PDB-8ze6: Crystal structure of MjHKU4r-CoV-1 RBD bound to MjDPP4

ID or keywords:

Entry

Database: PDB / ID: 8ze6

Title

Crystal structure of MjHKU4r-CoV-1 RBD bound to MjDPP4

Components

Dipeptidyl peptidase 4
Spike glycoprotein

Keywords

VIRAL PROTEIN / Virus protein and receptor complex

Function / homology

Function and homology information

host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function

Biological species

Manis javanica (Malayan pangolin)

Pangolin coronavirus HKU4

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Yang, M. / Li, Z. / Xu, Y. / Zhang, S.

Funding support

China, 1items

Citation

Journal: Plos Pathog. / Year: 2024
Title: Structural basis for human DPP4 receptor recognition by a pangolin MERS-like coronavirus.
Authors: Yang, M. / Li, Z. / Chen, J. / Li, Y. / Xu, R. / Wang, M. / Xu, Y. / Chen, R. / Ji, W. / Li, X. / Wei, J. / Zhou, Z. / Ren, M. / Ma, K. / Guan, J. / Mo, G. / Zhou, P. / Shu, B. / Guo, J. / ...

History

Deposition	May 4, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Oct 30, 2024	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_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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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ze/8ze6 ftp://data.pdbj.org/pub/pdb/validation_reports/ze/8ze6	HTTPS FTP

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Related structure data

Related structure data	8zdxC 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

Deposited unit

B: Dipeptidyl peptidase 4

C: Spike glycoprotein

D: Dipeptidyl peptidase 4

A: Spike glycoprotein

hetero molecules

218 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

B: Dipeptidyl peptidase 4

A: Spike glycoprotein

hetero molecules

C: Spike glycoprotein

D: Dipeptidyl peptidase 4

hetero molecules

defined by author&software
Evidence: surface plasmon resonance
218 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	96.532, 121.440, 110.624
Angle α, β, γ (deg.)	90.00, 105.13, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 2 types, 4 molecules BDCA

#1: Protein	Dipeptidyl peptidase 4 Mass: 84407.484 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Manis javanica (Malayan pangolin) / Production host: Baculovirus expression vector pFastBac1-HM
#2: Protein	Spike glycoprotein / S glycoprotein / E2 / Peplomer protein Mass: 22504.447 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Sequence reference for source organism Pangolin coronavirus HKU4 is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0AAE8ZFM2. Source: (gene. exp.) Pangolin coronavirus HKU4 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: A0AAE8ZFM2

#1: Protein

Dipeptidyl peptidase 4

Mass: 84407.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Manis javanica (Malayan pangolin) / Production host:

Baculovirus expression vector pFastBac1-HM

#2: Protein

Spike glycoprotein / S glycoprotein / E2 / Peplomer protein

Mass: 22504.447 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Sequence reference for source organism Pangolin coronavirus HKU4 is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0AAE8ZFM2.
Source: (gene. exp.)

Pangolin coronavirus HKU4 / Production host:

Baculovirus expression vector pFastBac1-HM / References: UniProt: A0AAE8ZFM2

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Sugars , 2 types, 11 molecules

#3: Polysaccharide

2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}	LINUCS	PDB-CARE

#4: 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: isolated from a genetically manipulated source
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

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Non-polymers , 2 types, 158 molecules

#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃ / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.94 Å³/Da / Density % sol: 58.13 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1 M Ammonium tartrate dibasic (pH 7.0) and 12% (wt/vol) PEG 3350.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 12, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979183 Å / Relative weight: 1
Reflection	Resolution: 2.7→47.49 Å / Num. obs: 66775 / % possible obs: 98.8 % / Redundancy: 3.88 % / CC_1/2: 0.971 / Net I/σ(I): 4.98
Reflection shell	Resolution: 2.7→2.87 Å / Num. unique obs: 10670 / CC_1/2: 0.372

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
XDS	Jun 30, 2023	data reduction
XDS	Jun 30, 2023	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.7→47.49 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.62 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2736	3342	5.01 %
R_work	0.2424	-	-
obs	0.244	66672	98.75 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.7→47.49 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15030	0	244	157	15431

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	15699
X-RAY DIFFRACTION	f_angle_d	0.482	21342
X-RAY DIFFRACTION	f_dihedral_angle_d	14.985	5648
X-RAY DIFFRACTION	f_chiral_restr	0.049	2310
X-RAY DIFFRACTION	f_plane_restr	0.004	2708

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 (%)
2.7-2.74	0.4002	153	0.3603	2562	X-RAY DIFFRACTION	96
2.74-2.78	0.3655	139	0.3485	2615	X-RAY DIFFRACTION	98
2.78-2.83	0.3597	125	0.342	2624	X-RAY DIFFRACTION	99
2.83-2.87	0.3569	124	0.329	2641	X-RAY DIFFRACTION	98
2.87-2.92	0.3685	157	0.3223	2620	X-RAY DIFFRACTION	99
2.92-2.97	0.3744	144	0.3302	2607	X-RAY DIFFRACTION	99
2.97-3.03	0.3791	129	0.3138	2637	X-RAY DIFFRACTION	99
3.03-3.09	0.3527	125	0.3097	2646	X-RAY DIFFRACTION	99
3.09-3.16	0.3405	139	0.2946	2659	X-RAY DIFFRACTION	99
3.16-3.23	0.3325	125	0.2941	2659	X-RAY DIFFRACTION	99
3.23-3.32	0.356	154	0.2974	2605	X-RAY DIFFRACTION	99
3.32-3.4	0.3452	133	0.2844	2634	X-RAY DIFFRACTION	99
3.4-3.5	0.3111	128	0.2687	2689	X-RAY DIFFRACTION	99
3.5-3.62	0.2755	125	0.255	2638	X-RAY DIFFRACTION	99
3.62-3.75	0.2733	146	0.2357	2631	X-RAY DIFFRACTION	99
3.75-3.9	0.2755	164	0.2392	2630	X-RAY DIFFRACTION	99
3.9-4.07	0.2765	146	0.2179	2663	X-RAY DIFFRACTION	99
4.07-4.29	0.2603	127	0.2158	2626	X-RAY DIFFRACTION	99
4.29-4.56	0.1994	129	0.1915	2658	X-RAY DIFFRACTION	99
4.56-4.91	0.2226	144	0.1897	2646	X-RAY DIFFRACTION	99
4.91-5.4	0.2031	162	0.1976	2642	X-RAY DIFFRACTION	99
5.4-6.18	0.2309	139	0.2176	2674	X-RAY DIFFRACTION	99
6.18-7.78	0.2823	149	0.2331	2660	X-RAY DIFFRACTION	99
7.79-47.49	0.2187	136	0.2016	2664	X-RAY DIFFRACTION	97

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	0.9501	0.9327	-0.1242	0.9022	-0.3342	2.5763	0.074	-0.1847	0.0467	-0.0746	-0.0519	0.0412	0.2271	-0.1641	0.0117	0.3503	-0.004	0.052	0.3806	-0.0128	0.4508	51.612	105.6043	92.0975
2	1.0156	0.4355	0.0752	1.2712	-0.197	1.4087	-0.0203	0.1404	-0.0561	-0.0354	0.0705	-0.131	-0.0416	0.1438	-0.0613	0.3086	-0.0063	0.0612	0.2927	-0.0172	0.406	66.0947	112.5981	110.7656
3	0.6684	0.0604	0.002	0.3882	-0.0134	1.5341	0	0.0153	0.0997	-0.0065	0.0204	0.0908	-0.2375	-0.3689	-0.0307	0.414	0.0639	0.051	0.4203	0.052	0.5033	38.5349	123.2402	108.975
4	1.0104	0.1912	-0.2696	0.1417	-0.1397	0.1469	-0.4539	0.1684	-0.6732	-0.0528	-0.3358	0.6662	0.6669	-1.268	0.6718	0.7576	-0.1842	0.1214	1.8959	-0.2862	1.2096	-55.9058	123.8682	59.4062
5	4.0486	0.0941	1.7679	0.3056	0.1699	0.8271	0.2106	0.4773	-1.0158	-0.3398	0.0461	0.6106	0.4946	-1.306	-0.1174	0.5436	-0.2494	0.0634	1.9358	-0.1716	1.5681	-60.4043	115.0904	58.1451
6	4.4009	-0.6823	0.1484	0.1087	-0.0268	0.0084	-0.0587	0.8504	0.5041	-0.154	-0.3722	0.1709	-0.1422	-0.608	0.3758	0.9342	0.345	-0.3093	2.0962	-0.1673	1.098	-55.4911	122.1453	45.2099
7	1.7561	-0.8503	-0.1733	0.4135	0.081	0.0237	0.2316	0.3431	-0.7059	-0.412	-0.3186	0.9243	0.2521	-1.1482	0.0886	1.1306	-0.2062	-0.4338	1.418	-0.4906	1.7809	-59.0288	109.741	46.5595
8	4.8249	-0.3506	2.2242	5.9269	2.0908	4.2524	0.1505	-0.0356	-0.3862	-0.5027	-0.2572	1.1238	-0.1906	-0.8278	0.2812	0.4393	0.0812	-0.0441	1.1246	-0.004	0.7137	-45.6899	122.7565	51.6277
9	5.3168	-3.7585	0.1583	7.6166	-0.3354	3.9489	0.3429	0.2416	-0.5834	-0.6794	-0.385	1.0851	0.3673	-1.2471	-0.04	0.4904	-0.0865	0.0632	1.0166	-0.0821	0.6621	-45.2257	122.3969	51.9739
10	6.7934	1.1774	2.9035	2.4816	0.2418	3.9773	0.2903	-0.0751	-0.6126	0.3913	0.0236	0.0323	0.7287	-0.4317	-0.1486	0.5945	0.0193	0.123	0.5502	-0.1399	0.5585	-30.6483	120.0172	64.7593
11	3.812	2.9623	-1.5017	2.663	-2.761	7.682	-0.0067	-0.2745	0.259	-0.5391	-0.351	-0.0518	0.2128	0.0067	0.4741	0.6579	-0.0004	0.085	0.5032	-0.1582	0.6221	-32.6608	126.0207	70.7866
12	5.4163	0.3199	1.1123	1.8769	-0.3895	4.5364	-0.3535	0.8746	0.4295	-0.1275	0.3143	0.6153	-0.3055	-0.8335	0.1163	0.5064	0.0805	-0.0163	0.6593	-0.0466	0.5786	-46.1664	123.0204	55.3887
13	0.9028	0.225	1.1095	0.3266	0.7773	2.2952	-0.1047	0.1141	0.0018	-0.0897	0.0117	-0.1166	-0.1998	0.2655	0.0653	0.5634	-0.0634	0.0752	0.523	-0.0106	0.5387	7.2093	155.2139	49.0062
14	1.8237	0.5151	-0.4286	2.0714	-0.4431	1.8642	-0.1247	0.427	0.1279	-0.2302	-0.0046	-0.0616	0.2484	-0.0521	0.0937	0.3876	0.0576	0.0529	0.4479	0.0135	0.5077	-13.9858	152.3802	51.4089
15	0.3306	0.3153	-0.0748	0.6013	0.4829	1.0701	-0.0297	-0.1135	0.1491	0.1518	-0.1367	0.1454	0.0448	0.0139	0.1392	0.3677	0.0373	0.0612	0.2892	-0.0012	0.3913	-13.1118	154.1961	73.2089
16	1.4975	-0.0621	0.1635	0.6489	0.087	0.8625	-0.1953	0.1948	-0.1796	-0.1096	0.0604	0.0062	0.1285	-0.0921	0.104	0.5783	-0.0419	0.1241	0.3825	-0.0724	0.5025	-13.1695	129.5775	57.7057
17	2.8307	0.336	-0.5018	0.4265	-0.0053	2.1597	-0.4387	-0.0254	-0.4596	0.1254	0.1805	-0.347	0.4202	0.1422	0.1441	0.6325	0.0952	0.1606	0.4003	-0.1124	0.6205	10.7888	125.4045	53.6116
18	3.0748	0.9529	0.1721	1.0398	0.4317	2.9754	-0.1397	0.4644	-0.3191	-0.107	0.2046	-0.01	-0.0833	0.5573	-0.0058	0.4216	0.0164	0.0759	0.5297	0.0085	0.4495	16.9758	140.7495	47.008
19	1.7796	0.3765	0.0098	0.9709	-0.2207	1.0516	-0.015	-0.072	-0.2517	0.0801	-0.089	-0.1323	0.1306	0.3305	0.1068	0.3749	0.0989	0.0475	0.4444	0.0209	0.4387	14.1014	139.0198	79.9423
20	1.8034	-0.2116	-0.7275	1.5788	-0.5594	1.9946	0.0181	-0.0994	0.0242	0.0245	0.1036	-0.1495	0.0034	0.3738	-0.0874	0.4301	0.0332	0.0377	0.3977	-0.0528	0.4425	9.2462	155.7598	83.3871
21	2.5714	-2.1963	-0.7659	2.3066	0.3894	0.3855	-0.0036	0.2544	-0.3123	0.3032	-0.0459	-1.3103	-0.5304	1.3423	0.0309	0.6913	-0.239	-0.0597	1.9649	-0.0204	1.1318	102.1544	140.7744	131.7949
22	9.3331	-3.9087	3.4093	1.6434	-1.3244	2.5671	0.3429	-0.6493	-0.6531	0.0068	0.1988	0.1943	-0.0084	1.153	-0.5642	0.7966	-0.0846	0.2345	2.2051	-0.0044	1.0933	105.1873	142.1002	118.0066
23	0.0584	0.1955	-0.1019	1.387	-0.3149	0.1782	0.5176	-0.2919	0.5714	0.7226	-0.6035	-1.1203	-0.3091	0.6003	-0.03	1.007	-0.5315	-0.2084	1.9119	-0.2986	1.5124	109.5405	152.9733	126.1572
24	5.1249	-1.0317	0.1433	4.0087	-0.7613	4.5651	-0.3037	-0.0117	0.056	-0.2324	0.0448	-0.9201	-0.419	1.8366	0.1575	0.6721	-0.1966	0.1012	1.1467	-0.0953	0.6629	93.1696	141.6539	119.2341
25	0.4193	0.5054	-0.2144	1.7596	0.5754	0.9805	-0.1847	-0.4862	-1.0311	0.3841	0.2042	-1.338	0.4981	1.977	-0.0608	1.0478	0.0984	-0.0849	1.5787	0.0088	1.1762	100.4574	125.3704	128.0288
26	5.6285	-0.2444	-0.1443	4.3595	1.8183	3.8416	-0.1673	-0.4441	-0.0947	0.1318	0.2046	-0.0161	-0.2518	0.5948	-0.0572	0.4265	-0.0889	0.0007	0.5103	0.0656	0.4393	75.198	137.8489	126.7693
27	3.2353	2.2139	-0.009	1.9812	-0.1046	3.0611	0.014	0.5486	-0.2029	-0.0088	0.9514	-0.5991	-0.5685	0.6347	-1.0823	0.7871	0.0815	0.1025	1.7402	0.0039	1.0325	100.3357	142.941	125.1741

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 41 through 130 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 131 through 317 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 318 through 766 )
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 388 through 407 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 408 through 418 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 419 through 434 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 435 through 447 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 448 through 463 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 464 through 503 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 504 through 537 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 538 through 560 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 561 through 588 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 40 through 130 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 131 through 221 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 222 through 264 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 265 through 388 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 389 through 456 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 457 through 503 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 504 through 697 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 698 through 767 )
21	X-RAY DIFFRACTION	21	chain 'A' and (resid 390 through 422 )
22	X-RAY DIFFRACTION	22	chain 'A' and (resid 423 through 438 )
23	X-RAY DIFFRACTION	23	chain 'A' and (resid 439 through 448 )
24	X-RAY DIFFRACTION	24	chain 'A' and (resid 449 through 492 )
25	X-RAY DIFFRACTION	25	chain 'A' and (resid 493 through 503 )
26	X-RAY DIFFRACTION	26	chain 'A' and (resid 504 through 569 )
27	X-RAY DIFFRACTION	27	chain 'A' and (resid 570 through 590 )

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