7VPQ: Deltacoronavirus spike protein

Structures of a deltacoronavirus spike protein bound to porcine and human receptors indicate the risk of virus adaptation to humans. Determined by X-ray diffraction at 3.1 Å resolution. Released 16 Mar 2022.

Method: X-ray diffraction
Resolution: 3.1 Å
Organisms: Homo sapiens, Porcine deltacoronavirus
Chains: 6
Atoms: 24,537
Mol. weight: 361.88 kDa
Ligands: ZN, NAG
Released: 16 Mar 2022

Explore 7VPQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7VPQ contains 146 α-helices and 146 β-strands across 6 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: 48 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	70-72	3
α-helix	76-77	2
β-strand	80-91	12	1
β-strand	102-113	12	1
β-strand	119-123	5	2
β-strand	128-129	2	1
α-helix	130-131	2
β-strand	137-141	5	1
α-helix	147-149	3
β-strand	150-156	7	2
β-strand	161-166	6	2
α-helix	170-171	2
β-strand	175-185	11	1
β-strand	192-200	9	3
β-strand	203-211	9	3
α-helix	217-219	3
β-strand	223	1	2
β-strand	231	1	4
β-strand	232-240	9	1
β-strand	244-246	3	3
β-strand	251	1	5
β-strand	256-258	3	1
β-strand	261-268	8	1
β-strand	269	1	5
β-strand	270-271	2	1
α-helix	272-273	2
β-strand	275	1	4
α-helix	277-279	3
β-strand	283-285	3	3
β-strand	288-293	6	6
β-strand	299-304	6	6
α-helix	306-310	5
α-helix	315-331	17
β-strand	340-346	7	6
β-strand	353-354	2	6
β-strand	359-363	5	6
α-helix	364-366	3
α-helix	376-392	17
β-strand	395	1	7
β-strand	399-401	3	7
α-helix	404-406	3
α-helix	408-425	18
α-helix	427-429	3
α-helix	431-434	4
α-helix	435	1
α-helix	436-440	5
α-helix	441-447	7
α-helix	459-461	3
α-helix	465-470	6
α-helix	474	1
α-helix	475-479	5
α-helix	480-491	12
α-helix	493-506	14
β-strand	510-512	3	7
α-helix	514-527	14
α-helix	536-544	9
β-strand	550-555	6	8
β-strand	560-565	6	8
β-strand	586-588	3	9
β-strand	590-592	3	10
β-strand	595-596	2	10
β-strand	600-602	3	9
β-strand	606-608	3	8
α-helix	610-612	3
β-strand	620-622	3	10
β-strand	631-634	4	8
α-helix	636-640	5
α-helix	655-670	16
α-helix	676-681	6
α-helix	684-688	5
α-helix	692-709	18
α-helix	715-736	22
β-strand	742-744	3	11
α-helix	747-762	16
α-helix	766-780	15
α-helix	790-803	14
α-helix	806-817	12
α-helix	822-831	10
α-helix	832-834	3
α-helix	838-848	11
α-helix	856-858	3
α-helix	859-868	10
α-helix	870-890	21
α-helix	898-906	9
α-helix	912-924	13
α-helix	931-933	3
α-helix	934-962	29

Chain B: 0 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	307	1	12
β-strand	310-316	7	13
β-strand	321-328	8	13
β-strand	331	1	13
β-strand	333-335	3	11
β-strand	342	1	12
β-strand	345-350	6	13
β-strand	353-358	6	11
β-strand	377-379	3	11
β-strand	387-394	8	11
β-strand	396-406	11	11

Chain C: 49 helices, 38 β-strands

Element	Residues	Length	Sheet
α-helix	70-72	3
α-helix	76-77	2
β-strand	80-91	12	14
β-strand	102-113	12	14
β-strand	119-123	5	15
β-strand	128-129	2	14
α-helix	130-131	2
β-strand	137-141	5	14
α-helix	147-149	3
β-strand	150-156	7	15
β-strand	161-166	6	15
α-helix	170-171	2
β-strand	175-185	11	14
β-strand	192-200	9	16
β-strand	203-211	9	16
α-helix	217-219	3
β-strand	223	1	15
β-strand	231	1	17
β-strand	232-240	9	14
β-strand	244-246	3	16
β-strand	251	1	18
β-strand	256-257	2	14
β-strand	264-268	5	14
β-strand	269	1	18
α-helix	270-273	4
β-strand	275	1	17
α-helix	277-279	3
β-strand	283-285	3	16
β-strand	288-293	6	19
β-strand	299-304	6	19
α-helix	306-310	5
α-helix	315-331	17
β-strand	340-346	7	19
β-strand	353-354	2	19
β-strand	359-363	5	19
α-helix	364-366	3
α-helix	376-392	17
β-strand	395	1	20
β-strand	399-401	3	20
α-helix	404-406	3
α-helix	408-425	18
α-helix	427-429	3
α-helix	431-434	4
α-helix	435	1
α-helix	436-440	5
α-helix	441-447	7
α-helix	459-461	3
α-helix	465-470	6
α-helix	474	1
α-helix	475-479	5
α-helix	480-491	12
α-helix	493-506	14
β-strand	510-512	3	20
α-helix	514-527	14
α-helix	536-544	9
β-strand	550-555	6	21
β-strand	560-565	6	21
β-strand	586-588	3	22
β-strand	590-592	3	23
β-strand	595-596	2	23
β-strand	600-602	3	22
β-strand	606-608	3	21
α-helix	610-612	3
β-strand	620-622	3	23
α-helix	624-626	3
β-strand	631-634	4	21
α-helix	636-640	5
α-helix	655-670	16
α-helix	676-681	6
α-helix	684-688	5
α-helix	692-709	18
α-helix	715-736	22
β-strand	743-744	2	24
α-helix	747-762	16
α-helix	766-781	16
α-helix	790-803	14
α-helix	806-817	12
α-helix	822-831	10
α-helix	832-834	3
α-helix	838-848	11
α-helix	856-858	3
α-helix	859-868	10
α-helix	870-890	21
α-helix	900-906	7
α-helix	912-924	13
α-helix	931-933	3
α-helix	934-962	29

Chain D: 0 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	310-316	7	25
β-strand	321-328	8	25
β-strand	335	1	26
β-strand	345-350	6	25
β-strand	353-358	6	24
β-strand	377	1	26
β-strand	378-380	3	24
β-strand	387-394	8	24
β-strand	396-406	11	24

Chain E: 49 helices, 40 β-strands

Element	Residues	Length	Sheet
α-helix	70-72	3
α-helix	76-77	2
β-strand	80-91	12	27
β-strand	102-113	12	27
β-strand	119-123	5	28
β-strand	128-129	2	27
α-helix	130-131	2
β-strand	137-141	5	27
α-helix	147-149	3
β-strand	150-156	7	28
β-strand	161-166	6	28
α-helix	170-171	2
β-strand	175-185	11	27
β-strand	192-200	9	29
β-strand	203-211	9	29
α-helix	217-219	3
β-strand	223	1	28
β-strand	231	1	30
β-strand	232-240	9	27
β-strand	244-246	3	29
β-strand	251	1	31
β-strand	256-258	3	27
β-strand	261-268	8	27
β-strand	269	1	31
α-helix	270-273	4
β-strand	275	1	30
α-helix	277-279	3
β-strand	283-285	3	29
β-strand	288-293	6	32
β-strand	299-304	6	32
α-helix	306-310	5
α-helix	315-331	17
β-strand	340-346	7	32
β-strand	353-354	2	32
β-strand	359-363	5	32
α-helix	364-367	4
α-helix	376-392	17
β-strand	395	1	33
β-strand	399-401	3	33
α-helix	404-406	3
α-helix	408-425	18
α-helix	431-434	4
α-helix	435	1
α-helix	436-440	5
α-helix	441-447	7
α-helix	459-461	3
α-helix	465-470	6
α-helix	474	1
α-helix	475-479	5
α-helix	480-491	12
α-helix	493-506	14
β-strand	510-512	3	33
α-helix	514-528	15
α-helix	536-544	9
β-strand	550	1	34
β-strand	551-555	5	35
β-strand	560-562	3	35
β-strand	565	1	34
β-strand	586-588	3	36
β-strand	590-592	3	37
β-strand	595-596	2	37
β-strand	600-602	3	36
β-strand	606-608	3	35
α-helix	610-612	3
β-strand	620-622	3	37
α-helix	624-626	3
β-strand	631-634	4	35
α-helix	636-641	6
α-helix	655-670	16
α-helix	676-681	6
α-helix	684-688	5
α-helix	692-709	18
α-helix	715-736	22
β-strand	742-744	3	38
α-helix	747-762	16
α-helix	766-781	16
α-helix	790-792	3
α-helix	793-803	11
α-helix	806-817	12
α-helix	822-831	10
α-helix	832-834	3
α-helix	838-848	11
α-helix	856-858	3
α-helix	859-868	10
α-helix	870-890	21
α-helix	898-905	8
α-helix	912-924	13
α-helix	931-933	3
α-helix	934-962	29

Chain F: 0 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	307-316	10	39
β-strand	321-328	8	39
β-strand	335	1	40
β-strand	342-350	9	39
β-strand	353-358	6	38
β-strand	377	1	40
β-strand	378-380	3	38
β-strand	387-394	8	38
β-strand	396-406	11	38

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Aminopeptidase N	A, C, E	protein	909	Homo sapiens	P15144 (AlphaFold model)
Spike protein	B, D, F	protein	127	Porcine deltacoronavirus	A0A4P8D758

Sequence of entity 1 (A, C, E), FASTA

>7VPQ_1 Aminopeptidase N (chains A, C, E)
ATTLDQSKAWNRYRLPNTLKPDSYRVTLRPYLTPNDRGLYVFKGSSTVRFTCKEATDVII
IHSKKLNYTLSQGHRVVLRGVGGSQPPDIDKTELVEPTEYLVVHLKGSLVKDSQYEMDSE
FEGELADDLAGFYRSEYMEGNVRKVVATTQMQAADARKSFPCFDEPAMKAEFNITLIHPK
DLTALSNMLPKGPSTPLPEDPNWNVTEFHTTPKMSTYLLAFIVSEFDYVEKQASNGVLIR
IWARPSAIAAGHGDYALNVTGPILNFFAGHYDTPYPLPKSDQIGLPDFNAGAMENWGLVT
YRENSLLFDPLSSSSSNKERVVTVIAHELAHQWFGNLVTIEWWNDLWLNEGFASYVEYLG
ADYAEPTWNLKDLMVLNDVYRVMAVDALASSHPLSTPASEINTPAQISELFDAISYSKGA
SVLRMLSSFLSEDVFKQGLASYLHTFAYQNTIYLNLWDHLQEAVNNRSIQLPTTVRDIMN
RWTLQMGFPVITVDTSTGTLSQEHFLLDPDSNVTRPSEFNYVWIVPITSIRDGRQQQDYW
LIDVRAQNDLFSTSGNEWVLLNLNVTGYYRVNYDEENWRKIQTQLQRDHSAIPVINRAQI
INDAFNLASAHKVPVTLALNNTLFLIEERQYMPWEAALSSLSYFKLMFDRSEVYGPMKNY
LKKQVTPLFIHFRNNTNNWREIPENLMDQYSEVNAISTACSNGVPECEEMVSGLFKQWME
NPNNNPIHPNLRSTVYCNAIAQGGEEEWDFAWEQFRNATLVNEADKLRAALACSKELWIL
NRYLSYTLNPDLIRKQDATSTIISITNNVIGQGLVWDFVQSNWKKLFNDYGGGSFSFSNL
IQAVTRRFSTEYELQQLEQFKKDNEETGFGSGTRALEQALEKTKANIKWVKENKEVVLQW
FTGHHHHHH

Sequence of entity 2 (B, D, F), FASTA

>7VPQ_2 Spike protein (chains B, D, F)
PKLPELEVVQLNISAHMDFGEARLDSVTINGNTSYCVTKPYFRLETNFMCTGCTMNLRTD
TCSFDLSAVNNGMSFSQFCLSTESGACEMKIIVTYVWNYLLRQRLYVTAVEGQTHTGTTS
GHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	18

Water and common crystallization additives (GOL) are not listed.

Primary citation

Structures of a deltacoronavirus spike protein bound to porcine and human receptors. Ji, W., Peng, Q., Fang, X. et al. Nat Commun (2022) 13:1467-1467. DOI 10.1038/s41467-022-29062-5 · PubMed

Other PDB entries of the same protein (UniProt P15144 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7AEW 1.2 Å, 14-3-3 sigma bound to bis-phosphorylated aminopeptidase N (APN, CD13) via canonical and…
6XWD 1.6 Å, 14-3-3 sigma bound to canonical mono-phosphorylated aminopeptidase N (APN, CD13) binding…
4FYT 1.85 Å, Human aminopeptidase N (CD13) in complex with amastatin
4FYQ 1.9 Å, Human aminopeptidase N (CD13)
4FYR 1.91 Å, Human aminopeptidase N (CD13) in complex with bestatin
4FYS 2.01 Å, Human aminopeptidase N (CD13) in complex with angiotensin IV
6U7G 2.35 Å, HCoV-229E RBD Class V in complex with human APN
5LHD 2.6 Å, Structure of glycosylated human aminopeptidase N
6U7F 2.75 Å, HCoV-229E RBD Class IV in complex with human APN
9CAM 2.96 Å, Aminopeptidase N close state
6U7E 3.0 Å, HCoV-229E RBD Class III in complex with human APN
9CAO 3.14 Å, Aminopeptidase N open state

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