6VYB: SARS-CoV-2 spike ectodomain structure

SARS-CoV-2 spike ectodomain structure (open state). Determined by electron microscopy at 3.2 Å resolution. Released 11 Mar 2020.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Severe acute respiratory syndrome coronavirus 2
Chains: 3
Atoms: 22,365
Mol. weight: 437.44 kDa
Ligands: NAG
Released: 11 Mar 2020

Explore 6VYB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VYB contains 93 α-helices and 196 β-strands across 3 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, 64 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	1
β-strand	37	1	2
β-strand	43	1	3
β-strand	47-55	9	4
α-helix	56-57	2
β-strand	61-65	5	1
β-strand	83-85	3	5
β-strand	90-96	7	1
β-strand	103-107	5	5
β-strand	117-122	6	5
β-strand	125-129	5	5
β-strand	169-171	3	5
β-strand	188-197	10	1
β-strand	200-209	10	1
α-helix	217	1
β-strand	223	1	2
β-strand	224-230	7	1
β-strand	237-241	5	5
β-strand	265-269	5	1
β-strand	271-279	9	4
β-strand	285-290	6	4
α-helix	295-302	8
β-strand	311-319	9	6
α-helix	320-322	3
β-strand	324-328	5	7
β-strand	335	1	8
α-helix	339-342	4
β-strand	349	1	9
β-strand	354-358	5	9
β-strand	361-362	2	8
α-helix	365-370	6
β-strand	376-379	4	9
β-strand	391-392	2	8
β-strand	394-403	10	9
α-helix	404-409	6
α-helix	417-421	5
β-strand	431-437	7	9
β-strand	452-454	3	10
α-helix	460-462	3
β-strand	492-494	3	10
β-strand	507-516	10	9
β-strand	524-525	2	8
β-strand	538-543	6	7
β-strand	546-554	9	7
β-strand	565-567	3	7
β-strand	573-577	5	7
β-strand	584-588	5	7
α-helix	589-591	3
β-strand	592-599	8	6
β-strand	609-613	5	6
β-strand	642-645	4	6
β-strand	648-651	4	6
β-strand	654-655	2	11
β-strand	664-667	4	11
β-strand	670-675	6	11
β-strand	691-696	6	11
α-helix	697-698	2
β-strand	701-702	2	12
β-strand	711-728	18	13
β-strand	733-736	4	14
α-helix	738-742	5
α-helix	747-753	7
α-helix	754-756	3
α-helix	761-782	22
β-strand	787-788	2	15
α-helix	817-823	7
β-strand	858-861	4	14
α-helix	862-863	2
α-helix	867-884	18
α-helix	887-890	4
α-helix	898-907	10
α-helix	914-918	5
α-helix	920-940	21
α-helix	942-945	4
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	1041	1	16
β-strand	1044	1	16
β-strand	1047-1056	10	13
β-strand	1059-1078	20	13
β-strand	1081-1082	2	17
β-strand	1086-1090	5	17
β-strand	1094-1097	4	13
β-strand	1102-1105	4	13
β-strand	1113-1114	2	13
β-strand	1116	1	18
β-strand	1120-1125	6	17
β-strand	1133-1134	2	17
β-strand	1138	1	18
α-helix	1141-1146	6

Chain B: 30 helices, 64 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	19
β-strand	36-37	2	20
β-strand	42-43	2	7
β-strand	47-55	9	21
α-helix	56-57	2
β-strand	61-65	5	19
β-strand	83-85	3	22
β-strand	89-96	8	19
β-strand	103-107	5	22
β-strand	117-122	6	22
β-strand	125-129	5	22
β-strand	169-171	3	22
β-strand	188-195	8	19
β-strand	201-209	9	19
β-strand	222-223	2	20
β-strand	224-229	6	19
β-strand	237-241	5	22
β-strand	264-269	6	19
β-strand	271-279	9	21
β-strand	285-290	6	21
α-helix	295-302	8
β-strand	311-319	9	23
α-helix	320-322	3
β-strand	325-328	4	24
β-strand	335	1	25
α-helix	338-340	3
β-strand	349	1	26
β-strand	354-358	5	26
β-strand	361-362	2	25
α-helix	366-370	5
β-strand	376-379	4	26
β-strand	391-392	2	25
β-strand	395-403	9	26
α-helix	404-409	6
α-helix	417-421	5
α-helix	424-426	3
β-strand	431-437	7	26
β-strand	448	1	27
β-strand	452-453	2	28
β-strand	493-494	2	28
β-strand	497	1	27
α-helix	503-505	3
β-strand	507-514	8	26
β-strand	524-525	2	25
β-strand	538-543	6	24
β-strand	546-554	9	24
β-strand	565-567	3	24
β-strand	573-577	5	24
β-strand	584-588	5	24
α-helix	589-591	3
β-strand	592-599	8	23
β-strand	609-613	5	23
β-strand	642-645	4	23
β-strand	648-651	4	23
α-helix	653	1
β-strand	654-655	2	29
β-strand	664-667	4	29
β-strand	670-675	6	29
β-strand	691-696	6	29
α-helix	697-698	2
β-strand	702-704	3	30
β-strand	711-728	18	31
β-strand	733-736	4	32
α-helix	738-742	5
α-helix	747-753	7
α-helix	754-756	3
α-helix	759-782	24
β-strand	787-788	2	12
α-helix	817-823	7
β-strand	858-861	4	32
α-helix	862-863	2
α-helix	867-884	18
α-helix	887-890	4
α-helix	898-907	10
α-helix	913-918	6
α-helix	920-940	21
α-helix	942-945	4
α-helix	946-964	19
α-helix	965-967	3
α-helix	977-981	5
α-helix	986-1028	43
α-helix	1029-1033	5
β-strand	1047-1056	10	31
β-strand	1059-1078	20	31
β-strand	1081-1082	2	33
β-strand	1086-1090	5	33
β-strand	1094-1097	4	31
β-strand	1102-1105	4	31
β-strand	1113-1114	2	31
β-strand	1116	1	34
β-strand	1120-1125	6	33
β-strand	1133-1134	2	33
β-strand	1138	1	34
α-helix	1141-1146	6

Chain C: 34 helices, 68 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	35
β-strand	36-37	2	36
β-strand	42-43	2	24
β-strand	47-55	9	37
α-helix	56-57	2
β-strand	61-65	5	35
β-strand	83-85	3	38
β-strand	90-96	7	35
β-strand	103-107	5	38
β-strand	117-122	6	38
β-strand	125-129	5	38
β-strand	169-171	3	38
β-strand	188-197	10	35
β-strand	200-209	10	35
α-helix	216-218	3
β-strand	222-223	2	36
β-strand	224-230	7	35
β-strand	237-241	5	38
β-strand	265-269	5	35
β-strand	271-279	9	37
β-strand	285-290	6	37
α-helix	295-303	9
β-strand	311-319	9	39
α-helix	320-322	3
β-strand	324-328	5	3
α-helix	334	1
β-strand	335	1	40
α-helix	336	1
α-helix	339-342	4
β-strand	348-349	2	41
α-helix	350-352	3
β-strand	354-358	5	41
β-strand	361-362	2	40
α-helix	366-370	5
β-strand	376-379	4	41
β-strand	391-392	2	40
β-strand	394-403	10	41
α-helix	404-409	6
α-helix	417-421	5
β-strand	431-437	7	41
β-strand	452-453	2	42
β-strand	493-494	2	42
α-helix	503-505	3
β-strand	507-516	10	41
β-strand	524-525	2	40
α-helix	528-530	3
β-strand	538-543	6	3
β-strand	546-554	9	3
β-strand	565-567	3	3
β-strand	573-577	5	3
β-strand	584-588	5	3
α-helix	589-591	3
β-strand	592-599	8	39
β-strand	609-613	5	39
β-strand	642-645	4	39
β-strand	648-651	4	39
α-helix	653	1
β-strand	654-655	2	43
β-strand	660	1	44
β-strand	664-667	4	43
β-strand	670-675	6	43
β-strand	691-696	6	43
β-strand	697	1	44
α-helix	698	1
β-strand	701-702	2	15
β-strand	711-715	5	45
β-strand	718-728	11	46
β-strand	733-736	4	47
α-helix	738-742	5
α-helix	747-753	7
α-helix	754-756	3
α-helix	759-782	24
β-strand	788-790	3	30
α-helix	817-823	7
β-strand	858-861	4	47
α-helix	862-863	2
α-helix	867-884	18
α-helix	887-890	4
α-helix	898-907	10
α-helix	914-918	5
α-helix	920-940	21
α-helix	942-945	4
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	1041-1042	2	48
β-strand	1044	1	48
β-strand	1047-1056	10	46
β-strand	1059-1069	11	46
β-strand	1072-1078	7	45
β-strand	1081-1082	2	49
β-strand	1086-1090	5	49
β-strand	1094-1097	4	45
β-strand	1102-1105	4	45
β-strand	1113	1	45
β-strand	1116	1	50
β-strand	1120-1125	6	49
β-strand	1133-1134	2	49
β-strand	1138	1	50
α-helix	1141-1146	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein	A, B, C	protein	1281	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)

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

>6VYB_1 Spike glycoprotein (chains A, B, C)
MGILPSPGMPALLSLVSLLSVLLMGCVAETGTQCVNLTTRTQLPPAYTNSFTRGVYYPDK
VFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNII
RGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYS
SANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFS
ALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNE
NGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEV
FNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFV
IRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNL
KPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAP
ATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQT
LEILDITPCSFGGVSVITPGTNTSNEVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSN
VFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPSGAGSVASQSIIAYTMSLGA
ENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCT
QLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDL
LFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGT
ITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSST
ASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRL
QSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVV
FLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTF
VSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQK
EIDRLNEVAKNLNESLIDLQELGKYEQYIKGSGRENLYFQGGGGSGYIPEAPRDGQAYVR
KDGEWVLLSTFLGHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	35

Primary citation

Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein. Walls, A.C., Park, Y.J., Tortorici, M.A. et al. Cell (2020) 181:281. DOI 10.1016/j.cell.2020.02.058 · PubMed

Other PDB entries of the same protein (UniProt P0DTC2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7Z8O 0.96 Å, Crystal structure of SARS-CoV-2 S RBD in complex with a stapled peptide
7Y8J 1.03 Å, 3D1 in complex with 6-mer HR1 peptide from SARS-CoV-2
9FC2 1.21 Å, The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the…
7EK6 1.24 Å, Structure of viral peptides IPB19/N52
7EAM 1.4 Å, immune complex of SARS-CoV-2 RBD and cross-neutralizing antibody 7D6
7M53 1.4 Å, B6 Fab fragment bound to the SARS-CoV/SARS-CoV-2 spike stem helix peptide
8CMC 1.42 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S511-530
7M8U 1.45 Å, Crystal Structure of HLA-B*35:01 in complex with IPFAMQMAY, an 9-mer epitope from…
7ZR2 1.45 Å, Crystal structure of a chimeric protein mimic of SARS-CoV-2 Spike HR1 in complex with HR2
8D36 1.45 Å, Crystal structure of SARS-CoV-2 fusion peptide in complex with neutralizing antibody…
8ENS 1.45 Å, Crystal structure of beta'-COPI-WD40 domain in complex with SARS-CoV-2 spike tail…
8ENW 1.45 Å, Crystal structure of beta'-COPI-WD40 domain in complex with SARS-CoV-2 clientized spike…

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6VYB is part of these collections:

SARS-CoV-2 and COVID-19

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