6U7K: Prefusion structure of PEDV spike

Prefusion structure of PEDV spike. Determined by electron microscopy at 3.14 Å resolution. Released 18 Sept 2019.

Method: Electron microscopy
Resolution: 3.14 Å
Organism: Porcine epidemic diarrhea virus (strain CV777)
Chains: 3
Atoms: 25,515
Mol. weight: 475.66 kDa
Ligands: NAG
Released: 18 Sept 2019

Explore 6U7K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6U7K contains 94 α-helices and 199 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: 32 helices, 66 β-strands

Element	Residues	Length	Sheet
β-strand	46-51	6	1
β-strand	75-77	3	2
β-strand	162-166	5	2
β-strand	169-173	5	2
β-strand	177-181	5	2
β-strand	202-204	3	2
β-strand	208-213	6	1
β-strand	223-227	5	1
α-helix	232-234	3
β-strand	241	1	3
α-helix	242	1
α-helix	243-245	3
α-helix	246-248	3
β-strand	260	1	4
β-strand	268-285	18	4
β-strand	291-295	5	5
β-strand	305	1	4
β-strand	306	1	3
β-strand	315-319	5	4
α-helix	323-325	3
β-strand	332-336	5	5
β-strand	341-347	7	5
β-strand	368-376	9	5
β-strand	379-388	10	5
β-strand	394-398	5	4
β-strand	403-405	3	4
β-strand	408-411	4	4
β-strand	416-422	7	5
β-strand	435-451	17	4
β-strand	454-460	7	4
α-helix	464-469	6
β-strand	480-485	6	6
α-helix	494-495	2
β-strand	496-499	4	7
β-strand	507-519	13	8
β-strand	525-533	9	8
β-strand	536	1	8
β-strand	538-540	3	8
β-strand	545-554	10	8
β-strand	562-567	6	8
α-helix	573-576	4
β-strand	581-588	8	8
β-strand	596-603	8	8
β-strand	610-627	18	8
β-strand	640	1	7
β-strand	647-651	5	7
β-strand	654-658	5	7
β-strand	659-663	5	9
β-strand	672-674	3	9
β-strand	680-684	5	9
β-strand	691-695	5	9
β-strand	700-706	7	6
β-strand	709-715	7	6
β-strand	724-727	4	6
β-strand	732-735	4	6
β-strand	744-748	5	10
β-strand	751-754	4	10
β-strand	759-761	3	10
α-helix	762-765	4
β-strand	766	1	11
α-helix	767-769	3
β-strand	778-782	5	12
β-strand	785-795	11	13
β-strand	801-803	3	14
α-helix	805-810	6
α-helix	814-820	7
α-helix	828-848	21
β-strand	851	1	15
α-helix	853-859	7
α-helix	872-875	4
α-helix	893-902	10
α-helix	926-932	7
β-strand	935-937	3	14
α-helix	938-940	3
α-helix	944-956	13
α-helix	968-970	3
α-helix	971-980	10
α-helix	994-1010	17
α-helix	1015-1017	3
α-helix	1020-1023	4
α-helix	1028-1039	12
α-helix	1041-1043	3
α-helix	1044-1051	8
α-helix	1052-1054	3
α-helix	1064-1067	4
α-helix	1073-1115	43
α-helix	1116-1120	5
β-strand	1135-1144	10	13
β-strand	1147-1157	11	13
β-strand	1160-1165	6	12
β-strand	1169-1171	3	16
β-strand	1175-1179	5	16
β-strand	1184-1188	5	12
β-strand	1200-1203	4	12
β-strand	1210	1	12
β-strand	1217-1220	4	16
β-strand	1228-1230	3	16
α-helix	1235-1238	4

Chain B: 33 helices, 65 β-strands

Element	Residues	Length	Sheet
β-strand	46-49	4	17
β-strand	75-77	3	18
β-strand	162-166	5	18
β-strand	169-173	5	18
β-strand	177-181	5	18
β-strand	202-204	3	18
β-strand	209-213	5	17
β-strand	224-227	4	17
α-helix	231-234	4
β-strand	241	1	19
α-helix	242	1
α-helix	243-245	3
α-helix	246-248	3
β-strand	260	1	20
β-strand	268-285	18	20
β-strand	290-295	6	21
β-strand	306	1	19
β-strand	315-318	4	20
α-helix	323-325	3
β-strand	332-336	5	21
β-strand	341-347	7	21
β-strand	368-376	9	21
β-strand	379-388	10	21
α-helix	389	1
β-strand	395-398	4	20
β-strand	403-405	3	20
β-strand	408-411	4	20
β-strand	416-423	8	21
β-strand	435-451	17	20
β-strand	454-460	7	20
α-helix	464-472	9
β-strand	480-485	6	22
α-helix	486-487	2
α-helix	494-495	2
β-strand	496-499	4	23
β-strand	507-519	13	24
β-strand	525-533	9	24
β-strand	536	1	24
β-strand	538-540	3	24
β-strand	545-554	10	24
β-strand	562-567	6	24
α-helix	573-576	4
β-strand	581-588	8	24
β-strand	596-603	8	24
β-strand	610-627	18	24
β-strand	640	1	23
β-strand	647-651	5	23
β-strand	654-658	5	23
β-strand	659-663	5	25
β-strand	672-674	3	25
β-strand	680-684	5	25
β-strand	691-695	5	25
β-strand	700-706	7	22
β-strand	709-715	7	22
β-strand	724-727	4	22
β-strand	732-735	4	22
β-strand	744-748	5	26
β-strand	751-754	4	26
β-strand	759-761	3	26
α-helix	763-765	3
β-strand	766	1	15
α-helix	767-769	3
β-strand	778-782	5	27
β-strand	785-795	11	28
β-strand	801-803	3	29
α-helix	805-810	6
α-helix	814-820	7
α-helix	828-846	19
β-strand	851	1	30
α-helix	853-859	7
α-helix	872-875	4
α-helix	893-903	11
α-helix	915-918	4
α-helix	926-932	7
β-strand	935-937	3	29
α-helix	938-940	3
α-helix	944-956	13
α-helix	968-970	3
α-helix	971-980	10
α-helix	992-1008	17
α-helix	1015-1017	3
α-helix	1020-1023	4
α-helix	1028-1040	13
α-helix	1044-1051	8
α-helix	1064-1069	6
α-helix	1073-1115	43
α-helix	1116-1120	5
β-strand	1135-1144	10	28
β-strand	1147-1157	11	28
β-strand	1160-1166	7	27
β-strand	1169-1171	3	31
β-strand	1175-1179	5	31
β-strand	1184-1188	5	27
β-strand	1200-1203	4	27
β-strand	1210	1	27
β-strand	1217-1220	4	31
β-strand	1228-1230	3	31
α-helix	1235-1238	4

Chain C: 29 helices, 68 β-strands

Element	Residues	Length	Sheet
β-strand	46-51	6	32
β-strand	75-77	3	33
β-strand	162-166	5	33
β-strand	169-173	5	33
β-strand	177-181	5	33
β-strand	202-204	3	33
β-strand	208-213	6	32
β-strand	223-226	4	32
β-strand	241	1	34
α-helix	246-248	3
β-strand	260	1	35
β-strand	268-285	18	35
β-strand	290-295	6	36
β-strand	305	1	35
β-strand	306	1	34
β-strand	315-318	4	35
α-helix	323-325	3
β-strand	332-336	5	36
β-strand	341-347	7	36
β-strand	368-376	9	36
β-strand	379-388	10	36
β-strand	395-398	4	35
β-strand	403-405	3	35
β-strand	408-411	4	35
β-strand	416-423	8	36
β-strand	435-451	17	35
β-strand	454-460	7	35
α-helix	464-471	8
β-strand	480-485	6	37
β-strand	496-499	4	38
β-strand	507	1	39
β-strand	510-519	10	40
β-strand	525-533	9	40
β-strand	536	1	40
β-strand	538-540	3	39
β-strand	545-546	2	39
β-strand	548-552	5	40
β-strand	555	1	40
β-strand	562-567	6	39
α-helix	573-576	4
β-strand	581-588	8	39
β-strand	596-603	8	39
β-strand	610-627	18	39
β-strand	640	1	38
β-strand	646-651	6	38
β-strand	654-663	10	38
β-strand	672-674	3	38
β-strand	680-684	5	38
β-strand	691-695	5	38
β-strand	700-706	7	37
β-strand	709-715	7	37
β-strand	724-727	4	37
β-strand	732-735	4	37
β-strand	744-748	5	41
β-strand	751-754	4	41
β-strand	759-761	3	41
α-helix	762-765	4
β-strand	766	1	30
α-helix	767-769	3
α-helix	771-773	3
β-strand	778-782	5	42
β-strand	785-795	11	43
β-strand	801-803	3	44
α-helix	805-810	6
α-helix	814-820	7
α-helix	826-848	23
β-strand	851	1	11
α-helix	853-859	7
α-helix	872-875	4
α-helix	893-900	8
α-helix	914-917	4
α-helix	926-932	7
β-strand	935-937	3	44
α-helix	938-940	3
α-helix	944-955	12
α-helix	956-959	4
α-helix	968-970	3
α-helix	971-980	10
α-helix	992-1008	17
α-helix	1015-1017	3
α-helix	1020-1023	4
α-helix	1028-1041	14
α-helix	1044-1051	8
α-helix	1064-1068	5
α-helix	1073-1115	43
α-helix	1116-1120	5
β-strand	1135-1144	10	43
β-strand	1147-1157	11	43
β-strand	1160-1165	6	42
β-strand	1169-1171	3	45
β-strand	1175-1179	5	45
β-strand	1184-1188	5	42
β-strand	1200-1203	4	42
β-strand	1210	1	42
β-strand	1217-1220	4	45
β-strand	1228-1230	3	45
α-helix	1235-1238	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein	A, B, C	protein	1399	Porcine epidemic diarrhea virus (strain CV777)	Q91AV1 (AlphaFold model)

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

>6U7K_1 Spike glycoprotein (chains A, B, C)
MRSLIYFWLLLPVLPTLSLPQDVTRCQSTTNFRRFFSKFNVQAPAVVVLGGYLPSMNSSS
WYCGTGIETASGVHGIFLSYIDSGQGFEIGISQEPFDPSGYQLYLHKATNGNTNAIARLR
ICQFPDNKTLGPTVNDVTTGRNCLFNKAIPAYMRDGKDIVVGITWDNDRVTVFADKIYHF
YLKNDWSRVATRCYNRRSCAMQYVYTPTYYMLNVTSAGEDGIYYEPCTANCTGYAANVFA
TDSNGHIPEGFSFNNWFLLSNDSTLLHGKVVSNQPLLVNCLLAIPKIYGLGQFFSFNHTM
DGVCNGAAVDRAPEALRFNINDTSVILAEGSIVLHTALGTNLSFVCSNSSDPHLAIFAIP
LGATEVPYYCFLKVDTYNSTVYKFLAVLPPTVREIVITKYGDVYVNGFGYLHLGLLDAVT
INFTGHGTDDDVSGFWTIASTNFVDALIEVQGTSIQRILYCDDPVSQLKCSQVAFDLDDG
FYPISSRNLLSHEQPISFVTLPSFNDHSFVNITVSAAFGGLSSANLVASDTTINGFSSFC
VDTRQFTITLFYNVTNSYGYVSKSQDSNCPFTLQSVNDYLSFSKFCVSTSLLAGACTIDL
FGYPAFGSGVKLTSLYFQFTKGELITGTPKPLEGITDVSFMTLDVCTKYTIYGFKGEGII
TLTNSSILAGVYYTSDSGQLLAFKNVTSGAVYSVTPCSFSEQAAYVNDDIVGVISSLSNS
TFNNTRELPGFFYHSNDGSNCTEPVLVYSNIGVCKSGSIGYVPSQYGQVKIAPTVTGNIS
IPTNFSMSIRTEYLQLYNTPVSVDCATYVCNGNSRCKQLLTQYTAACKTIESALQLSARL
ESVEVNSMLTISEEALQLATISSFNGDGYNFTNVLGASVYDPASGRVVQKRSVIEDLLFN
KVVTNGLGTVDEDYKRCSNGRSVADLVCAQYYSGVMVLPGVVDAEKLHMYSASLIGGMAL
GGITAAAALPFSYAVQARLNYLALQTDVLQRNQQLLAESFNSAIGNITSAFESVKEAISQ
TSKGLNTVAHALTKVQEVVNSQGSALNQLTVQLQHNFQAISSSIDDIYSRLDILSADVQV
DRLITGRLSALNAFVAQTLTKYTEVQASRKLAQQKVNECVKSQSQRYGFCGGDGEHIFSL
VQAAPQGLLFLHTVLVPGDFVNVLAIAGLCVNGEIALTLREPGLVLFTHELQTYTATEYF
VSSRRMFEPRKPTVSDFVQIESCVVTYVNLTSDQLPDVIPDYIDVNKTLDEILASLPNRT
GPSLPLDVFNATYLNLTGEIADLEQRSESLRNTTEELRSLINNINNTLVDLEWLNRVETG
SGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHSAWSHPQFEKGG
GSGGGGSGGSAWSHPQFEK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	39

Primary citation

The 3.1-Angstrom Cryo-electron Microscopy Structure of the Porcine Epidemic Diarrhea Virus Spike Protein in the Prefusion Conformation. Wrapp, D., McLellan, J.S. J Virol (2019) 93. DOI 10.1128/JVI.00923-19 · PubMed

Other PDB entries of the same protein (UniProt Q91AV1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4J79 1.56 Å, Crystal structure of beta'-COP/PEDVspike complex

Browse structure collections

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