
β-strand	61-66	6	22
β-strand	84-85	2	25
β-strand	90-94	5	22
β-strand	103-107	5	25
β-strand	116-121	6	25
β-strand	126-131	6	25
β-strand	141-145	5	26
β-strand	152-154	3	26
β-strand	170	1	25
β-strand	188-197	10	22
β-strand	200-209	10	22
β-strand	223	1	23
β-strand	225-230	6	22
β-strand	237-240	4	25
β-strand	243-246	4	26
β-strand	259	1	26
β-strand	264-269	6	22
β-strand	271-279	9	24
β-strand	285-290	6	24
α-helix	295-302	8
β-strand	311-319	9	27
β-strand	324-327	4	28
β-strand	354-358	5	29
β-strand	361-362	2	30
α-helix	366-370	5
β-strand	374-376	3	29
α-helix	384-387	4
β-strand	392	1	30
β-strand	394-403	10	29
α-helix	407-410	4
α-helix	417-421	5
β-strand	432-437	6	29
β-strand	452-454	3	31
α-helix	460-462	3
α-helix	472	1
β-strand	473-474	2	32
β-strand	485	1	32
β-strand	488-489	2	32
β-strand	492-494	3	31
β-strand	507-516	10	29
α-helix	521-522	2
β-strand	524-525	2	30
β-strand	539-542	4	28
β-strand	548-550	3	28
β-strand	551	1	33
α-helix	553	1
β-strand	554	1	34
α-helix	555	1
β-strand	566	1	34
β-strand	575-578	4	34
β-strand	583-586	4	34
β-strand	588	1	33
α-helix	589-591	3
β-strand	592-599	8	27
β-strand	609-612	4	27
β-strand	642-645	4	27
β-strand	648-651	4	27
β-strand	654-655	2	35
β-strand	660	1	36
β-strand	664-667	4	35
β-strand	670-675	6	35
β-strand	691-696	6	35
β-strand	697	1	36
β-strand	701-704	4	37
β-strand	711-727	17	38
β-strand	734-736	3	39
α-helix	738-741	4
α-helix	747-752	6
α-helix	753-755	3
α-helix	757-782	26
β-strand	787-789	3	16
α-helix	790-792	3
α-helix	817-825	9
β-strand	855	1	39
β-strand	858-860	3	39
α-helix	861-863	3
α-helix	867-883	17
α-helix	898-908	11
α-helix	913-915	3
α-helix	920-939	20
α-helix	947-964	18
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	38
β-strand	1059-1078	20	38
β-strand	1081-1082	2	40
β-strand	1087-1090	4	40
β-strand	1094-1097	4	38
β-strand	1102-1105	4	38
β-strand	1120-1122	3	40
β-strand	1133-1134	2	40
α-helix	1141-1145	5

Chain C: 29 helices, 74 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	41
β-strand	37	1	42
β-strand	49-55	7	43
α-helix	56-57	2
β-strand	61-66	6	41
β-strand	84-85	2	44
β-strand	90-94	5	41
β-strand	103-107	5	44
β-strand	117-121	5	44
β-strand	126-129	4	44
β-strand	132-133	2	45
β-strand	140-145	6	46
β-strand	152-158	7	46
β-strand	163-164	2	45
β-strand	169-171	3	44
β-strand	188-197	10	41
β-strand	200-209	10	41
α-helix	222	1
β-strand	223	1	42
β-strand	224-225	2	41
β-strand	230	1	41
β-strand	237-240	4	44
β-strand	243-246	4	46
β-strand	259	1	46
β-strand	264-269	6	41
β-strand	271-279	9	43
β-strand	285-290	6	43
α-helix	295-302	8
β-strand	311-319	9	47
α-helix	320-322	3
β-strand	325-326	2	48
β-strand	335	1	49
α-helix	339-342	4
β-strand	354-358	5	50
β-strand	362	1	49
α-helix	366-369	4
β-strand	374-376	3	50
β-strand	379	1	50
β-strand	392	1	51
β-strand	394-403	10	50
α-helix	405-410	6
α-helix	417-421	5
β-strand	432-437	6	50
β-strand	452-454	3	52
β-strand	473-474	2	53
β-strand	485	1	53
β-strand	488-489	2	53
β-strand	492-494	3	52
β-strand	507-516	10	50
α-helix	521-522	2
β-strand	524	1	51
α-helix	531-533	3
β-strand	539-542	4	48
β-strand	547-550	4	48
β-strand	551-554	4	3
β-strand	565-566	2	3
β-strand	575-577	3	3
β-strand	584-588	5	3
β-strand	592-599	8	47
β-strand	609-612	4	47
β-strand	642-645	4	47
β-strand	648-651	4	47
β-strand	654-655	2	54
β-strand	664-667	4	54
β-strand	670-675	6	54
β-strand	691-696	6	54
α-helix	697-698	2
β-strand	701-702	2	20
β-strand	711-712	2	55
β-strand	715	1	56
β-strand	718-727	10	57
β-strand	733-735	3	58
α-helix	738-741	4
α-helix	747-751	5
α-helix	757-777	21
α-helix	779-782	4
β-strand	787-790	4	37
α-helix	791-792	2
α-helix	817-825	9
β-strand	859-861	3	58
α-helix	862-863	2
α-helix	867-883	17
α-helix	888-890	3
α-helix	898-908	11
α-helix	914-918	5
α-helix	920-939	20
α-helix	947-964	18
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	57
β-strand	1059-1069	11	57
β-strand	1072	1	56
β-strand	1075-1078	4	55
β-strand	1080-1082	3	59
β-strand	1087-1090	4	59
β-strand	1094-1097	4	55
β-strand	1102-1105	4	55
β-strand	1114	1	55
β-strand	1120-1122	3	59
β-strand	1132-1134	3	59
α-helix	1141-1145	5

Chain F: 1 helix, 9 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	66
β-strand	17-25	9	66
β-strand	34-39	6	67
β-strand	45-51	7	67
β-strand	58-60	3	67
β-strand	69-73	5	66
β-strand	78-84	7	66
α-helix	88-90	3
β-strand	92-98	7	67
β-strand	114-116	3	67

Chain G: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	68
β-strand	9	1	69
β-strand	18-24	7	68
β-strand	35-39	5	69
β-strand	45-49	5	69
β-strand	50	1	70
β-strand	54	1	70
β-strand	63-68	6	68
β-strand	73-78	6	68
α-helix	84-86	3
β-strand	87-92	6	69
β-strand	93	1	71
β-strand	100	1	71
β-strand	105-107	3	69

Chain H: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	60
β-strand	17-20	4	60
β-strand	22-25	4	60
β-strand	34-39	6	61
β-strand	45-51	7	61
β-strand	58-60	3	61
β-strand	69-73	5	60
β-strand	78-84	7	60
α-helix	88-90	3
β-strand	92-98	7	61
β-strand	114-116	3	61

Chain L: 0 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	62
β-strand	9	1	63
β-strand	18-24	7	62
β-strand	35-39	5	63
β-strand	45-49	5	63
β-strand	50	1	64
β-strand	54	1	64
β-strand	63-68	6	62
β-strand	73-78	6	62
β-strand	87-92	6	63
β-strand	93-94	2	65
β-strand	99-100	2	65
β-strand	105-107	3	63

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 R1-26 Fab	F, H	protein	243	Homo sapiens
Light chain of R1-26 Fab	G, L	protein	240	Homo sapiens

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

>8ZHD_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 (F, H), FASTA

>8ZHD_2 Heavy chain of R1-26 Fab (chains F, H)
MGWSLILLFLVAVATRVLSEVQLVESGGGLVQPGGSLRLSCAASGFTFSSYWMSWVRQAP
GKGLEWVANIKQDGSEKYYVDSVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCARGQL
GPWVGVDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSW
NSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK
SCD

Sequence of entity 3 (G, L), FASTA

>8ZHD_3 Light chain of R1-26 Fab (chains G, L)
MGWSCIILFLVATATGVNFMLTQPHSVSESPGKTVTISCTGSSGSIASNYVQWYQQRPGS
APTTVIYEDNQRPSGVPDRFSGSIDSSSNSASLTISGLKTEDEADYYCQSYDSSNWVFGG
GTQLTVLGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADS
SPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	30

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
8ZHM 3.39 Å, SARS-CoV-2 spike trimer (6P) in complex with three H18 and three R1-32 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

Browse structure collections

About this viewer

MolViewer shows 8ZHD directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.