7VPP: 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 2.69 Å resolution. Released 16 Mar 2022.

Method: X-ray diffraction
Resolution: 2.69 Å
Organisms: Sus scrofa, Porcine deltacoronavirus
Chains: 3
Atoms: 15,615
Mol. weight: 227.87 kDa
Ligands: ZN, NAG
Released: 16 Mar 2022

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

Secondary structure: helices and β-sheets

7VPP contains 103 α-helices and 85 β-strands across 3 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: 51 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	66-68	3
α-helix	72-73	2
β-strand	76-87	12	1
β-strand	98-109	12	1
β-strand	115-119	5	2
β-strand	124-125	2	1
β-strand	133-136	4	1
β-strand	145-151	7	2
β-strand	156-161	6	2
α-helix	165-166	2
β-strand	170-180	11	1
β-strand	182	1	3
β-strand	187-195	9	3
β-strand	198-206	9	3
α-helix	212-214	3
β-strand	218	1	2
β-strand	226	1	4
β-strand	227-235	9	1
β-strand	239-242	4	3
α-helix	245	1
β-strand	246	1	5
β-strand	251-252	2	1
β-strand	259-263	5	1
β-strand	264	1	5
α-helix	265-267	3
β-strand	270	1	4
α-helix	272-274	3
β-strand	277-280	4	3
β-strand	283-288	6	6
β-strand	294-299	6	6
α-helix	301-305	5
α-helix	310-326	17
β-strand	335-341	7	6
β-strand	348-349	2	6
β-strand	354-358	5	6
α-helix	359-362	4
α-helix	371-386	16
β-strand	390	1	7
β-strand	394-396	3	7
α-helix	399-401	3
α-helix	403-420	18
α-helix	422-424	3
α-helix	426-429	4
α-helix	430	1
α-helix	431-435	5
α-helix	436-442	7
α-helix	454-456	3
α-helix	460-465	6
α-helix	469	1
α-helix	470-474	5
α-helix	475-485	11
α-helix	488-501	14
β-strand	505-507	3	7
α-helix	509-520	12
α-helix	532-540	9
β-strand	546-551	6	8
β-strand	556-561	6	8
α-helix	573-574	2
β-strand	582-584	3	9
β-strand	586-588	3	10
β-strand	591-592	2	10
β-strand	596-598	3	9
β-strand	603-605	3	8
α-helix	607-609	3
β-strand	617-619	3	10
α-helix	621-623	3
β-strand	628-631	4	8
α-helix	633-645	13
α-helix	652-667	16
α-helix	673-677	5
α-helix	678-685	8
α-helix	689-706	18
α-helix	712-733	22
β-strand	739-740	2	11
α-helix	744-759	16
α-helix	763-778	16
α-helix	787-789	3
α-helix	790-800	11
α-helix	803-814	12
α-helix	819-828	10
α-helix	829-831	3
α-helix	835-844	10
α-helix	853-855	3
α-helix	856-865	10
α-helix	869-878	10
α-helix	881-884	4
α-helix	895-903	9
α-helix	909-921	13
α-helix	928-930	3
α-helix	931-960	30

Chain B: 0 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	308-316	9	12
β-strand	321-328	8	12
β-strand	343-350	8	12
β-strand	353-358	6	11
β-strand	380	1	13
β-strand	388-394	7	11
β-strand	396-399	4	11
β-strand	404	1	11
β-strand	405	1	13

Chain C: 52 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	66-68	3
α-helix	72-73	2
β-strand	76-87	12	14
β-strand	98-109	12	14
β-strand	115-119	5	15
β-strand	124-125	2	14
β-strand	133-136	4	14
α-helix	141-144	4
β-strand	145-151	7	15
β-strand	156-161	6	15
α-helix	165-166	2
β-strand	170-180	11	14
β-strand	187-195	9	16
β-strand	198-206	9	16
α-helix	212-214	3
β-strand	218	1	15
β-strand	226	1	17
β-strand	227-235	9	14
β-strand	239-242	4	16
α-helix	245	1
β-strand	246	1	18
β-strand	251-253	3	14
β-strand	256-263	8	14
β-strand	264	1	18
α-helix	265-268	4
β-strand	270	1	17
α-helix	272-274	3
β-strand	277-280	4	16
β-strand	283-288	6	19
β-strand	294-299	6	19
α-helix	301-305	5
α-helix	310-326	17
β-strand	335-341	7	19
β-strand	348-349	2	19
β-strand	354-358	5	19
α-helix	359-361	3
α-helix	371-387	17
β-strand	390	1	20
β-strand	394-396	3	20
α-helix	399-401	3
α-helix	403-420	18
α-helix	422-424	3
α-helix	426-429	4
α-helix	430	1
α-helix	431-435	5
α-helix	436-442	7
α-helix	454-456	3
α-helix	460-465	6
α-helix	469	1
α-helix	470-474	5
α-helix	475-486	12
α-helix	488-501	14
β-strand	505-507	3	20
α-helix	509-521	13
α-helix	532-540	9
β-strand	546-551	6	21
β-strand	556-561	6	21
β-strand	582-584	3	22
β-strand	586-588	3	23
β-strand	591-592	2	23
β-strand	596-598	3	22
β-strand	603-605	3	21
α-helix	607-609	3
β-strand	617-619	3	23
α-helix	621-623	3
β-strand	628-631	4	21
α-helix	633-643	11
α-helix	647-649	3
α-helix	652-667	16
α-helix	673-677	5
α-helix	678-685	8
α-helix	689-706	18
α-helix	712-733	22
α-helix	744-759	16
α-helix	763-778	16
α-helix	787-789	3
α-helix	790-800	11
α-helix	803-813	11
α-helix	819-828	10
α-helix	829-831	3
α-helix	835-844	10
α-helix	853-855	3
α-helix	856-865	10
α-helix	869-879	11
α-helix	881-885	5
α-helix	895-903	9
α-helix	909-920	12
α-helix	928-930	3
α-helix	931-960	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Aminopeptidase	A, C	protein	911	Sus scrofa	P15145 (AlphaFold model)
Spike protein	B	protein	127	Porcine deltacoronavirus	A0A4P8D758

Sequence of entity 1 (A, C), FASTA

>7VPP_1 Aminopeptidase (chains A, C)
AITLDQSKPWNRYRLPTTLLPDSYNVTLRPYLTPNADGLYIFKGKSIVRFICQEPTDVII
IHSKKLNYTTQGHMVVLRGVGDSQVPEIDRTELVELTEYLVVHLKGSLQPGHMYEMESEF
QGELADDLAGFYRSEYMEGNVKKVLATTQMQSTDARKSFPCFDEPAMKATFNITLIHPNN
LTALSNMPPKGSSTPLAEDPNWSVTEFETTPVMSTYLLAYIVSEFQSVNETAQNGVLIRI
WARPNAIAEGHGMYALNVTGPILNFFANHYNTPYPLPKSDQIALPDFNAGAMENWGLVTY
RENALLFDPQSSSISNKERVVTVIAHELAHQWFGNLVTLAWWNDLWLNEGFASYVEYLGA
DHAEPTWNLKDLIVPGDVYRVMAVDALASSHPLTTPAEEVNTPAQISEMFDSISYSKGAS
VIRMLSNFLTEDLFKEGLASYLHAFAYQNTTYLDLWEHLQKAVDAQTSIRLPDTVRAIMD
RWTLQMGFPVITVDTKTGNISQKHFLLDSESNVTRSSAFDYLWIVPISSIKNGVMQDHYW
LRDVSQAQNDLFKTASDDWVLLNINVTGYFQVNYDEDNWRMIQHQLQTNLSVIPVINRAQ
VIYDSFNLATAHMVPVTLALDNTLFLNGEKEYMPWQAALSSLSYFSLMFDRSEVYGPMKK
YLRKQVEPLFQHFETLTKNWTERPENLMDQYSEINAISTACSNGLPQCENLAKTLFDQWM
SDPENNPIHPNLRSTIYCNAIAQGGQDQWDFAWGQLQQAQLVNEADKLRSALACSNEVWL
LNRYLGYTLNPDLIRKQDATSTINSIASNVIGQPLAWDFVQSNWKKLFQDYGGGSFSFSN
LIQGVTRRFSSEFELQQLEQFKKNNMDVGFGSGTRALEQALEKTKANIKWVKENKEVVLN
WFIEGHHHHHH

Sequence of entity 2 (B), FASTA

>7VPP_2 Spike protein (chains B)
PKLPELEVVQLNISAHMDFGEARLDSVTINGNTSYCVTKPYFRLETNFMCTGCTMNLRTD
TCSFDLSAVNNGMSFSQFCLSTESGACEMKIIVTYVWNYLLRQRLYVTAVEGQTHTGTTS
GHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

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 P15145 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4FKE 1.85 Å, Crystal structure of porcine aminopeptidase-N
6BV0 1.86 Å, Crystal structure of porcine aminopeptidase-N with Arginine
4HOM 1.9 Å, Crystal structure of porcine aminopeptidase-N complexed with substance P
4OU3 1.95 Å, Crystal structure of porcine aminopeptidase N complexed with CNGRCG tumor-homing peptide
4NZ8 2.0 Å, Crystal structure of porcine aminopeptidase-N complexed with cleaved poly-alanine
5LDS 2.0 Å, Structure of the porcine aminopeptidase N ectodomain
6BV1 2.0 Å, Crystal structure of porcine aminopeptidase-N with Aspartic acid
6BV4 2.02 Å, Crystal structure of porcine aminopeptidase-N with Methionine
4FKH 2.05 Å, Crystal structure of porcine aminopeptidase-N complexed with alanine
4NAQ 2.1 Å, Crystal structure of porcine aminopeptidase-N complexed with poly-alanine
6BUY 2.1 Å, Crystal structure of porcine aminopeptidase-N with Glycine
6BV2 2.14 Å, Crystal structure of porcine aminopeptidase-N with Isoleucine

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