PDB-9jr7: Crystal structure of PCoV-GX receptor-binding domain complexed wi...

ID or keywords:

Entry

Database: PDB / ID: 9jr7

Title

Crystal structure of PCoV-GX receptor-binding domain complexed with squirrel ACE2

Components

Angiotensin-converting enzyme
Spike glycoprotein

Keywords

VIRAL PROTEIN / PCoV-GX / receptor-binding domain / squirrel ACE2

Function / homology

Function and homology information

Hydrolases; Acting on peptide bonds (peptidases) / positive regulation of L-proline import across plasma membrane / angiotensin-mediated drinking behavior / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / peptidyl-dipeptidase activity / transporter activator activity / angiotensin maturation / metallocarboxypeptidase activity ...
Similarity search - Function

Biological species

Petaurus norfolcensis (squirrel glider)

Pangolin coronavirus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.429 Å

Authors

Lan, J. / Nan, X.

Funding support

1items

Citation

Journal: Structure / Year: 2025
Title: Cross-species recognition of squirrel ACE2 by the receptor binding domains of SARS-CoV-2, RaTG13, PCoV-GD and PCoV-GX
Authors: Wang, C. / Nan, X. / Deng, Y. / Fan, S. / Lan, J.

History

Deposition	Sep 29, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Aug 6, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9jr7.cif.gz	339.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9jr7.ent.gz	278.9 KB	Display	PDB format
PDBx/mmJSON format	9jr7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9jr7_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	9jr7_full_validation.pdf.gz	1.5 MB	Display
Data in XML	9jr7_validation.xml.gz	36.4 KB	Display
Data in CIF	9jr7_validation.cif.gz	47.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jr/9jr7 ftp://data.pdbj.org/pub/pdb/validation_reports/jr/9jr7	HTTPS FTP

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Related structure data

Related structure data	9jr4C 9jr5C 9jrcC 9kudC 6m0jS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#246 - Jun 2020 SARS-CoV-2 Spike similarity (4) #264 - Dec 2021 SARS-CoV-2 Spike Variants similarity (4)

Deposited unit

A: Angiotensin-converting enzyme

E: Spike glycoprotein

hetero molecules

93.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	196.281, 196.281, 144.629
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	98
Space group name H-M	I4₁22

#1: Protein

Angiotensin-converting enzyme

Mass: 70724.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The sequence of organism Petaurus norfolcensis is not available during the biocuration, replaced by A0A8D2KIZ1 temporarily.
Source: (gene. exp.)

Petaurus norfolcensis (squirrel glider)
Gene: ACE2 / Production host:

Trichoplusia ni (cabbage looper)
References: UniProt: A0A8D2KIZ1, Hydrolases; Acting on peptide bonds (peptidases)

#2: Protein

Spike glycoprotein / S glycoprotein / E2 / Peplomer protein

Mass: 21687.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pangolin coronavirus / Gene: S / Production host:

Trichoplusia ni (cabbage looper) / References: UniProt: A0A6G6A1M4

#3: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₈H₁₅NO₆ / Feature type: SUBJECT OF INVESTIGATION

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

Has ligand of interest

Y

Has protein modification

Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.76 Å³/Da / Density % sol: 67.29 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 0.2M Sodium bromide, 20% w/v Polyethylene glycol 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.98 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 3.429→50 Å / Num. obs: 19172 / % possible obs: 99.6 % / Redundancy: 24.2 % / CC_1/2: 0.987 / Net I/σ(I): 9.33
Reflection shell	Resolution: 3.429→3.552 Å / Num. unique obs: 1847 / CC_1/2: 0.847

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6M0J

6m0j

Resolution: 3.429→38.811 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.14 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2558	912	4.76 %
R_work	0.2043	-	-
obs	0.2068	19148	99.71 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 3.429→38.811 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6429	0	14	0	6443

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	6624
X-RAY DIFFRACTION	f_angle_d	1.271	8999
X-RAY DIFFRACTION	f_dihedral_angle_d	19.555	3912
X-RAY DIFFRACTION	f_chiral_restr	0.065	954
X-RAY DIFFRACTION	f_plane_restr	0.008	1159

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.4292-3.6098	0.3582	123	0.2795	2532	X-RAY DIFFRACTION	99
3.6098-3.8358	0.2763	126	0.2443	2575	X-RAY DIFFRACTION	100
3.8358-4.1317	0.2275	127	0.2091	2585	X-RAY DIFFRACTION	100
4.1317-4.5469	0.2582	126	0.1867	2584	X-RAY DIFFRACTION	100
4.5469-5.2035	0.2287	128	0.1746	2609	X-RAY DIFFRACTION	100
5.2035-6.5507	0.2498	139	0.217	2622	X-RAY DIFFRACTION	100
6.5507-38.81	0.2513	143	0.1867	2729	X-RAY DIFFRACTION	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	3.0733	-1.4175	-3.1481	2.2882	2.0877	6.9892	0.053	0.4974	-0.2289	-0.1196	-0.4592	0.2946	-0.1328	-0.9006	0.4058	0.8872	0.0268	0.0087	0.8153	-0.0017	0.9288	35.8969	0.8835	24.976
2	3.7079	0.9497	-1.3527	2.9284	-1.7673	3.1042	0.0585	0.6424	1.5743	-0.0635	0.4276	0.504	-0.7816	-0.1283	-0.3994	0.8624	-0.136	-0.135	0.9852	0.0496	1.1247	48.7431	16.5639	18.7317
3	2.8618	0.5844	0.0413	1.7332	-0.2356	0.7652	-0.1544	0.3564	0.538	-0.1102	0.0902	0.1805	-0.1495	-0.0442	0.1083	0.6575	-0.0479	0.0418	0.761	0.1086	0.8928	65.5587	14.7362	21.1155
4	3.621	-0.0303	0.1096	2.5228	-0.6533	2.4205	-0.0808	0.5615	0.3645	-0.352	-0.2333	0.1402	0.9191	-0.2379	0.1318	0.835	-0.0334	0.1307	0.7872	-0.126	0.7753	55.4702	-7.962	18.2649
5	2.0241	-0.3311	-0.1684	2.7618	-0.1493	2.4139	0.2	0.2086	-0.1115	-0.0933	-0.0785	-0.5217	-0.185	0.3695	0.1317	0.6668	0.0824	0.106	0.678	0.0509	0.9295	67.3833	-4.5734	25.8042
6	4.373	1.2129	-0.6628	3.8754	-0.6576	2.3822	-0.1518	0.1385	0.8355	-0.1075	0.1197	-0.0445	-0.0835	-0.0549	0.0016	0.5118	-0.036	0.0353	0.6104	-0.0189	0.5797	64.9459	13.0174	27.6984
7	5.8145	1.6861	-1.3959	3.8188	-0.7084	2.3819	0.1917	-0.2987	-0.1517	0.0127	-0.5804	-0.7386	-0.084	0.2973	0.3049	0.634	-0.0132	0.1625	0.6983	-0.0132	1.0481	79.8168	15.0729	30.4359
8	-0.0118	0.0084	-0.0168	0.1432	-0.2196	0.3457	0.1222	0.3769	-1.174	-0.2227	0.3512	0.5938	0.8417	-0.4831	0.0685	1.0929	-0.0595	0.0279	0.9581	-0.3964	1.761	25.2632	-36.259	26.49
9	0.5479	-0.0258	-1.6632	0.895	0.1735	6.7694	-0.551	0.0657	-0.942	-0.0946	0.4	0.7703	1.8199	-0.2769	-0.3183	1.0339	-0.1687	-0.087	0.7963	0.0594	1.7783	22.279	-34.5531	33.827
10	8.1215	6.424	-4.2969	5.0766	-3.395	2.2737	-1.1767	-0.1424	-1.2156	-0.8084	-0.2984	-2.057	1.2049	1.3584	1.2265	1.2184	0.124	0.5217	1.1802	0.0373	2.4688	38.1078	-39.8904	29.9448
11	1.4192	-1.1017	-0.0405	5.7091	-0.0407	5.921	-0.7777	0.0845	-1.7364	0.2001	-0.2522	-0.292	1.3415	1.7419	1.2445	1.2662	0.2999	0.1314	1.3099	0.1041	1.7242	34.1823	-41.8587	40.2666
12	3.7851	-0.7033	-0.3349	2.3198	0.4456	4.7528	-0.4837	-0.2289	-0.4712	0.6706	-0.131	-0.6234	0.2139	0.3629	0.4085	0.9112	0.0121	0.0889	0.8919	0.0499	0.8618	31.8514	-23.3473	38.1991
13	4.1593	0.0995	-0.8389	2.4996	0.0044	3.9841	-0.128	0.0319	-0.1592	-0.2906	-0.0329	0.155	0.2584	0.2118	0.2978	0.7812	-0.0491	0.1206	0.7704	0.0069	0.9154	30.5136	-21.4271	32.7749
14	2.3675	2.068	0.6554	3.0038	-0.1517	1.3758	-0.1168	-0.0598	0.207	0.2144	0.3037	0.5883	0.076	-0.1757	-0.1861	0.6832	0.0544	0.2992	0.8115	-0.0412	1.1962	20.4148	-12.0402	42.2574
15	2.6967	3.2829	2.4715	4.1558	2.0763	7.0804	-0.3943	0.6869	0.6334	-0.9715	0.4992	0.4233	-2.0048	0.2541	0.2588	0.7366	0.0655	-0.0875	0.8985	0.0722	1.1407	21.4239	-2.2355	35.3398
16	9.0878	3.6341	1.49	3.8415	-1.7804	2.6184	-0.4853	-0.6698	-0.0216	0.5437	-0.2791	-0.1623	-0.213	-0.3906	0.8186	0.6394	-0.0129	0.1702	0.9436	0.026	0.6792	38.8367	-15.9106	24.7667
17	2.617	-0.7037	2.6941	7.6715	1.3978	4.2076	-0.2884	-0.2274	-0.9248	1.4928	0.3264	-0.1083	1.1755	-1.5985	0.1144	1.1305	-0.0399	0.291	1.0494	0.0475	1.1244	25.9435	-37.9686	38.2656

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 19 through 82 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 83 through 157 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 158 through 317 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 318 through 387 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 388 through 431 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 432 through 574 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 575 through 609 )
8	X-RAY DIFFRACTION	8	chain 'E' and (resid 333 through 349 )
9	X-RAY DIFFRACTION	9	chain 'E' and (resid 350 through 364 )
10	X-RAY DIFFRACTION	10	chain 'E' and (resid 365 through 375 )
11	X-RAY DIFFRACTION	11	chain 'E' and (resid 376 through 393 )
12	X-RAY DIFFRACTION	12	chain 'E' and (resid 394 through 421 )
13	X-RAY DIFFRACTION	13	chain 'E' and (resid 422 through 459 )
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 460 through 479 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 480 through 494 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 495 through 506 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 507 through 526 )

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