8HFY: Spike protein S1

SARS-CoV-2 Omicron BA.1 spike protein receptor-binding domain in complex with white-tailed deer ACE2. Determined by electron microscopy at 3.21 Å resolution. Released 30 Aug 2023.

Method: Electron microscopy
Resolution: 3.21 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, Odocoileus virginianus texanus
Chains: 2
Atoms: 6,568
Mol. weight: 93.56 kDa
Ligands: ZN, NAG
Released: 30 Aug 2023

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

Secondary structure: helices and β-sheets

8HFY contains 41 α-helices and 26 β-strands across 2 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: 36 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	22-53	32
α-helix	57-81	25
α-helix	92-102	11
α-helix	105-108	4
α-helix	111-129	19
β-strand	133-134	2	6
α-helix	136-138	3
β-strand	141-142	2	6
α-helix	144-148	5
α-helix	149-154	6
α-helix	158-193	36
α-helix	199-204	6
α-helix	205-207	3
β-strand	209	1	7
β-strand	217	1	7
α-helix	219-251	33
β-strand	260	1	8
α-helix	261	1
β-strand	262-263	2	9
α-helix	264-266	3
α-helix	276-278	3
α-helix	279-282	4
α-helix	289-290	2
α-helix	294-299	6
α-helix	304-317	14
α-helix	325-330	6
β-strand	332	1	10
β-strand	347-352	6	10
β-strand	355-359	5	10
α-helix	366-384	19
α-helix	385-387	3
α-helix	390-392	3
α-helix	400-411	12
α-helix	415-420	6
α-helix	432-447	16
α-helix	449-465	17
α-helix	475-480	6
α-helix	481-485	5
β-strand	487-488	2	9
α-helix	499-502	4
α-helix	504-507	4
α-helix	517-532	16
α-helix	548-558	11
α-helix	566-573	8
α-helix	582-587	6
α-helix	589-598	10
β-strand	607	1	8

Chain B: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	335	1	1
β-strand	354-358	5	2
β-strand	362	1	1
α-helix	368-370	3
β-strand	376-380	5	2
β-strand	391-392	2	1
β-strand	394-403	10	2
α-helix	405-408	4
β-strand	431-437	7	2
α-helix	439-442	4
β-strand	448	1	3
β-strand	452-454	3	4
α-helix	460-462	3
β-strand	473-474	2	5
β-strand	488-489	2	5
β-strand	492-494	3	4
β-strand	497	1	3
α-helix	503-505	3
β-strand	507-516	10	2
β-strand	524-525	2	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike protein S1	B	protein	194	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)
Angiotensin-converting enzyme	A	protein	595	Odocoileus virginianus texanus	Q58DD0 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>8HFY_1 Spike protein S1 (chains B)
TNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCF
TNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYL
YRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVV
LSFELLHAPATVCG

Sequence of entity 2 (A), FASTA

>8HFY_2 Angiotensin-converting enzyme (chains A)
STTEEQAKTFLEKFNHEAEDLSYQSSLASWNYNTNITDENVQKMNEARAKWSAFYEEQSR
MAKTYSLEEIQNLTLKRQLKALQQSGTSVLSAEKSKRLNTILNTMSTIYSTGKVLDPNTQ
ECLALEPGLDDIMENSRDYNRRLWAWEGWRAEVGKQLRPLYEEYVVLENEMARANNYEDY
GDYWRGDYEVTEAGDYDYSRDQLMKDVENTFAEIKPLYEQLHAYVRAKLMDTYPSYISPT
GCLPAHLLGDMWGRFWTNLYSLTVPFKHKPSIDVTEKMKNQSWDAERIFKEAEKFFVSIS
LPHMTQGFWDNSMLTEPGDGRKVVCHPTAWDLGKGDFRIKMCTKVTMDDFLTAHHEMGHI
QYDMAYAAQPYLLRDGANEGFHEAVGEIMSLSAATPHYLKALGLLEPDFYEDNETEINFL
LKQALTIVGTLPFTYMLEKWRWMVFKGEIPKEQWMEKWWEMKREIVGVVEPLPHDETYCD
PACLFHVAEDYSFIRYYTRTIYQFQFHEALCKTANHEGALFKCDISNSTEAGQRLLQMLS
LGKSEPWTLALESIVGIKTMDVKPLLNYFEPLFTWLKEQNRNSFVGWSTEWTPYS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

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 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 structure collections

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