7T9J: SARS-CoV-2 Omicron spike protein

Cryo-EM structure of the SARS-CoV-2 Omicron spike protein. Determined by electron microscopy at 2.79 Å resolution. Released 29 Dec 2021.

Method: Electron microscopy
Resolution: 2.79 Å
Organism: Severe acute respiratory syndrome coronavirus 2
Chains: 3
Atoms: 21,960
Mol. weight: 440.26 kDa
Ligands: NAG
Released: 29 Dec 2021

Explore 7T9J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7T9J contains 85 α-helices and 185 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: 26 helices, 54 β-strands

Element	Residues	Length	Sheet
α-helix	25-26	2
β-strand	27-30	4	1
β-strand	37	1	2
β-strand	42-43	2	3
β-strand	47-55	9	4
α-helix	56-57	2
β-strand	61-67	7	1
β-strand	79	1	1
β-strand	84-85	2	5
β-strand	89-96	8	1
β-strand	103-107	5	5
β-strand	116-121	6	5
β-strand	126-141	16	5
β-strand	157-172	16	5
β-strand	188-197	10	1
β-strand	200-209	10	1
α-helix	216-217	2
α-helix	222	1
β-strand	223	1	2
β-strand	224-229	6	1
β-strand	237-241	5	5
β-strand	243	1	5
β-strand	245	1	6
β-strand	259	1	6
α-helix	260-261	2
β-strand	263-269	7	1
β-strand	271-279	9	4
β-strand	285-290	6	4
α-helix	295-303	9
β-strand	311-318	8	7
β-strand	325-328	4	8
β-strand	538-543	6	8
β-strand	546-554	9	8
β-strand	565-567	3	8
β-strand	573-577	5	8
β-strand	584-588	5	8
α-helix	589-590	2
β-strand	593-599	7	7
β-strand	609-613	5	7
α-helix	617-619	3
β-strand	642-644	3	7
β-strand	648-651	4	7
β-strand	654-655	2	9
β-strand	664-667	4	9
β-strand	670-674	5	9
β-strand	692-696	5	9
α-helix	697-698	2
β-strand	701-704	4	10
β-strand	711-728	18	11
β-strand	733-736	4	12
α-helix	738-743	6
α-helix	747-753	7
α-helix	754-756	3
α-helix	759-782	24
β-strand	787-790	4	13
α-helix	807-808	2
α-helix	817-825	9
β-strand	858-861	4	12
α-helix	862-863	2
α-helix	867-883	17
α-helix	898-908	11
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	1047-1056	10	11
β-strand	1059-1078	20	11
β-strand	1081-1083	3	14
β-strand	1086-1090	5	14
β-strand	1093-1097	5	11
β-strand	1102-1106	5	11
β-strand	1113-1114	2	11
β-strand	1116	1	15
β-strand	1120-1122	3	14
β-strand	1133-1134	2	14
β-strand	1138	1	15
α-helix	1142-1146	5

Chain B: 25 helices, 57 β-strands

Element	Residues	Length	Sheet
α-helix	25-26	2
β-strand	27-30	4	16
β-strand	37	1	17
β-strand	42-44	3	8
β-strand	48-55	8	18
α-helix	56-57	2
β-strand	61-67	7	16
β-strand	79	1	16
β-strand	83-85	3	19
β-strand	89-96	8	16
β-strand	103-107	5	19
β-strand	116-121	6	19
β-strand	126-141	16	19
β-strand	157-172	16	19
β-strand	188-197	10	16
β-strand	200-209	10	16
α-helix	216-218	3
α-helix	222	1
β-strand	223	1	17
β-strand	224-230	7	16
β-strand	237-243	7	19
β-strand	245	1	20
β-strand	259	1	20
α-helix	260-262	3
β-strand	263-269	7	16
β-strand	271-279	9	18
β-strand	285-290	6	18
α-helix	295-303	9
β-strand	311-319	9	21
β-strand	325-328	4	22
β-strand	538-543	6	22
β-strand	546-554	9	22
β-strand	565-567	3	22
β-strand	573-577	5	22
β-strand	584-588	5	22
α-helix	589-591	3
β-strand	592-599	8	21
β-strand	609-613	5	21
α-helix	617-619	3
β-strand	642-644	3	21
β-strand	648-651	4	21
β-strand	654-660	7	23
β-strand	664-667	4	23
β-strand	670-674	5	23
β-strand	692-697	6	23
β-strand	701-704	4	24
β-strand	711-728	18	25
β-strand	733-736	4	26
α-helix	738-743	6
α-helix	747-753	7
α-helix	754-756	3
α-helix	759-782	24
β-strand	787-790	4	10
β-strand	797	1	27
β-strand	800	1	27
α-helix	807-808	2
α-helix	817-825	9
β-strand	858-861	4	26
α-helix	862-863	2
α-helix	867-883	17
α-helix	898-908	11
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	1041	1	28
β-strand	1044	1	28
β-strand	1047-1056	10	25
β-strand	1059-1078	20	25
β-strand	1081-1083	3	29
β-strand	1086-1090	5	29
β-strand	1094-1097	4	25
β-strand	1102-1105	4	25
β-strand	1113-1114	2	25
β-strand	1116	1	30
β-strand	1120-1122	3	29
β-strand	1133-1134	2	29
β-strand	1138	1	30
α-helix	1142-1146	5

Chain C: 34 helices, 74 β-strands

Element	Residues	Length	Sheet
α-helix	25-26	2
β-strand	27-30	4	31
β-strand	37	1	32
β-strand	42-44	3	22
β-strand	48-55	8	33
α-helix	56-57	2
β-strand	61-67	7	31
β-strand	79	1	31
β-strand	83-85	3	34
β-strand	89-96	8	31
β-strand	103-107	5	34
β-strand	116-121	6	34
β-strand	126-131	6	34
β-strand	133-141	9	35
β-strand	157-163	7	35
β-strand	168-172	5	34
β-strand	188-197	10	31
β-strand	200-209	10	31
α-helix	216-218	3
α-helix	222	1
β-strand	223	1	32
β-strand	224-230	7	31
β-strand	237-241	5	34
β-strand	243	1	35
β-strand	245-246	2	36
β-strand	258-259	2	36
α-helix	260-261	2
β-strand	263-269	7	31
β-strand	271-279	9	33
β-strand	285-290	6	33
α-helix	295-303	9
β-strand	311-319	9	37
α-helix	320-322	3
β-strand	325-328	4	3
β-strand	335	1	38
α-helix	338-342	5
β-strand	354-358	5	39
β-strand	361-362	2	38
α-helix	366-369	4
β-strand	376-379	4	39
α-helix	387-389	3
β-strand	391-392	2	38
β-strand	393-402	10	39
α-helix	405-408	4
α-helix	417-421	5
β-strand	424	1	40
β-strand	431-437	7	39
β-strand	448	1	41
β-strand	452-454	3	42
α-helix	460-462	3
β-strand	463	1	40
β-strand	473-474	2	43
β-strand	485	1	43
β-strand	488-489	2	43
β-strand	492-494	3	42
β-strand	497	1	41
β-strand	508-516	9	39
β-strand	524-525	2	38
α-helix	528-533	6
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	584-589	6	3
α-helix	590-591	2
β-strand	592-599	8	37
β-strand	609-613	5	37
α-helix	617-619	3
β-strand	642-644	3	37
β-strand	648-651	4	37
β-strand	654-655	2	44
β-strand	664-667	4	44
β-strand	670-674	5	44
β-strand	692-696	5	44
α-helix	697-698	2
β-strand	701-704	4	13
β-strand	711-728	18	45
β-strand	733-736	4	46
α-helix	738-743	6
α-helix	747-753	7
α-helix	754-756	3
α-helix	759-782	24
β-strand	787-790	4	24
α-helix	807-808	2
α-helix	817-825	9
β-strand	858-861	4	46
α-helix	862-863	2
α-helix	867-883	17
α-helix	898-908	11
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	1047-1056	10	45
β-strand	1059-1078	20	45
β-strand	1081-1083	3	47
β-strand	1086-1090	5	47
β-strand	1094-1097	4	45
β-strand	1102-1105	4	45
β-strand	1113-1114	2	45
β-strand	1116	1	48
β-strand	1120-1122	3	47
β-strand	1133-1134	2	47
β-strand	1138	1	48
α-helix	1142-1146	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein	A, B, C	protein	1285	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)

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

>7T9J_1 Spike glycoprotein (chains A, B, C)
MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFS
NVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNN
ATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGN
FKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLA
LHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTL
KSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVA
DYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNY
KLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGV
AGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNF
NGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTN
TSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECD
IPIGAGICASYQTQTKSHGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVT
TEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFA
QVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGD
IAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMA
YRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLV
KQLSSKFGAISSVLNDIFSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASAN
LAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICH
DGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQP
ELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQEL
GKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHSAWSHP
QFEKGGGSGGGGSGGSAWSHPQFEK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	22

Primary citation

SARS-CoV-2 Omicron variant: Antibody evasion and cryo-EM structure of spike protein-ACE2 complex. Mannar, D., Saville, J.W., Zhu, X. et al. Science (2022) 375:760-764. DOI 10.1126/science.abn7760 · 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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7T9J is part of these collections:

SARS-CoV-2 and COVID-19

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