PDB-8z9i: Crystal structure of RaTG13 RBD bound to Rhinolophus affinis ACE2

ID or keywords:

Entry

Database: PDB / ID: 8z9i

Title

Crystal structure of RaTG13 RBD bound to Rhinolophus affinis ACE2

Components

Angiotensin-converting enzyme
RaTG13 Spike glycoprotein

Keywords

VIRAL PROTEIN/HYDROLASE / RaTG13 RBD / Rhinolophus affinis ACE2 / VIRAL PROTEIN-HYDROLASE complex

Function / homology

Function and homology information

Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / cilium / apical plasma membrane / proteolysis / extracellular space / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Bat coronavirus RaTG13

Rhinolophus affinis (intermediate horseshoe bat)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.011 Å

Authors

Lan, J. / Wang, C.H.

Funding support

1items

Citation

Journal: Protein Sci. / Year: 2025
Title: Molecular mechanisms of RaTG13 and SARS-CoV-2 RBD bound to Rhinolophus affinis bat ACE2.
Authors: Wang, C. / Li, M. / Nan, X. / Deng, Y. / Fan, S. / Lan, J.

History

Deposition	Apr 23, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Apr 30, 2025	Provider: repository / Type: Initial release
Revision 1.1	May 14, 2025	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8z9i.cif.gz	647.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8z9i.ent.gz	538.1 KB	Display	PDB format
PDBx/mmJSON format	8z9i.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8z9i_validation.pdf.gz	938 KB	Display	wwPDB validaton report
Full document	8z9i_full_validation.pdf.gz	966.1 KB	Display
Data in XML	8z9i_validation.xml.gz	63.6 KB	Display
Data in CIF	8z9i_validation.cif.gz	81.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z9/8z9i ftp://data.pdbj.org/pub/pdb/validation_reports/z9/8z9i	HTTPS FTP

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Related structure data

Related structure data	8z9lC 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

O: RaTG13 Spike glycoprotein

A: Angiotensin-converting enzyme

E: RaTG13 Spike glycoprotein

F: Angiotensin-converting enzyme

hetero molecules

184 kDa, 4 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)	100.925, 273.391, 165.103
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein

RaTG13 Spike glycoprotein

Mass: 22108.818 Da / Num. of mol.: 2 / Fragment: RBD domain
Source method: isolated from a genetically manipulated source
Details: Current sequence reference is from UniProt ID A0A6B9WHD3 with TAX ID 2709072 (Bat coronavirus RaTG13) which matches the entry title. However, UniProt ID A0A6B9WHD3 is deleted from UniProtKB ...
Source: (gene. exp.)

Bat coronavirus RaTG13 / Production host:

Trichoplusia ni (cabbage looper)

#2: Protein

Angiotensin-converting enzyme

Mass: 69525.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Rhinolophus affinis (intermediate horseshoe bat)
Production host:

Trichoplusia ni (cabbage looper)
References: UniProt: A0A7D7J6S6, Hydrolases; Acting on peptide bonds (peptidases)

#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.: 2 / 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: 3.11 Å³/Da / Density % sol: 60.47 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.0,30% v/v Jeffamine ED-2001 pH 7.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 13, 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: 3.011→50 Å / Num. obs: 44473 / % possible obs: 98.7 % / Redundancy: 12 % / CC_1/2: 0.99 / Net I/σ(I): 8.2
Reflection shell	Resolution: 3.011→3.119 Å / Num. unique obs: 3985 / CC_1/2: 0.685

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Processing

Software

Name	Version	Classification
PHENIX	1.18.2	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.011→28.653 Å / SU ML: 0.35 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 23.42 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2385	2201	4.95 %
R_work	0.194	-	-
obs	0.1962	44424	97.55 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.011→28.653 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12890	0	31	0	12921

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	13471
X-RAY DIFFRACTION	f_angle_d	1.33	18323
X-RAY DIFFRACTION	f_dihedral_angle_d	19.34	7916
X-RAY DIFFRACTION	f_chiral_restr	0.066	1932
X-RAY DIFFRACTION	f_plane_restr	0.008	2348

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 (%)
3.0114-3.0768	0.2916	106	0.2487	2218	X-RAY DIFFRACTION	83
3.0768-3.1483	0.2893	135	0.259	2621	X-RAY DIFFRACTION	98
3.1483-3.2269	0.3084	139	0.2438	2627	X-RAY DIFFRACTION	98
3.2269-3.314	0.318	163	0.2391	2560	X-RAY DIFFRACTION	97
3.314-3.4114	0.2951	140	0.2396	2623	X-RAY DIFFRACTION	98
3.4114-3.5213	0.2492	128	0.2219	2626	X-RAY DIFFRACTION	98
3.5213-3.6469	0.2618	135	0.2173	2649	X-RAY DIFFRACTION	98
3.6469-3.7926	0.2699	133	0.1947	2639	X-RAY DIFFRACTION	98
3.7926-3.9648	0.2521	113	0.1866	2665	X-RAY DIFFRACTION	99
3.9648-4.1733	0.2322	135	0.1846	2679	X-RAY DIFFRACTION	99
4.1733-4.4338	0.2287	152	0.1705	2665	X-RAY DIFFRACTION	99
4.4338-4.7747	0.2072	145	0.1625	2700	X-RAY DIFFRACTION	100
4.7747-5.2526	0.2127	145	0.1668	2726	X-RAY DIFFRACTION	100
5.2526-6.0065	0.2211	142	0.1816	2727	X-RAY DIFFRACTION	100
6.0065-7.5447	0.2057	143	0.191	2761	X-RAY DIFFRACTION	100
7.5447-28.653	0.2043	147	0.1806	2737	X-RAY DIFFRACTION	96

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	1.2154	-0.2295	0.3262	1.0554	0.2999	2.2604	-0.0028	-0.2152	-0.4183	0.1017	0.3481	0.7058	-0.3683	-0.075	-0.1204	0.415	0.1047	0.0695	0.4204	0.0362	0.8199	-15.3458	53.065	23.9883
2	6.5941	4.3432	0.0816	4.3685	-2.7445	7.7562	-0.6376	0.3905	-0.9433	-0.4646	1.0905	1.1265	0.7097	-0.2676	0.6408	0.486	-0.0533	0.0778	1.1436	0.1624	0.8512	-21.0465	41.2436	24.8656
3	3.501	0.8288	-2.3642	5.4321	-0.5391	3.3162	-1.1364	0.9947	-0.086	-0.6515	0.2913	0.156	0.4768	-0.7468	0.5039	0.4602	-0.1622	0.084	0.455	-0.0747	0.5897	-9.7314	39.1551	18.1336
4	1.4695	1.0639	0.1371	2.83	0.0023	0.6353	0.1552	-0.2259	0.2755	0.4497	-0.0948	0.2077	0.0313	-0.0344	-0.1092	0.4291	0.0471	0.0353	0.363	-0.0656	0.5024	-1.6408	52.0532	25.1373
5	1.7627	0.2812	0.0412	2.2175	-0.0781	0.4365	0.0813	-0.0449	0.3383	0.1961	-0.0366	-0.1845	0.1677	0.2781	-0.0322	0.3608	0.0479	0.056	0.4048	-0.0373	0.5371	2.7802	58.5794	19.0615
6	1.0704	-0.633	-1.5777	1.7246	0.1079	3.5273	0.6801	-0.9563	-0.359	0.4253	0.1116	-0.0658	-0.6823	0.3061	-0.6684	0.674	-0.1659	0.4366	0.8693	0.0227	1.2859	-20.9909	41.6411	37.5473
7	0.6026	-0.3064	0.4661	1.6529	-0.2472	0.2499	0.1098	0.1284	-0.0187	0.0987	-0.2191	-0.065	-0.0255	0.129	0.0958	0.4763	0.0476	0.0374	0.5083	0.0222	0.4082	82.3711	20.9946	-36.1926
8	0.7182	-0.0076	-0.6172	1.4564	-0.1704	1.1799	-0.0609	-0.2342	0.1718	0.1049	0.0331	-0.1073	-0.0668	0.4475	0.0269	0.2183	0.067	-0.0826	0.4977	-0.0295	0.3131	70.2181	40.0684	-19.6843
9	1.987	-0.3092	-0.176	0.7787	0.114	1.6862	-0.0754	-0.2628	0.3501	0.3856	-0.0024	-0.2016	0.3191	0.0943	0.1216	0.4841	0.0682	-0.0571	0.5123	-0.1566	0.3981	68.2611	42.1797	-1.0649
10	1.6957	-0.1032	-1.8821	1.5231	-0.3931	2.5402	-0.1118	-0.7689	0.1613	0.3538	0.1567	0.0066	-0.2003	0.6079	0.0196	0.4764	0.2035	-0.0336	0.5839	-0.0816	0.3911	84.5676	16.9114	-7.6684
11	1.1994	-0.4009	-0.4084	0.9563	0.4618	0.801	-0.0829	-0.2854	0.0238	0.1033	0.1055	0.0038	0.1178	0.0518	-0.0243	0.2989	0.0635	-0.0169	0.4035	-0.0072	0.2863	68.3689	33.1518	-14.4364
12	1.4531	-0.3293	-0.3241	1.6963	0.5843	1.493	-0.1143	-0.2619	-0.2974	0.3201	0.0976	0.0188	0.2476	-0.0957	-0.0144	0.4521	0.0668	0.062	0.3571	0.0456	0.3356	60.0718	23.5798	-9.8148
13	1.5943	-0.4895	0.4147	2.8292	-0.164	1.8929	0.2586	-0.077	-0.3484	-0.4638	-0.1585	-0.1162	0.4783	0.2011	-0.0515	0.392	0.0473	-0.011	0.4016	0.0137	0.5599	102.5212	-15.2516	-32.1044
14	1.8777	-2.2283	0.174	5.4198	0.0692	0.0867	-0.4078	-0.4798	-0.2547	0.9071	0.661	-0.8191	-0.3362	-0.2494	-0.1133	0.6414	0.2211	-0.0474	0.5939	0.0573	0.7195	99.747	-21.474	-20.5477
15	0.3846	-0.47	-0.1202	2.5067	0.0622	0.9677	0.0561	-0.2282	-0.2719	0.1564	-0.0861	0.364	0.1693	0.0136	-0.0159	0.406	0.0359	0.0288	0.4601	0.0821	0.5058	89.5339	-16.5815	-28.7969
16	2.6482	-0.4661	0.1322	2.7029	-0.5427	2.8345	-0.2036	-0.4127	-0.0205	0.438	0.304	-0.2178	0.1778	0.1736	-0.0412	0.4483	0.0959	-0.0173	0.4105	-0.0922	0.4545	91.7543	-11.9712	-28.5606
17	1.6741	-0.3886	-0.5923	1.6039	0.4643	1.2491	0.2364	0.183	-0.0759	-0.0994	-0.0167	-0.7111	-0.051	0.5419	-0.1113	0.3445	-0.0387	-0.0391	0.3565	0.0696	0.4578	93.0363	1.771	-36.7209
18	2.0052	0.2314	-1.2741	2.0909	0.909	1.356	0.2206	0.4595	-0.1871	-0.185	-0.2546	-0.3105	-0.374	-0.1457	0.0626	0.3535	0.041	-0.0153	0.3695	-0.0543	0.5608	86.5715	-5.0278	-48.4598
19	1.1341	-0.714	-0.0707	1.0559	1.131	1.8727	-0.062	-0.0715	0.4125	-0.0261	0.0273	-0.2518	-0.5492	-0.0079	0.0665	0.3979	-0.0039	0.0341	0.2752	-0.0116	0.5698	91.1287	1.0375	-35.7964
20	3.5282	-0.0193	-1.3788	1.13	2.3444	5.4899	-0.049	-0.6532	-1.3309	0.9904	-0.0112	-0.3255	0.5649	-0.6972	-0.0223	0.7773	0.0755	-0.0816	0.5328	0.1505	0.5656	98.0489	-32.5113	-30.6687
21	0.3947	-0.2631	-0.4792	1.4114	0.6958	0.8139	0.1649	-0.0887	0.2945	-0.1659	0.1054	-0.3307	-0.2098	0.2741	-0.1285	0.3575	-0.0483	0.0698	0.4094	-0.0492	0.5706	19.7002	63.185	9.6877
22	1.0342	-0.2505	-0.6599	1.9524	-0.2017	1.4383	-0.0454	-0.0577	0.275	-0.0378	0.0447	0.0403	-0.3248	-0.0662	-0.0289	0.281	0.0255	-0.0093	0.2839	-0.0305	0.3093	30.2828	59.2006	-15.7428
23	1.0921	-0.4279	0.027	1.0163	0.1871	1.7441	-0.1273	0.0028	-0.1106	-0.0397	-0.0857	0.1215	0.0346	0.0372	0.1823	0.3298	-0.0101	0.049	0.3518	-0.031	0.326	37.5164	38.085	-20.611
24	1.5774	-0.7623	-0.7341	1.4598	0.3199	1.5244	0.0101	0.0557	-0.1014	-0.2249	-0.1743	0.3561	0.1448	-0.2253	0.14	0.3582	0.0124	0.0513	0.4355	-0.0126	0.4221	15.2945	39.5543	-6.7382
25	1.3905	0.2981	-0.0106	1.7265	-0.1373	1.3931	-0.0189	0.0066	0.1246	0.0955	0.0871	-0.1574	-0.1257	0.0144	-0.0707	0.3663	-0.0068	0.0288	0.3535	-0.0419	0.3241	38.1489	50.2542	-16.8714
26	1.5183	-0.4038	-0.4496	1.621	0.4065	1.0718	-0.0319	-0.1177	-0.1847	0.1002	0.0404	-0.025	0.2463	0.0945	0.0251	0.3743	0.0091	0.064	0.3004	0.0187	0.2615	34.7811	34.0405	-4.8549

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'O' and (resid 333 through 358 )
2	X-RAY DIFFRACTION	2	chain 'O' and (resid 359 through 369 )
3	X-RAY DIFFRACTION	3	chain 'O' and (resid 370 through 380 )
4	X-RAY DIFFRACTION	4	chain 'O' and (resid 381 through 479 )
5	X-RAY DIFFRACTION	5	chain 'O' and (resid 480 through 516 )
6	X-RAY DIFFRACTION	6	chain 'O' and (resid 517 through 527 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 19 through 128 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 129 through 251 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 252 through 293 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 294 through 384 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 385 through 512 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 513 through 614 )
13	X-RAY DIFFRACTION	13	chain 'E' and (resid 333 through 358 )
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 359 through 375 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 376 through 421 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 422 through 442 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 443 through 459 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 460 through 479 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 480 through 515 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 516 through 528 )
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 19 through 109 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 110 through 218 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 219 through 293 )
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 294 through 431 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 432 through 513 )
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 514 through 615 )

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