7QTI: P2G3 Heavy Chain

SARS-CoV-2 S Omicron Spike B.1.1.529 - 3-P2G3 and 1-P5C3 Fabs (Global). Determined by electron microscopy at 3.04 Å resolution. Released 3 Aug 2022.

Method: Electron microscopy
Resolution: 3.04 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 11
Atoms: 40,094
Mol. weight: 631.69 kDa
Ligands: NAG
Released: 3 Aug 2022

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

Secondary structure: helices and β-sheets

7QTI contains 137 α-helices and 408 β-strands across 11 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, 76 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	97
β-strand	36-37	2	98
β-strand	43-44	2	60
β-strand	48-55	8	99
α-helix	56-57	2
β-strand	61-63	3	97
β-strand	66-67	2	100
α-helix	70-72	3
β-strand	82-83	2	101
β-strand	87-88	2	102
β-strand	91-92	2	102
β-strand	104-105	2	101
β-strand	113-114	2	101
β-strand	126-133	8	101
α-helix	134	1
β-strand	139	1	103
β-strand	155-165	11	101
β-strand	186-192	7	102
β-strand	195-201	7	102
β-strand	219-220	2	98
β-strand	221-226	6	102
β-strand	234-235	2	101
β-strand	240	1	103
β-strand	260-261	2	100
β-strand	262-263	2	102
β-strand	264	1	97
β-strand	266	1	102
β-strand	268-276	9	99
β-strand	282-287	6	99
α-helix	292-299	8
β-strand	308-310	3	104
β-strand	321-322	2	105
β-strand	325	1	105
β-strand	332	1	106
α-helix	336-339	4
β-strand	346	1	107
β-strand	351-355	5	107
β-strand	359	1	106
α-helix	362-367	6
β-strand	376-377	2	108
α-helix	381-383	3
β-strand	391-399	9	107
α-helix	402-407	6
α-helix	414-415	2
α-helix	416-420	5
β-strand	428-429	2	108
β-strand	430-434	5	107
β-strand	449-451	3	109
α-helix	457-459	3
α-helix	469-470	2
β-strand	482	1	110
β-strand	485	1	110
β-strand	489-491	3	109
α-helix	500-502	3
β-strand	505-513	9	107
β-strand	535-540	6	105
β-strand	543-551	9	105
β-strand	562	1	105
β-strand	572-574	3	105
β-strand	581-585	5	105
β-strand	594-596	3	104
β-strand	606-610	5	104
α-helix	617-620	4
β-strand	640-641	2	104
β-strand	645-648	4	104
β-strand	651-652	2	111
β-strand	661-664	4	111
β-strand	667-672	6	111
β-strand	688-693	6	111
β-strand	698-699	2	92
β-strand	709-710	2	112
β-strand	714-725	12	113
β-strand	730-733	4	114
α-helix	735-739	5
α-helix	744-750	7
α-helix	751-753	3
α-helix	758-779	22
β-strand	784-785	2	62
β-strand	794	1	115
β-strand	797	1	115
α-helix	814-823	10
α-helix	847-851	5
β-strand	855-858	4	114
α-helix	859-860	2
α-helix	864-880	17
α-helix	884-886	3
α-helix	895-904	10
α-helix	911-936	26
α-helix	943-961	19
α-helix	962-964	3
α-helix	974-979	6
α-helix	983-1025	43
α-helix	1026-1030	5
β-strand	1044-1053	10	113
β-strand	1056-1067	12	113
β-strand	1071-1072	2	112
β-strand	1073	1	116
β-strand	1078-1079	2	117
β-strand	1084-1087	4	117
β-strand	1091-1094	4	116
β-strand	1099-1102	4	116
β-strand	1110	1	116
β-strand	1113	1	118
β-strand	1117-1119	3	117
β-strand	1130-1131	2	117
β-strand	1135	1	118

Chain B: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	11-12	2	12
β-strand	19-25	7	11
β-strand	34-39	6	13
β-strand	46-51	6	13
β-strand	60	1	13
β-strand	68-73	6	11
β-strand	78-83	6	11
α-helix	88-90	3
β-strand	92-98	7	13
β-strand	115	1	13
β-strand	119-121	3	13
β-strand	122-123	2	12
β-strand	132-136	5	14
α-helix	140-142	3
β-strand	143-144	2	14
β-strand	147-157	11	14
β-strand	163-166	4	15
β-strand	171	1	15
β-strand	175-177	3	14
α-helix	178-180	3
β-strand	181-182	2	14
β-strand	188-197	10	14
α-helix	198-200	3
β-strand	201	1	16
β-strand	204	1	16
β-strand	206-212	7	15
β-strand	217-223	7	15

Chain C: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	17
β-strand	10-12	3	18
β-strand	19-25	7	17
β-strand	33-38	6	18
β-strand	45-49	5	18
β-strand	53-54	2	18
β-strand	62-67	6	17
β-strand	70-75	6	17
α-helix	80-82	3
β-strand	85-90	6	18
β-strand	98	1	18
β-strand	102-105	4	18
α-helix	112-113	2
β-strand	114-118	5	19
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	19
β-strand	144-150	7	20
β-strand	153-155	3	20
β-strand	159-163	5	19
α-helix	164-167	4
β-strand	173-182	10	19
α-helix	183-187	5
β-strand	191-198	8	20
β-strand	205-210	6	20

Chain D: 31 helices, 80 β-strands

Element	Residues	Length	Sheet
α-helix	21-23	3
β-strand	28-30	3	42
β-strand	36-37	2	43
β-strand	43	1	44
β-strand	50-55	6	45
α-helix	56-57	2
β-strand	61-63	3	42
β-strand	66-67	2	46
β-strand	70	1	47
β-strand	74	1	47
β-strand	82-83	2	48
β-strand	88	1	49
β-strand	91-92	2	49
β-strand	99-100	2	50
β-strand	104-105	2	48
β-strand	114-116	3	48
β-strand	120	1	51
β-strand	123	1	51
β-strand	126-131	6	48
α-helix	132-134	3
β-strand	139	1	52
α-helix	151-154	4
β-strand	158-165	8	48
α-helix	173-175	3
β-strand	186-192	7	49
β-strand	195-201	7	49
β-strand	219-220	2	43
β-strand	221-226	6	49
β-strand	234-235	2	48
β-strand	238-239	2	50
β-strand	240	1	52
β-strand	260-261	2	46
β-strand	262-263	2	49
β-strand	264	1	42
β-strand	268-276	9	45
β-strand	282-287	6	45
α-helix	292-300	9
β-strand	308-316	9	53
β-strand	322-323	2	54
α-helix	331	1
β-strand	332	1	55
α-helix	333	1
α-helix	335-339	5
β-strand	351-355	5	56
β-strand	359	1	55
α-helix	363-368	6
β-strand	376-377	2	57
α-helix	381-383	3
β-strand	392-400	9	56
α-helix	402-406	5
α-helix	414-418	5
β-strand	428-429	2	57
β-strand	430-434	5	56
β-strand	449-451	3	58
α-helix	457-459	3
β-strand	470-471	2	59
β-strand	485-486	2	59
β-strand	489-491	3	58
α-helix	500-502	3
β-strand	504-511	8	56
β-strand	536-538	3	54
α-helix	540-542	3
β-strand	546-547	2	54
β-strand	548-551	4	60
β-strand	562-564	3	60
β-strand	570-574	5	60
β-strand	581-585	5	60
α-helix	586-588	3
β-strand	589-596	8	53
β-strand	606-610	5	53
β-strand	640-641	2	53
β-strand	645-648	4	53
β-strand	651-652	2	61
β-strand	661-664	4	61
β-strand	667-672	6	61
β-strand	688-693	6	61
β-strand	698-699	2	62
β-strand	709-710	2	63
β-strand	714-725	12	64
β-strand	730-733	4	65
α-helix	735-739	5
α-helix	744-751	8
α-helix	758-779	22
β-strand	784-785	2	66
β-strand	794	1	67
β-strand	797	1	67
α-helix	814-823	10
β-strand	855-858	4	65
α-helix	859-860	2
α-helix	864-881	18
α-helix	884-887	4
α-helix	895-904	10
α-helix	911-936	26
α-helix	943-961	19
α-helix	962-964	3
α-helix	974-980	7
α-helix	983-1025	43
α-helix	1026-1030	5
β-strand	1044-1053	10	64
β-strand	1056-1067	12	64
β-strand	1071-1072	2	63
β-strand	1073-1075	3	68
β-strand	1078-1079	2	69
β-strand	1083-1087	5	69
β-strand	1091-1094	4	68
β-strand	1099-1102	4	68
β-strand	1110	1	68
β-strand	1113	1	70
β-strand	1117-1122	6	69
β-strand	1130-1131	2	69
β-strand	1135	1	70

Chain E: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	21
β-strand	10	1	22
β-strand	13	1	23
β-strand	19-25	7	21
β-strand	34-39	6	22
β-strand	46-50	5	22
β-strand	54-55	2	22
α-helix	56	1
β-strand	63-68	6	21
β-strand	71-76	6	21
β-strand	86-91	6	22
β-strand	99	1	22
β-strand	103-104	2	22
β-strand	107	1	23
α-helix	113-114	2
β-strand	115-119	5	24
α-helix	120-122	3
α-helix	123-127	5
β-strand	130-140	11	24
β-strand	147-151	5	25
β-strand	154-156	3	25
β-strand	160-164	5	24
α-helix	165-168	4
β-strand	174-183	10	24
α-helix	184-188	5
β-strand	192-197	6	25
β-strand	206-211	6	25

Chain F: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	26
α-helix	7-9	3
β-strand	10-12	3	27
β-strand	18-25	8	26
α-helix	29-31	3
β-strand	33-39	7	27
β-strand	46-52	7	27
β-strand	58-59	2	27
β-strand	68-73	6	26
β-strand	78-83	6	26
α-helix	88-90	3
β-strand	92-98	7	27
β-strand	101	1	28
β-strand	106	1	28
β-strand	112-113	2	27
β-strand	117-121	5	27
α-helix	124-126	3
α-helix	128-129	2
β-strand	130-134	5	29
α-helix	138-140	3
β-strand	141-142	2	29
β-strand	145-155	11	29
β-strand	161-164	4	30
β-strand	169	1	30
β-strand	174-175	2	29
α-helix	176-178	3
β-strand	179-180	2	29
β-strand	186-195	10	29
α-helix	196-198	3
β-strand	199	1	31
β-strand	202	1	31
β-strand	205-210	6	30
β-strand	215-220	6	30

Chain G: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	19-25	7	1
β-strand	34-39	6	3
β-strand	46-51	6	3
β-strand	59-60	2	3
α-helix	62-64	3
β-strand	69-73	5	1
β-strand	78-82	5	1
α-helix	88-90	3
β-strand	92-98	7	3
β-strand	114-115	2	3
β-strand	119-121	3	3
β-strand	122-123	2	2
β-strand	132-136	5	4
β-strand	143-144	2	4
β-strand	147-157	11	4
β-strand	163-166	4	5
α-helix	167-169	3
β-strand	171	1	5
β-strand	175-177	3	4
α-helix	178-180	3
β-strand	181-182	2	4
β-strand	188-197	10	4
α-helix	198-200	3
β-strand	201	1	6
β-strand	204	1	6
β-strand	206-212	7	5
β-strand	217-223	7	5

Chain H: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	7
β-strand	10-12	3	8
β-strand	19-25	7	7
β-strand	33-38	6	8
β-strand	44-49	6	8
β-strand	53-54	2	8
β-strand	62-67	6	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	85-90	6	8
β-strand	98	1	8
β-strand	102-105	4	8
α-helix	112-113	2
β-strand	114-118	5	9
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	9
β-strand	145-150	6	10
β-strand	153-155	3	10
β-strand	159-163	5	9
α-helix	164-167	4
β-strand	173-182	10	9
α-helix	183-187	5
β-strand	191-197	7	10
β-strand	205-210	6	10

3 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
P2G3 Heavy Chain	B, G, I	protein	228	Homo sapiens
P2G3 Light Chain	C, H, J	protein	214	Homo sapiens
P5C3 Light Chain	E	protein	215	Homo sapiens
P5C3 Heavy Chain	F	protein	221	Homo sapiens
Spike glycoprotein,Envelope glycoprotein	A, D, K	protein	1285	Severe acute respiratory syndrome coronavirus 2	M1E1E4 (AlphaFold model), P0DTC2 (AlphaFold model)

Sequence of entity 1 (B, G, I), FASTA

>7QTI_1 P2G3 Heavy Chain (chains B, G, I)
EVQLVESGGGLVQPGRSLRLSCAASGFRFDDYALHWVRQAPEKGLEWVSGISWNSNNIGY
AESVKGRFTISRDTAKKSLYLQMNDLRAEDTALYYCVKDRHYDSSGYFVNGFDIWGQGTL
VTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
VLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

Sequence of entity 2 (C, H, J), FASTA

>7QTI_2 P2G3 Light Chain (chains C, H, J)
DIQLTQSPSFLSASVGDRVTVTCRASQGISSYVAWYQQKAGKAPTLLIYTASTLQSGVPS
RFSGSGSGTEFTLTISSLQPEDFATYYCQQLHSYPVTFGQGTRLDIERTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (E), FASTA

>7QTI_3 P5C3 Light Chain (chains E)
EIVLTQSPGTLSLSPGERATLSCRGSQSVRSSYLGWYQQKPGQAPRLLIYGASSRATGIP
DRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPWTFGQGTKVEIKGTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 4 (F), FASTA

>7QTI_4 P5C3 Heavy Chain (chains F)
QMQLVQSGPEVKKPGTSVKVSCKASGFTFTSSAVQWVRQARGQRLEWIGWIVVGSGNTDY
AQQFQERVTITRDMSTSTAYMELSSLGSEDTAVYYCAAPNCSGGSCYDGFDLWGQGTMVT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKV

Sequence of entity 5 (A, D, K), FASTA

>7QTI_5 Spike glycoprotein,Envelope glycoprotein (chains A, D, K)
MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFS
NVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNN
ATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGN
FKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLA
LHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTL
KSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVA
DYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNY
KLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGV
AGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNF
NGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTN
TSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECD
IPIGAGICASYQTQTKSHGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVT
TEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFA
QVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGD
IAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMA
YRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNHNAQALNTLV
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	26

Primary citation

Patient-derived monoclonal antibody neutralizes SARS-CoV-2 Omicron variants and confers full protection in monkeys. Fenwick, C., Turelli, P., Ni, D. et al. Nat Microbiol (2022) 7:1376-1389. DOI 10.1038/s41564-022-01198-6 · PubMed

Other PDB entries of the same protein (UniProt M1E1E4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9BJM 2.07 Å, Crystal Structure of Inhibitor 5c in Complex with Prefusion RSV F Glycoprotein
6VKE 2.1 Å, Crystal Structure of Inhibitor JNJ-40012665 in Complex with Prefusion RSV F Glycoprotein
6A0Z 2.33 Å, Crystal structure of broadly neutralizing antibody 13D4 bound to H5N1 influenza…
5KWW 2.5 Å, Crystal Structure of Inhibitor JNJ-53718678 In Complex with Prefusion RSV F Glycoprotein
6VKD 2.5 Å, Crystal Structure of Inhibitor JNJ-36689282 in Complex with Prefusion RSV F Glycoprotein
6VKC 2.6 Å, Crystal Structure of Inhibitor JNJ-36811054 in Complex with Prefusion RSV F Glycoprotein
7ZRV 2.8 Å, cryo-EM structure of omicron spike in complex with de novo designed binder, full map
7AD1 2.92 Å, Cryo-EM structure of a prefusion stabilized SARS-CoV-2 Spike (D614N, R682S, R685G,…
5U68 3.08 Å, Structural basis for antibody cross-neutralization of respiratory syncytial virus and…
6W16 3.1 Å, Crystal structure of a human metapneumovirus monomeric fusion protein complexed with 458…
7FJN 3.25 Å, Cryo-EM structure of South African (B.1.351) SARS-CoV-2 spike glycoprotein in complex…
6OUS 3.4 Å, Structure of fusion glycoprotein from human respiratory syncytial virus

Browse structure collections

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