9JRC: SARS-CoV-2 receptor-binding domain

Crystal structure of SARS-CoV-2 receptor-binding domain complexed with squirrel ACE2. Determined by X-ray diffraction at 3.16 Å resolution. Released 6 Aug 2025.

Method
X-ray diffraction
Resolution
3.16 Å
Organisms
Petaurus norfolcensis, Severe acute respiratory syndrome coronavirus 2
Chains
2
Atoms
6,544
Mol. weight
93.13 kDa
Ligands
ZN, NAG
Released
6 Aug 2025

Explore 9JRC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9JRC contains 48 α-helices and 24 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 B: 38 helices, 9 β-strands

ElementResiduesLengthSheet
α-helix21-5131
α-helix56-8025
α-helix85-873
α-helix91-10111
α-helix110-1156
α-helix118-12912
β-strand131-13441
β-strand137-14371
α-helix144-1485
α-helix149-1546
α-helix158-17114
α-helix173-19321
α-helix199-2035
α-helix204-2074
β-strand20912
β-strand21712
α-helix219-25133
α-helix2611
β-strand262-26323
α-helix264-2663
α-helix275-2784
α-helix279-2824
α-helix294-2996
α-helix304-31815
α-helix320-3245
α-helix325-3306
β-strand33214
β-strand347-35044
β-strand356-35944
α-helix366-38419
α-helix385-3873
α-helix390-3923
α-helix400-41314
α-helix415-4217
α-helix432-46433
α-helix470-4723
α-helix473-4808
α-helix481-4855
β-strand487-48823
α-helix499-5024
α-helix504-5074
α-helix513-53520
α-helix542-5443
α-helix551-56111
α-helix564-5663
α-helix569-5779
α-helix585-60117
Chain E: 10 helices, 15 β-strands
ElementResiduesLengthSheet
β-strand33515
α-helix338-3425
β-strand34916
α-helix350-3523
β-strand354-35856
β-strand361-36225
α-helix366-3694
β-strand376-38056
α-helix385-3895
β-strand391-39225
β-strand394-403106
α-helix404-4096
α-helix417-4215
β-strand431-43776
α-helix439-4424
β-strand452-45437
α-helix460-4623
α-helix471-4722
β-strand473-47428
β-strand48518
β-strand488-48928
β-strand492-49437
α-helix503-5053
β-strand507-516106
β-strand524-52525

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Angiotensin-converting enzymeBprotein593Petaurus norfolcensisA0A8D2KIZ1 (AlphaFold model)
Spike protein S1Eprotein196Severe acute respiratory syndrome coronavirus 2P0DTC2 (AlphaFold model)
Sequence of entity 1 (B), FASTA
>9JRC_1 Angiotensin-converting enzyme (chains B)
PSTIEELAKTFLDKFNQEAEDLDHQRSLAAWNYNTNITKENTEKMNEAEAKWSAFYEEQS
KLAKDYPLQEIQNFTLKRQLQALQQSGSSALSANKREQLNTILNTMSTIYSTGKVCNPKK
PQECLLLEPGLDEIMANSTDYSERLWVWEGWRSEVGKQLRPLYEEYVVLKNEMARANNYE
DYGDYWRGDYEAEGADGYGYNRNQLIEDVERTFAEIKPLYEHLHAYVRAKLMNTYPSYIS
PTGCLPAHLLGDMWGRFWTNLYSLTVPFPEKPNIDVTDAMINQNWNAVRIFKEAEKFFVS
VGLPNMTQGFWENSMLTEPTDGRKVVCHPTAWDLQKGDFRIKMCTKVTMDNFLTAHHEMG
HIQYDMAYAMQPYLLRNGANEGFHEAVGEIMSLSASTPKHLKSIGLLPSDFREDNETEIN
FLLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEMKREIVGVMEPVPHDETY
CDPAALYHVSNDFSFIRYYTRTIYQFQFQEALCQAAKHEGPLHKCDISNSTEAGQKLLNM
LRLGKSKPWTLALENVVGARNMDVRPLLNYFEPLFGWLKDQNRNSFVGWNTDW
Sequence of entity 2 (E), FASTA
>9JRC_2 Spike protein S1 (chains E)
TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSTSFSTFKCYGVSPTKLNDLCF
TNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYL
YRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVV
LSFELLHAPATVCGPH

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn1
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O64

Primary citation

Cross-species recognition of squirrel ACE2 by the receptor binding domains of SARS-CoV-2, RaTG13, PCoV-GD and PCoV-GX. Wang, C., Nan, X., Deng, Y. et al. Structure (2025) 33:1750-1759.e2. DOI 10.1016/j.str.2025.07.003 · PubMed

Other PDB entries of the same protein (UniProt A0A8D2KIZ1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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