9JR5: PCoV-GD receptor-binding domain

Crystal structure of PCoV-GD receptor-binding domain complexed with squirrel ACE2. Determined by X-ray diffraction at 3.41 Å resolution. Released 6 Aug 2025.

Method: X-ray diffraction
Resolution: 3.41 Å
Organisms: Pangolin coronavirus, Petaurus norfolcensis
Chains: 2
Atoms: 6,408
Mol. weight: 92.28 kDa
Ligands: NAG
Released: 6 Aug 2025

Explore 9JR5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9JR5 contains 41 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 A: 33 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	21-52	32
α-helix	56-81	26
α-helix	85-87	3
α-helix	91-100	10
α-helix	110-128	19
β-strand	131	1	5
β-strand	143	1	5
α-helix	144-148	5
α-helix	149-152	4
α-helix	158-193	36
α-helix	199-203	5
α-helix	204-207	4
β-strand	209	1	6
β-strand	217	1	6
α-helix	219-249	31
β-strand	262-263	2	7
α-helix	264-267	4
α-helix	275-278	4
α-helix	279-282	4
α-helix	294-299	6
α-helix	304-318	15
α-helix	320-324	5
α-helix	325-330	6
β-strand	332	1	8
β-strand	348-350	3	9
β-strand	356-358	3	9
β-strand	359	1	8
α-helix	366-384	19
α-helix	390-392	3
α-helix	400-413	14
α-helix	415-420	6
α-helix	432-464	33
α-helix	473-480	8
α-helix	481-485	5
β-strand	487-488	2	7
α-helix	500-502	3
α-helix	504-507	4
α-helix	514-532	19
α-helix	539-541	3
α-helix	548-558	11
α-helix	561-563	3
α-helix	566-574	9
α-helix	582-598	17

Chain E: 8 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	339-342	4
β-strand	349	1	1
α-helix	350-352	3
β-strand	354-357	4	1
α-helix	366-369	4
β-strand	376	1	1
β-strand	379-380	2	1
β-strand	395-403	9	1
α-helix	404-409	6
α-helix	417-421	5
β-strand	431-437	7	1
α-helix	439-442	4
β-strand	448	1	2
β-strand	453-454	2	3
α-helix	460-462	3
β-strand	473-474	2	4
α-helix	479-480	2
β-strand	485	1	4
β-strand	488-489	2	4
β-strand	492-493	2	3
β-strand	497	1	2
β-strand	507-515	9	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein	E	protein	185	Pangolin coronavirus	P0DTC2 (AlphaFold model)
Angiotensin-converting enzyme	A	protein	598	Petaurus norfolcensis	A0A8D2KIZ1 (AlphaFold model)

Sequence of entity 1 (E), FASTA

>9JR5_1 Spike glycoprotein (chains E)
TNLCTFGEVFNATTFASVYAWNRKRISNCVADYSVLYNSTSFSTFKCYGVSPTKLNDLCF
TNVYADSFVVRGDEVRQIAPGQTGRIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYL
YRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFHPTNGVGYQPYRVVV
LSFEL

Sequence of entity 2 (A), FASTA

>9JR5_2 Angiotensin-converting enzyme (chains A)
PSTIEELAKTFLDKFNQEAEDLDHQRSLAAWNYNTNITKENTEKMNEAEAKWSAFYEEQS
KLAKDYPLQEIQNFTLKRQLQALQQSGSSALSANKREQLNTILNTMSTIYSTGKVCNPKK
PQECLLLEPGLDEIMANSTDYSERLWVWEGWRSEVGKQLRPLYEEYVVLKNEMARANNYE
DYGDYWRGDYEAEGADGYGYNRNQLIEDVERTFAEIKPLYEHLHAYVRAKLMNTYPSYIS
PTGCLPAHLLGDMWGRFWTNLYSLTVPFPEKPNIDVTDAMINQNWNAVRIFKEAEKFFVS
VGLPNMTQGFWENSMLTEPTDGRKVVCHPTAWDLQKGDFRIKMCTKVTMDNFLTAHHEMG
HIQYDMAYAMQPYLLRNGANEGFHEAVGEIMSLSASTPKHLKSIGLLPSDFREDNETEIN
FLLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEMKREIVGVMEPVPHDETY
CDPAALYHVSNDFSFIRYYTRTIYQFQFQEALCQAAKHEGPLHKCDISNSTEAGQKLLNM
LRLGKSKPWTLALENVVGARNMDVRPLLNYFEPLFGWLKDQNRNSFVGWNTDWSPYTD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

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 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…

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