8GRY: SARS-CoV-2 Omicron BA.2 RBD

Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with rat ACE2 (local refinement). Determined by electron microscopy at 3.29 Å resolution. Released 19 Jul 2023.

Method
Electron microscopy
Resolution
3.29 Å
Organisms
Rattus norvegicus, Severe acute respiratory syndrome coronavirus 2
Chains
2
Atoms
6,444
Mol. weight
91.52 kDa
Ligands
ZN, NAG
Released
19 Jul 2023

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

Secondary structure: helices and β-sheets

8GRY contains 39 α-helices and 25 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: 34 helices, 8 β-strands

ElementResiduesLengthSheet
α-helix20-5233
α-helix56-7924
α-helix80-823
α-helix93-1019
α-helix104-1063
α-helix110-12819
β-strand14311
β-strand14711
α-helix148-1536
α-helix158-19235
α-helix199-2046
β-strand20912
β-strand21712
α-helix221-23010
α-helix234-25118
β-strand262-26323
α-helix264-2663
α-helix276-2783
α-helix279-2824
α-helix294-3007
α-helix304-31714
α-helix320-3245
α-helix327-3304
β-strand347-35044
β-strand356-35944
α-helix366-38419
α-helix385-3873
α-helix390-3923
α-helix400-41213
α-helix415-4217
α-helix432-44615
α-helix450-46415
α-helix473-4808
α-helix481-4855
β-strand487-48823
α-helix500-5023
α-helix504-5085
α-helix514-53118
α-helix539-5413
α-helix548-55811
α-helix566-5738
α-helix582-59817
Chain B: 5 helices, 17 β-strands
ElementResiduesLengthSheet
β-strand33515
β-strand354-35856
β-strand36215
β-strand376-38056
β-strand39217
β-strand394-403106
α-helix405-4095
α-helix418-4214
β-strand431-43776
β-strand44818
β-strand452-45439
α-helix460-4623
α-helix471-4722
β-strand473-474210
β-strand485110
β-strand488-489210
β-strand492-49439
β-strand49718
α-helix503-5053
β-strand507-516106
β-strand52417
β-strand52515

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Processed angiotensin-converting enzyme 2Aprotein597Rattus norvegicusQ5EGZ1 (AlphaFold model)
Spike protein S1Bprotein195Severe acute respiratory syndrome coronavirus 2P0DTC2 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>8GRY_1 Processed angiotensin-converting enzyme 2 (chains A)
SLIEEKAESFLNKFNQEAEDLSYQSSLASWNYNTNITEENAQKMNEAAAKWSAFYEEQSK
IAQNFSLQEIQNATIKRQLKALQQSGSSALSPDKNKQLNTILNTMSTIYSTGKVCNSMNP
QECFLLEPGLDEIMATSTDYNRRLWAWEGWRAEVGKQLRPLYEEYVVLKNEMARANNYED
YGDYWRGDYEAEGVEGYNYNRNQLIEDVENTFKEIKPLYEQLHAYVRTKLMEVYPSYISP
TGCLPAHLLGDMWGRFWTNLYPLTTPFLQKPNIDVTDAMVNQSWDAERIFKEAEKFFVSV
GLPQMTPGFWTNSMLTEPGDDRKVVCHPTAWDLGHGDFRIKMCTKVTMDNFLTAHHEMGH
IQYDMAYAKQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKSIGLLPSNFQEDNETEINF
LLKQALTIVGTLPFTYMLEKWRWMVFQDKIPREQWTKKWWEMKREIVGVVEPLPHDETYC
DPASLFHVSNDYSFIRYYTRTIYQFQFQEALCQAAKHDGPLHKCDISNSTEAGQKLLNML
SLGNSGPWTLALENVVGSRNMDVKPLLNYFQPLFVWLKEQNRNSTVGWSTDWSPYAD
Sequence of entity 2 (B), FASTA
>8GRY_2 Spike protein S1 (chains B)
TNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCF
TNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYL
YRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYGFRPTYGVGHQPYRVVV
LSFELLHAPATVCGP

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn1
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O61

Primary citation

Structural basis for receptor binding and broader interspecies receptor recognition of currently circulating Omicron sub-variants. Zhao, Z., Xie, Y., Bai, B. et al. Nat Commun (2023) 14:4405-4405. DOI 10.1038/s41467-023-39942-z · PubMed

Other PDB entries of the same protein (UniProt Q5EGZ1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

About this viewer

MolViewer shows 8GRY 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.