6VSB: Spike glycoprotein

Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up. Determined by electron microscopy at 3.46 Å resolution. Released 26 Feb 2020.

Method: Electron microscopy
Resolution: 3.46 Å
Organism: Severe acute respiratory syndrome coronavirus 2
Chains: 3
Atoms: 22,854
Mol. weight: 440.39 kDa
Ligands: NAG
Released: 26 Feb 2020

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

Secondary structure: helices and β-sheets

6VSB contains 93 α-helices and 206 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: 30 helices, 69 β-strands

Element	Residues	Length	Sheet
β-strand	28-31	4	1
β-strand	37	1	2
β-strand	43	1	3
β-strand	48-51	4	4
β-strand	54-55	2	5
β-strand	60-65	6	1
β-strand	84	1	6
β-strand	90-94	5	1
β-strand	101-107	7	6
β-strand	116-121	6	6
β-strand	126-129	4	6
β-strand	132	1	7
α-helix	133-135	3
β-strand	164	1	7
β-strand	169-172	4	6
β-strand	188-197	10	1
β-strand	200-209	10	1
β-strand	223	1	2
β-strand	224-225	2	1
β-strand	230	1	1
β-strand	238-242	5	6
α-helix	262-264	3
β-strand	265-269	5	1
β-strand	271-272	2	5
β-strand	275-279	5	4
β-strand	285-290	6	4
α-helix	297-303	7
β-strand	311-319	9	8
α-helix	320-322	3
α-helix	339-342	4
β-strand	349	1	9
α-helix	350-352	3
β-strand	354-358	5	9
β-strand	361-362	2	10
β-strand	376-379	4	9
α-helix	384-389	6
β-strand	391-392	2	10
β-strand	394-402	9	9
α-helix	405-409	5
α-helix	417-421	5
β-strand	432-437	6	9
β-strand	452-453	2	11
β-strand	493-494	2	11
β-strand	508-516	9	9
β-strand	524-525	2	10
β-strand	538-540	3	12
β-strand	549-554	6	12
β-strand	565-567	3	12
β-strand	573-577	5	12
β-strand	584-588	5	12
α-helix	589-591	3
β-strand	592-599	8	8
β-strand	609-612	4	8
β-strand	642-643	2	8
β-strand	650-651	2	8
α-helix	653	1
β-strand	654-655	2	13
α-helix	656	1
β-strand	660	1	14
β-strand	665-667	3	15
β-strand	670-671	2	15
β-strand	693-694	2	13
β-strand	695-696	2	15
β-strand	697	1	14
α-helix	698	1
β-strand	701	1	16
β-strand	711-728	18	17
β-strand	733-736	4	18
α-helix	738-742	5
α-helix	747-753	7
α-helix	754-756	3
α-helix	759-782	24
β-strand	788	1	19
β-strand	807	1	20
β-strand	816	1	20
α-helix	817-823	7
β-strand	858-861	4	18
α-helix	862-863	2
α-helix	867-883	17
α-helix	885-889	5
α-helix	898-909	12
α-helix	914-918	5
α-helix	920-940	21
α-helix	946-964	19
α-helix	965-967	3
α-helix	977-982	6
α-helix	986-1032	47
β-strand	1047-1054	8	17
β-strand	1059-1076	18	17
β-strand	1081-1083	3	21
β-strand	1086-1090	5	21
β-strand	1094-1098	5	17
β-strand	1101-1105	5	17
β-strand	1116	1	22
α-helix	1117-1119	3
β-strand	1120-1125	6	21
β-strand	1133-1134	2	21
β-strand	1138	1	22
α-helix	1141-1144	4

Chain B: 31 helices, 70 β-strands

Element	Residues	Length	Sheet
β-strand	28-31	4	23
β-strand	37	1	24
β-strand	47-55	9	25
α-helix	56-57	2
β-strand	60-65	6	23
β-strand	85	1	26
β-strand	90-94	5	23
β-strand	103	1	27
β-strand	106-107	2	26
β-strand	116-117	2	26
β-strand	120-121	2	27
β-strand	126-129	4	27
β-strand	132	1	28
α-helix	133-135	3
β-strand	164	1	28
β-strand	169-172	4	27
β-strand	189-197	9	23
β-strand	200-208	9	23
β-strand	223	1	24
β-strand	224-229	6	23
β-strand	237	1	26
α-helix	239-241	3
β-strand	265-267	3	23
β-strand	271-279	9	25
β-strand	285-290	6	25
α-helix	297-303	7
β-strand	311-319	9	29
β-strand	323-328	6	30
β-strand	335	1	31
α-helix	339-342	4
β-strand	354-358	5	32
β-strand	361-362	2	31
α-helix	366-369	4
β-strand	376-379	4	32
α-helix	384-389	6
β-strand	392	1	31
β-strand	394-403	10	32
α-helix	405-409	5
α-helix	417-421	5
β-strand	432-437	6	32
β-strand	451-453	3	33
β-strand	493-495	3	33
α-helix	496-497	2
β-strand	507-516	10	32
β-strand	524-525	2	31
β-strand	538-543	6	30
β-strand	547-554	8	30
β-strand	565-567	3	30
β-strand	573-577	5	30
β-strand	584-588	5	30
α-helix	589-591	3
β-strand	592-599	8	29
β-strand	609-613	5	29
β-strand	642-645	4	29
β-strand	648-651	4	29
α-helix	653	1
β-strand	654-655	2	34
β-strand	660	1	35
β-strand	665-667	3	36
β-strand	670-671	2	36
β-strand	688	1	37
β-strand	691	1	37
β-strand	693-694	2	34
β-strand	695-696	2	36
β-strand	697	1	35
α-helix	698	1
α-helix	705-707	3
β-strand	711-728	18	38
β-strand	733-736	4	39
α-helix	738-742	5
α-helix	747-754	8
α-helix	759-782	24
β-strand	787	1	16
β-strand	807	1	40
β-strand	816	1	40
α-helix	817-822	6
β-strand	858-861	4	39
α-helix	862-863	2
α-helix	867-883	17
α-helix	885-889	5
α-helix	898-909	12
α-helix	914-918	5
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	1047-1054	8	38
β-strand	1059-1078	20	38
β-strand	1081-1083	3	41
β-strand	1086-1088	3	41
β-strand	1094-1097	4	38
β-strand	1102-1106	5	38
β-strand	1109-1113	5	38
β-strand	1116	1	42
α-helix	1117-1119	3
β-strand	1122-1125	4	41
β-strand	1133-1134	2	41
β-strand	1138	1	42
α-helix	1141-1144	4

Chain C: 32 helices, 67 β-strands

Element	Residues	Length	Sheet
β-strand	29-31	3	43
β-strand	43	1	30
β-strand	48-55	8	44
β-strand	60-62	3	43
β-strand	65	1	45
β-strand	84	1	46
β-strand	90-94	5	45
β-strand	104-107	4	46
β-strand	116-121	6	46
β-strand	126-129	4	46
α-helix	133-135	3
β-strand	169-172	4	46
β-strand	188-197	10	45
β-strand	200-209	10	45
α-helix	216-218	3
β-strand	224-227	4	45
β-strand	230	1	45
β-strand	237-240	4	46
β-strand	265-267	3	45
β-strand	271-279	9	44
β-strand	285-290	6	44
α-helix	295-303	9
β-strand	311-319	9	47
α-helix	320-322	3
β-strand	328	1	48
β-strand	335	1	49
α-helix	339-342	4
α-helix	347-348	2
β-strand	349	1	50
α-helix	350-352	3
β-strand	354-358	5	50
β-strand	361-362	2	49
α-helix	366-370	5
β-strand	376-380	5	50
α-helix	384-389	6
β-strand	392	1	49
β-strand	394-403	10	50
α-helix	405-409	5
α-helix	417	1
α-helix	418-422	5
β-strand	430-437	8	50
β-strand	451-453	3	51
β-strand	493-495	3	51
β-strand	507-516	10	50
β-strand	524-525	2	49
β-strand	538-543	6	48
β-strand	546-554	9	48
β-strand	566	1	3
β-strand	567	1	52
β-strand	573	1	52
β-strand	575-577	3	48
β-strand	584-588	5	48
α-helix	589-591	3
β-strand	592-599	8	47
β-strand	609-613	5	47
β-strand	642-644	3	47
β-strand	648-651	4	47
α-helix	653	1
β-strand	654-655	2	53
β-strand	660	1	54
β-strand	665-667	3	55
β-strand	670-671	2	55
β-strand	693-694	2	53
β-strand	695-696	2	55
β-strand	697	1	54
α-helix	698	1
β-strand	702	1	19
β-strand	711-728	18	56
β-strand	733-736	4	57
α-helix	738-742	5
α-helix	747-753	7
α-helix	754-756	3
α-helix	759-782	24
β-strand	807	1	58
β-strand	816	1	58
α-helix	817-823	7
β-strand	858-861	4	57
α-helix	862-863	2
α-helix	867-883	17
α-helix	885-887	3
α-helix	898-909	12
α-helix	914-918	5
α-helix	920-940	21
α-helix	946-964	19
α-helix	965-967	3
α-helix	977-982	6
α-helix	986-1028	43
α-helix	1029-1033	5
β-strand	1047-1054	8	56
β-strand	1059-1078	20	56
β-strand	1081-1083	3	59
β-strand	1086-1090	5	59
β-strand	1094-1097	4	56
β-strand	1102-1105	4	56
β-strand	1116	1	60
β-strand	1120-1125	6	59
β-strand	1133-1134	2	59
β-strand	1138	1	60
α-helix	1142-1144	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein	A, B, C	protein	1288	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)

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

>6VSB_1 Spike glycoprotein (chains A, B, C)
MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFS
NVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIV
NNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLE
GKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT
LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETK
CTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISN
CVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIAD
YNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPC
NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVN
FNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITP
GTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSY
ECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTI
SVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQE
VFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDC
LGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAM
QMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALN
TLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA
SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPA
ICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP
LQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL
QELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHSAW
SHPQFEKGGGSGGGGSGGSAWSHPQFEK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	27

Primary citation

Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Wrapp, D., Wang, N., Corbett, K.S. et al. Science (2020) 367:1260-1263. DOI 10.1126/science.abb2507 · 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…

Browse more

6VSB is part of these collections:

SARS-CoV-2 and COVID-19

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