7ZRV: Omicron spike

cryo-EM structure of omicron spike in complex with de novo designed binder, full map. Determined by electron microscopy at 2.8 Å resolution. Released 8 Mar 2023.

Method: Electron microscopy
Resolution: 2.8 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, Tequatrovirus T4, Drosophila melanogaster
Chains: 5
Atoms: 28,055
Mol. weight: 463.55 kDa
Ligands: NAG
Released: 8 Mar 2023

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

Secondary structure: helices and β-sheets

7ZRV contains 107 α-helices and 246 β-strands across 5 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: 33 helices, 84 β-strands

Element	Residues	Length	Sheet
α-helix	24-26	3
β-strand	31-33	3	1
β-strand	39-40	2	2
β-strand	46	1	3
β-strand	51-58	8	4
α-helix	59-60	2
β-strand	64-70	7	1
β-strand	73	1	5
β-strand	77	1	5
β-strand	85-86	2	6
β-strand	91	1	1
β-strand	94-95	2	1
β-strand	102-103	2	7
β-strand	107-108	2	6
β-strand	117	1	8
β-strand	120	1	8
β-strand	123	1	9
β-strand	126	1	9
β-strand	129-133	5	8
β-strand	136	1	10
β-strand	142	1	11
α-helix	146-148	3
α-helix	153-157	5
β-strand	158	1	10
β-strand	163-168	6	8
α-helix	176-178	3
β-strand	189-195	7	1
β-strand	198-204	7	1
β-strand	222-223	2	2
β-strand	224-229	6	1
β-strand	237-238	2	6
β-strand	241-242	2	7
β-strand	243	1	11
β-strand	263-267	5	1
β-strand	271-279	9	4
β-strand	285-290	6	4
α-helix	295-303	9
β-strand	311-316	6	12
β-strand	320	1	13
α-helix	321-322	2
β-strand	325-328	4	14
α-helix	334	1
β-strand	335	1	15
α-helix	336	1
α-helix	338-342	5
α-helix	347-349	3
β-strand	354-358	5	16
β-strand	362	1	15
α-helix	366-370	5
β-strand	379-380	2	16
α-helix	384-389	6
β-strand	395-403	9	16
β-strand	412	1	17
α-helix	417-421	5
β-strand	425	1	17
β-strand	431-437	7	16
β-strand	448	1	18
β-strand	452-454	3	19
α-helix	460-462	3
β-strand	473	1	20
β-strand	489	1	20
β-strand	492-494	3	19
β-strand	497	1	18
α-helix	503-505	3
β-strand	507-515	9	16
β-strand	538-543	6	14
β-strand	549-554	6	14
β-strand	565-567	3	14
β-strand	573-577	5	14
β-strand	584-588	5	14
α-helix	589-591	3
β-strand	594-599	6	12
β-strand	609-613	5	12
β-strand	628	1	13
β-strand	642-644	3	12
β-strand	648-651	4	12
β-strand	654-660	7	21
β-strand	664-667	4	21
β-strand	670-675	6	21
β-strand	691-697	7	21
β-strand	701-704	4	22
β-strand	712-713	2	23
β-strand	717-728	12	24
β-strand	733-736	4	25
α-helix	738-741	4
α-helix	747-755	9
α-helix	760-782	23
β-strand	787-788	2	26
β-strand	797	1	27
β-strand	800	1	27
α-helix	817-826	10
α-helix	850-854	5
β-strand	858-861	4	25
α-helix	862-863	2
α-helix	867-884	18
α-helix	887-890	4
α-helix	898-908	11
α-helix	913-917	5
α-helix	920-939	20
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	24
β-strand	1059-1070	12	24
β-strand	1074-1075	2	23
β-strand	1076-1077	2	28
β-strand	1081-1082	2	29
β-strand	1086-1090	5	29
β-strand	1093-1097	5	28
β-strand	1102-1106	5	28
β-strand	1113	1	28
β-strand	1116	1	30
β-strand	1120-1125	6	29
β-strand	1133-1134	2	29
β-strand	1138	1	30

Chain B: 34 helices, 76 β-strands

Element	Residues	Length	Sheet
α-helix	24-26	3
β-strand	31-33	3	31
β-strand	45-46	2	32
β-strand	50-58	9	33
α-helix	59-60	2
β-strand	64-66	3	31
β-strand	69-70	2	34
β-strand	85-86	2	35
β-strand	90-95	6	36
β-strand	102	1	37
β-strand	107-108	2	35
β-strand	118-119	2	38
β-strand	123	1	39
β-strand	126	1	39
β-strand	129-132	4	38
β-strand	135-136	2	40
β-strand	142	1	41
α-helix	146-148	3
β-strand	158-160	3	40
β-strand	164-168	5	38
β-strand	189-193	5	36
β-strand	199-202	4	36
β-strand	225-229	5	36
β-strand	237-238	2	35
β-strand	242	1	37
β-strand	243	1	41
β-strand	263-264	2	34
β-strand	265-266	2	36
β-strand	267	1	31
β-strand	271-279	9	33
β-strand	285-290	6	33
α-helix	295-303	9
β-strand	313-319	7	42
β-strand	325-326	2	43
α-helix	334	1
β-strand	335	1	44
α-helix	336	1
α-helix	338-342	5
α-helix	347-349	3
β-strand	354-358	5	45
β-strand	362	1	44
α-helix	366-370	5
β-strand	376	1	45
β-strand	379-380	2	46
α-helix	384-389	6
β-strand	395-403	9	45
α-helix	407-409	3
α-helix	417-421	5
β-strand	431-432	2	46
β-strand	433-437	5	45
β-strand	448	1	47
β-strand	452-454	3	48
α-helix	460-462	3
α-helix	472-473	2
β-strand	492-494	3	48
β-strand	497	1	47
α-helix	503-505	3
β-strand	507-514	8	45
α-helix	529-533	5
β-strand	538-543	6	43
β-strand	546-554	9	43
β-strand	565	1	43
β-strand	566	1	3
β-strand	575-577	3	43
β-strand	584-588	5	43
α-helix	589-591	3
β-strand	592-597	6	42
β-strand	610-613	4	42
β-strand	643-645	3	42
β-strand	648-651	4	42
β-strand	654-655	2	49
β-strand	664-666	3	49
β-strand	670-675	6	49
β-strand	691-696	6	49
α-helix	697-698	2
β-strand	701-702	2	26
β-strand	712-728	17	50
β-strand	734-736	3	51
α-helix	738-741	4
α-helix	747-754	8
α-helix	760-782	23
β-strand	787-790	4	52
β-strand	797	1	53
β-strand	800	1	53
α-helix	817-826	10
α-helix	827-829	3
β-strand	858-860	3	51
α-helix	861-863	3
α-helix	867-883	17
α-helix	887-889	3
α-helix	898-908	11
α-helix	913-918	6
α-helix	920-939	20
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	50
β-strand	1059-1075	17	50
β-strand	1076-1077	2	54
β-strand	1081-1082	2	55
β-strand	1086-1090	5	55
β-strand	1094-1097	4	54
β-strand	1102-1105	4	54
β-strand	1113	1	54
β-strand	1116	1	56
β-strand	1120-1125	6	55
β-strand	1133-1134	2	55
β-strand	1138	1	56

Chain C: 32 helices, 86 β-strands

Element	Residues	Length	Sheet
β-strand	31-33	3	57
β-strand	40	1	58
β-strand	46	1	14
β-strand	52-58	7	59
α-helix	59-60	2
β-strand	64-66	3	57
β-strand	69-70	2	60
β-strand	73	1	61
β-strand	77	1	61
β-strand	85-86	2	62
β-strand	90-91	2	63
β-strand	94-95	2	63
β-strand	102	1	64
β-strand	107-108	2	62
β-strand	116-117	2	65
β-strand	131-133	3	65
β-strand	136	1	66
β-strand	142	1	67
α-helix	146-148	3
β-strand	158	1	66
β-strand	164-166	3	65
β-strand	185	1	68
β-strand	188-195	8	63
β-strand	198-204	7	63
β-strand	208	1	68
β-strand	223	1	58
β-strand	224-229	6	63
β-strand	237-238	2	62
β-strand	242	1	64
β-strand	243	1	67
β-strand	263-264	2	60
β-strand	265-266	2	63
β-strand	267	1	57
β-strand	271-279	9	59
β-strand	285-290	6	59
α-helix	295-302	8
β-strand	311-313	3	69
β-strand	324-325	2	32
β-strand	328	1	32
β-strand	335	1	70
α-helix	338-342	5
α-helix	347-349	3
β-strand	354-358	5	71
β-strand	362	1	70
α-helix	366-369	4
β-strand	375-377	3	72
β-strand	380	1	73
α-helix	384-389	6
β-strand	395-399	5	71
β-strand	400-403	4	72
α-helix	417	1
α-helix	418-422	5
β-strand	431	1	73
β-strand	433-437	5	72
β-strand	448	1	74
β-strand	452-454	3	75
α-helix	460-462	3
α-helix	471-472	2
β-strand	473	1	76
β-strand	489	1	76
β-strand	492-494	3	75
β-strand	497	1	74
β-strand	507-512	6	72
β-strand	513-515	3	71
β-strand	525	1	70
β-strand	538-543	6	32
β-strand	546-554	9	32
β-strand	565-566	2	32
β-strand	575-577	3	32
β-strand	584-588	5	32
β-strand	597-599	3	69
β-strand	609-613	5	69
α-helix	617-619	3
α-helix	620-623	4
α-helix	631-633	3
β-strand	643-644	2	69
β-strand	648-651	4	69
β-strand	654-655	2	77
β-strand	664-667	4	77
β-strand	670-675	6	77
β-strand	691-696	6	77
α-helix	697-698	2
β-strand	701-704	4	52
β-strand	712-728	17	78
β-strand	733-736	4	79
α-helix	738-741	4
α-helix	747-753	7
α-helix	754-756	3
α-helix	760-781	22
β-strand	787-790	4	22
β-strand	797	1	80
β-strand	800	1	80
α-helix	817-826	10
α-helix	849-854	6
β-strand	858-861	4	79
α-helix	862-863	2
α-helix	867-883	17
α-helix	887-890	4
α-helix	898-908	11
α-helix	913-918	6
α-helix	920-939	20
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	78
β-strand	1059-1075	17	78
β-strand	1076-1077	2	81
β-strand	1081-1082	2	82
β-strand	1086-1090	5	82
β-strand	1094-1097	4	81
β-strand	1102-1105	4	81
β-strand	1113-1114	2	81
β-strand	1116	1	83
β-strand	1120-1125	6	82
β-strand	1133-1134	2	82
β-strand	1138	1	83

Chain E: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	4-24	21
α-helix	27-48	22
α-helix	51-54	4
α-helix	59-61	3

Chain F: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	4-24	21
α-helix	27-48	22
α-helix	52-54	3
α-helix	59-61	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein,Envelope glycoprotein	A, B, C	protein	1285	Severe acute respiratory syndrome coronavirus 2, Tequatrovirus T4	M1E1E4 (AlphaFold model), P0DTC2 (AlphaFold model)
de novo designed binder	E, F	protein	79	Drosophila melanogaster	Q9VKJ9 (AlphaFold model)

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

>7ZRV_1 Spike glycoprotein,Envelope glycoprotein (chains A, B, C)
MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFS
NVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNN
ATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGN
FKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLA
LHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTL
KSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVA
DYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNY
KLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGV
AGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNF
NGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTN
TSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECD
IPIGAGICASYQTQTKSHGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVT
TEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFA
QVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGD
IAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMA
YRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNHNAQALNTLV
KQLSSKFGAISSVLNDIFSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASAN
LAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICH
DGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQP
ELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQEL
GKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHSAWSHP
QFEKGGGSGGGGSGGSAWSHPQFEK

Sequence of entity 2 (E, F), FASTA

>7ZRV_2 de novo designed binder (chains E, F)
ETGASSTNMLEALQQRLQFYHGQVARAALENNSGKARRFGRIVKQYEDAIKLYKAGKPVP
YDELPVPPGFGGSENLYFQ

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	16

Primary citation

De novo design of protein interactions with learned surface fingerprints. Gainza, P., Wehrle, S., Van Hall-Beauvais, A. et al. Nature (2023) 617:176-184. DOI 10.1038/s41586-023-05993-x · 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
7AD1 2.92 Å, Cryo-EM structure of a prefusion stabilized SARS-CoV-2 Spike (D614N, R682S, R685G,…
7QTI 3.04 Å, SARS-CoV-2 S Omicron Spike B.1.1.529 - 3-P2G3 and 1-P5C3 Fabs (Global)
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

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