8HFX: SARS-CoV-2 Omicron BA.1 spike protein

Cryo-EM structure of SARS-CoV-2 Omicron BA.1 spike protein in complex with white-tailed deer ACE2. Determined by electron microscopy at 2.98 Å resolution. Released 30 Aug 2023.

Method: Electron microscopy
Resolution: 2.98 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, Human immunodeficiency virus 1, Odocoileus virginianus texanus
Chains: 4
Atoms: 30,807
Mol. weight: 505.4 kDa
Ligands: ZN, NAG
Released: 30 Aug 2023

Explore 8HFX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8HFX contains 131 α-helices and 221 β-strands across 4 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: 31 helices, 75 β-strands

Element	Residues	Length	Sheet
α-helix	25-26	2
β-strand	27-31	5	1
β-strand	37	1	2
β-strand	43	1	3
β-strand	47-55	9	4
β-strand	60-67	8	1
β-strand	82-83	2	5
β-strand	88-92	5	1
β-strand	99-105	7	5
β-strand	114-119	6	5
β-strand	124-128	5	5
β-strand	131	1	6
β-strand	139	1	7
β-strand	158	1	6
β-strand	164-167	4	5
β-strand	183-192	10	1
β-strand	195-204	10	1
α-helix	213-215	3
β-strand	220	1	2
β-strand	221-227	7	1
β-strand	234-239	6	5
β-strand	240	1	7
β-strand	243	1	8
β-strand	255	1	8
β-strand	260-266	7	1
β-strand	268-276	9	4
β-strand	282-284	3	4
β-strand	287	1	4
α-helix	292-300	9
β-strand	308-316	9	9
β-strand	317	1	10
α-helix	318-319	2
β-strand	322-325	4	11
β-strand	332	1	12
β-strand	351-355	5	13
β-strand	358-359	2	12
α-helix	363-367	5
β-strand	373-378	6	13
β-strand	388-389	2	12
β-strand	391-400	10	13
α-helix	402-406	5
β-strand	428-434	7	13
α-helix	436-439	4
β-strand	445	1	14
β-strand	449-451	3	15
α-helix	457-459	3
α-helix	477	1
β-strand	489-491	3	15
β-strand	494	1	14
α-helix	500-502	3
β-strand	504-513	10	13
β-strand	521-522	2	12
α-helix	528-530	3
β-strand	536-540	5	11
β-strand	543-547	5	11
β-strand	548-551	4	16
β-strand	562-564	3	16
β-strand	570-574	5	16
β-strand	581-585	5	16
α-helix	586-588	3
β-strand	589-596	8	9
β-strand	606-610	5	9
β-strand	625	1	10
β-strand	640-641	2	9
β-strand	645-648	4	9
β-strand	651-657	7	17
β-strand	661-664	4	17
β-strand	667-672	6	17
β-strand	688-694	7	17
α-helix	695	1
β-strand	699	1	18
β-strand	708-725	18	19
β-strand	730-733	4	20
α-helix	735-740	6
α-helix	744-750	7
α-helix	751-753	3
α-helix	757-779	23
β-strand	784-785	2	21
β-strand	794	1	22
β-strand	797	1	22
α-helix	814-822	9
α-helix	846-851	6
β-strand	855-858	4	20
α-helix	859-860	2
α-helix	864-880	17
α-helix	884-886	3
α-helix	895-904	10
α-helix	911-914	4
α-helix	917-937	21
α-helix	943-961	19
α-helix	962-964	3
α-helix	974-978	5
α-helix	983-1025	43
α-helix	1026-1030	5
β-strand	1044-1053	10	19
β-strand	1056-1073	18	19
β-strand	1078-1080	3	23
β-strand	1083-1087	5	23
β-strand	1091-1094	4	19
β-strand	1099-1102	4	19
β-strand	1110	1	19
β-strand	1113	1	24
β-strand	1117-1119	3	23
β-strand	1130-1131	2	23
β-strand	1135	1	24
α-helix	1138-1143	6

Chain B: 35 helices, 71 β-strands

Element	Residues	Length	Sheet
α-helix	25-26	2
β-strand	27-31	5	25
β-strand	36-37	2	26
β-strand	42-43	2	16
β-strand	48-55	8	27
α-helix	56-57	2
β-strand	60-67	8	25
β-strand	77	1	25
β-strand	82-83	2	28
β-strand	88-94	7	25
β-strand	99-105	7	28
β-strand	114-119	6	28
β-strand	124-129	6	28
β-strand	133	1	29
β-strand	139	1	30
β-strand	152	1	30
β-strand	155	1	29
β-strand	163-167	5	28
β-strand	183-192	10	25
β-strand	195-203	9	25
β-strand	219-220	2	26
β-strand	221-226	6	25
β-strand	234-239	6	28
β-strand	240	1	30
β-strand	260-266	7	25
β-strand	268-276	9	27
β-strand	282-287	6	27
α-helix	292-300	9
β-strand	308-316	9	31
α-helix	317-319	3
β-strand	322	1	32
β-strand	325	1	32
α-helix	331	1
β-strand	332	1	33
α-helix	333	1
α-helix	336-339	4
β-strand	351-355	5	34
β-strand	358	1	35
β-strand	359	1	33
α-helix	363-366	4
α-helix	369-371	3
β-strand	376-377	2	34
α-helix	384-386	3
β-strand	389	1	35
β-strand	392-400	9	34
α-helix	401-404	4
α-helix	414-418	5
β-strand	428-434	7	34
β-strand	449-451	3	36
α-helix	457-459	3
α-helix	468-470	3
β-strand	489-491	3	36
β-strand	504-511	8	34
β-strand	521	1	35
β-strand	535-540	6	32
β-strand	543-551	9	32
β-strand	563	1	37
β-strand	572-574	3	32
β-strand	581-585	5	32
α-helix	586-588	3
β-strand	589-596	8	31
β-strand	606-610	5	31
α-helix	614-616	3
β-strand	639-641	3	31
β-strand	645-648	4	31
β-strand	651-652	2	38
β-strand	661-664	4	38
β-strand	667-672	6	38
β-strand	688-693	6	38
α-helix	694-695	2
β-strand	698-701	4	39
β-strand	708-725	18	40
β-strand	730-733	4	41
α-helix	735-739	5
α-helix	744-750	7
α-helix	751-753	3
α-helix	757-779	23
β-strand	785	1	18
β-strand	794-795	2	42
β-strand	797	1	42
α-helix	814-822	9
α-helix	846-851	6
β-strand	855-858	4	41
α-helix	859-860	2
α-helix	864-880	17
α-helix	884-886	3
α-helix	895-906	12
α-helix	911-914	4
α-helix	917-937	21
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	40
β-strand	1056-1074	19	40
β-strand	1078-1080	3	43
β-strand	1083-1087	5	43
β-strand	1091-1094	4	40
β-strand	1099-1102	4	40
β-strand	1110	1	40
β-strand	1113	1	44
β-strand	1117-1119	3	43
β-strand	1130-1131	2	43
β-strand	1135	1	44
α-helix	1139-1143	5

Chain C: 32 helices, 71 β-strands

Element	Residues	Length	Sheet
β-strand	27-31	5	45
β-strand	36-37	2	46
β-strand	43	1	37
β-strand	48-55	8	47
α-helix	56-57	2
β-strand	60-67	8	45
β-strand	82-83	2	48
β-strand	88-94	7	45
β-strand	99-105	7	48
β-strand	114-119	6	48
β-strand	124-128	5	48
β-strand	139	1	49
β-strand	163-167	5	48
β-strand	183-190	8	45
β-strand	197-204	8	45
β-strand	219-220	2	46
β-strand	221-225	5	45
β-strand	234-239	6	48
β-strand	240	1	49
α-helix	241-242	2
β-strand	243	1	50
β-strand	255	1	50
β-strand	260-266	7	45
β-strand	268-276	9	47
β-strand	282-287	6	47
α-helix	292-300	9
β-strand	308-316	9	51
β-strand	317	1	52
α-helix	318-319	2
β-strand	322	1	53
β-strand	325	1	53
α-helix	331	1
β-strand	332	1	54
α-helix	333	1
α-helix	335-339	5
α-helix	344-346	3
β-strand	351-355	5	55
β-strand	359	1	54
β-strand	373-377	5	55
β-strand	392-400	9	55
α-helix	404-406	3
α-helix	414-418	5
β-strand	428-434	7	55
β-strand	449-451	3	56
α-helix	457-459	3
β-strand	470-471	2	57
β-strand	482	1	57
β-strand	485-486	2	57
β-strand	489-491	3	56
α-helix	500-502	3
β-strand	504-511	8	55
α-helix	518-519	2
β-strand	522	1	54
β-strand	536-540	5	53
β-strand	543-547	5	53
β-strand	548-551	4	3
β-strand	563-564	2	3
β-strand	570-574	5	3
β-strand	581-585	5	3
α-helix	586-588	3
β-strand	589-596	8	51
β-strand	606-610	5	51
β-strand	625	1	52
β-strand	640-641	2	51
β-strand	645-648	4	51
β-strand	651-652	2	58
β-strand	661-664	4	58
β-strand	667-672	6	58
β-strand	688-693	6	58
α-helix	694-695	2
β-strand	698-699	2	21
β-strand	708-725	18	59
β-strand	731-733	3	60
α-helix	735-739	5
α-helix	744-750	7
α-helix	756-779	24
β-strand	784-787	4	39
α-helix	814-822	9
α-helix	846-851	6
β-strand	855-857	3	60
α-helix	858-860	3
α-helix	864-880	17
α-helix	884-886	3
α-helix	895-906	12
α-helix	910-915	6
α-helix	917-937	21
α-helix	939-942	4
α-helix	943-961	19
α-helix	974-980	7
α-helix	983-1025	43
α-helix	1026-1030	5
β-strand	1044-1053	10	59
β-strand	1056-1075	20	59
β-strand	1078-1080	3	61
β-strand	1083-1087	5	61
β-strand	1091-1094	4	59
β-strand	1099-1102	4	59
β-strand	1110	1	59
β-strand	1113	1	62
β-strand	1117-1119	3	61
β-strand	1130-1131	2	61
β-strand	1135	1	62
α-helix	1138-1142	5

Chain E: 33 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	23-53	31
α-helix	57-81	25
α-helix	92-101	10
α-helix	111-129	19
α-helix	145	1
α-helix	147	1
α-helix	148-154	7
α-helix	158-193	36
α-helix	199-204	6
α-helix	205-207	3
α-helix	221-251	31
β-strand	262-263	2	63
α-helix	264-267	4
α-helix	279-281	3
α-helix	289-290	2
α-helix	295-298	4
α-helix	306-315	10
α-helix	316-318	3
β-strand	347	1	64
β-strand	359	1	64
α-helix	366-385	20
α-helix	390-392	3
α-helix	400-412	13
α-helix	415-421	7
α-helix	428-430	3
α-helix	433-448	16
α-helix	450-465	16
α-helix	470-473	4
α-helix	475-484	10
β-strand	487-488	2	63
α-helix	500-502	3
α-helix	504-507	4
α-helix	516-532	17
α-helix	549-558	10
α-helix	566-573	8
α-helix	583-587	5
α-helix	589-598	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein,Envelope glycoprotein	A, B, C	protein	1253	Severe acute respiratory syndrome coronavirus 2, Human immunodeficiency virus 1	A0A7T8KZF1
Angiotensin-converting enzyme	E	protein	613	Odocoileus virginianus texanus	Q58DD0 (AlphaFold model)

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

>8HFX_1 Spike glycoprotein,Envelope glycoprotein (chains A, B, C)
MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFS
NVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNN
ATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGN
FKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLA
LHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTL
KSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVA
DYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNY
KLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGV
AGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNF
NGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTN
TSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECD
IPIGAGICASYQTQTKSHRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVT
TEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFA
QVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGD
IAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMA
YRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLV
KQLSSKFGAISSVLNDIFSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASAN
LAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICH
DGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQP
ELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQEL
GKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGSAWSHPQFEKHHHHHHHH

Sequence of entity 2 (E), FASTA

>8HFX_2 Angiotensin-converting enzyme (chains E)
MTGSFWLLLSLVAVTAAQSTTEEQAKTFLEKFNHEAEDLSYQSSLASWNYNTNITDENVQ
KMNEARAKWSAFYEEQSRMAKTYSLEEIQNLTLKRQLKALQQSGTSVLSAEKSKRLNTIL
NTMSTIYSTGKVLDPNTQECLALEPGLDDIMENSRDYNRRLWAWEGWRAEVGKQLRPLYE
EYVVLENEMARANNYEDYGDYWRGDYEVTEAGDYDYSRDQLMKDVENTFAEIKPLYEQLH
AYVRAKLMDTYPSYISPTGCLPAHLLGDMWGRFWTNLYSLTVPFKHKPSIDVTEKMKNQS
WDAERIFKEAEKFFVSISLPHMTQGFWDNSMLTEPGDGRKVVCHPTAWDLGKGDFRIKMC
TKVTMDDFLTAHHEMGHIQYDMAYAAQPYLLRDGANEGFHEAVGEIMSLSAATPHYLKAL
GLLEPDFYEDNETEINFLLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKEQWMEKWWEMK
REIVGVVEPLPHDETYCDPACLFHVAEDYSFIRYYTRTIYQFQFHEALCKTANHEGALFK
CDISNSTEAGQRLLQMLSLGKSEPWTLALESIVGIKTMDVKPLLNYFEPLFTWLKEQNRN
SFVGWSTEWTPYS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	31

Primary citation

Structural basis of white-tailed deer, Odocoileus virginianus , ACE2 recognizing all the SARS-CoV-2 variants of concern with high affinity. Han, P., Meng, Y., Zhang, D. et al. J Virol (2023) 97:e0050523-e0050523. DOI 10.1128/jvi.00505-23 · PubMed

Other PDB entries of the same protein (UniProt A0A7T8KZF1), best resolution first:

7CN8 2.5 Å, Cryo-EM structure of PCoV_GX spike glycoprotein
8UPX 3.4 Å, Omicron-S-MERS-RBD

Browse structure collections

About this viewer

MolViewer shows 8HFX directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.