7CN8: PCoV_GX spike glycoprotein

Cryo-EM structure of PCoV_GX spike glycoprotein. Determined by electron microscopy at 2.5 Å resolution. Released 3 Mar 2021.

Method: Electron microscopy
Resolution: 2.5 Å
Organism: Pangolin coronavirus
Chains: 3
Atoms: 27,675
Mol. weight: 451.32 kDa
Ligands: NAG, EIC
Released: 3 Mar 2021

Explore 7CN8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7CN8 contains 119 α-helices and 242 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: 39 helices, 80 β-strands

Element	Residues	Length	Sheet
α-helix	25-26	2
β-strand	27-31	5	1
β-strand	36-37	2	2
β-strand	43	1	3
β-strand	48-55	8	4
α-helix	56-57	2
β-strand	60-67	8	1
β-strand	81-83	3	5
β-strand	88-94	7	1
β-strand	99-105	7	5
β-strand	109	1	6
β-strand	114-119	6	5
β-strand	124-129	6	5
β-strand	132	1	6
β-strand	133-142	10	5
β-strand	143-144	2	7
β-strand	149-150	2	7
β-strand	156-158	3	5
β-strand	166-169	4	5
α-helix	170-172	3
β-strand	188-195	8	1
β-strand	198-205	8	1
β-strand	220-221	2	2
β-strand	222-227	6	1
β-strand	235-244	10	5
β-strand	261-267	7	1
β-strand	269-277	9	4
α-helix	278	1
β-strand	283-288	6	4
α-helix	293-301	9
β-strand	309	1	8
β-strand	312	1	9
β-strand	322-326	5	10
β-strand	333	1	11
α-helix	334	1
α-helix	336-340	5
β-strand	347	1	12
β-strand	352-356	5	12
β-strand	359-360	2	11
α-helix	366-369	4
β-strand	374-377	4	12
α-helix	382-387	6
β-strand	389-390	2	11
β-strand	393-401	9	12
α-helix	402-404	3
α-helix	415-419	5
β-strand	429-435	7	12
α-helix	437-440	4
β-strand	446	1	13
β-strand	450-452	3	14
α-helix	458-460	3
α-helix	469-470	2
β-strand	471-472	2	15
β-strand	486-487	2	15
β-strand	490-492	3	14
β-strand	495	1	13
α-helix	501-503	3
β-strand	505-512	8	12
β-strand	522-523	2	11
β-strand	536-541	6	10
β-strand	544-552	9	10
β-strand	563-564	2	10
β-strand	573-575	3	10
β-strand	582-586	5	10
β-strand	594-596	3	9
β-strand	597	1	8
β-strand	607-610	4	9
α-helix	615-617	3
α-helix	618-622	5
α-helix	624-626	3
α-helix	629-635	7
β-strand	641-642	2	9
β-strand	647-649	3	9
β-strand	652-653	2	16
β-strand	658	1	17
β-strand	662-665	4	16
β-strand	668-673	6	16
α-helix	677-679	3
β-strand	685-690	6	16
β-strand	691	1	17
α-helix	692	1
β-strand	696-697	2	18
β-strand	705-709	5	19
β-strand	712-722	11	20
β-strand	727-730	4	21
α-helix	732-737	6
α-helix	747-776	30
β-strand	782-784	3	22
α-helix	785-786	2
α-helix	788	1
β-strand	801	1	23
β-strand	810	1	23
α-helix	811-819	9
α-helix	831-836	6
α-helix	843-849	7
β-strand	852-855	4	21
α-helix	856-857	2
α-helix	861-878	18
α-helix	879-882	4
α-helix	892-902	11
α-helix	907-912	6
α-helix	914-934	21
α-helix	940-959	20
α-helix	971-977	7
α-helix	980-1022	43
α-helix	1023-1027	5
β-strand	1041-1050	10	20
β-strand	1053-1063	11	20
β-strand	1066-1072	7	19
β-strand	1075-1076	2	24
β-strand	1080-1084	5	24
β-strand	1088-1091	4	19
β-strand	1096-1099	4	19
β-strand	1107-1108	2	19
β-strand	1110	1	25
β-strand	1114-1119	6	24
α-helix	1120-1122	3
β-strand	1127-1128	2	24
β-strand	1132	1	25

Chain B: 40 helices, 82 β-strands

Element	Residues	Length	Sheet
α-helix	25-26	2
β-strand	27-31	5	26
β-strand	36-37	2	27
β-strand	43	1	10
β-strand	48-55	8	28
α-helix	56-57	2
β-strand	60-67	8	26
β-strand	81-83	3	29
β-strand	88-94	7	26
β-strand	99-105	7	29
β-strand	109	1	30
β-strand	114-119	6	29
β-strand	124-129	6	29
β-strand	132	1	30
β-strand	133-138	6	31
β-strand	139-142	4	32
β-strand	143-144	2	33
β-strand	149-150	2	33
β-strand	156-158	3	31
β-strand	166-169	4	29
α-helix	170-172	3
β-strand	188-195	8	26
β-strand	198-205	8	26
β-strand	220-221	2	27
β-strand	222-227	6	26
β-strand	235-240	6	29
β-strand	241-244	4	32
β-strand	261-267	7	26
β-strand	269-277	9	28
α-helix	278	1
β-strand	283-288	6	28
α-helix	293-301	9
β-strand	309	1	34
β-strand	312	1	35
β-strand	322-326	5	36
β-strand	333	1	37
α-helix	334	1
α-helix	336-340	5
β-strand	347	1	38
β-strand	352-356	5	38
β-strand	359-360	2	37
α-helix	366-369	4
β-strand	374-377	4	38
α-helix	382-387	6
β-strand	389-390	2	37
β-strand	393-401	9	38
α-helix	402-404	3
α-helix	415-419	5
β-strand	429-435	7	38
α-helix	437-440	4
β-strand	446	1	39
β-strand	450-452	3	40
α-helix	458-460	3
α-helix	469-470	2
β-strand	471-472	2	41
β-strand	486-487	2	41
β-strand	490-492	3	40
β-strand	495	1	39
α-helix	501-503	3
β-strand	505-512	8	38
β-strand	522-523	2	37
β-strand	536-541	6	36
β-strand	544-552	9	36
β-strand	563-564	2	36
β-strand	573-575	3	36
β-strand	582-586	5	36
β-strand	594-596	3	35
β-strand	597	1	34
β-strand	607-610	4	35
α-helix	615-617	3
α-helix	618-622	5
α-helix	624-626	3
α-helix	629-635	7
β-strand	641-642	2	35
β-strand	647-649	3	35
β-strand	652-653	2	42
β-strand	658	1	43
β-strand	662-665	4	42
β-strand	668-673	6	42
α-helix	677-679	3
β-strand	685-690	6	42
β-strand	691	1	43
α-helix	692	1
β-strand	696-698	3	44
β-strand	705-709	5	45
β-strand	712-722	11	46
β-strand	727-730	4	47
α-helix	732-737	6
α-helix	747-776	30
β-strand	782-783	2	18
α-helix	784-786	3
α-helix	788	1
β-strand	801	1	48
β-strand	810	1	48
α-helix	811-819	9
α-helix	831-836	6
α-helix	843-849	7
β-strand	852-855	4	47
α-helix	856-857	2
α-helix	861-878	18
α-helix	879-882	4
α-helix	892-902	11
α-helix	907-912	6
α-helix	914-934	21
α-helix	940-959	20
α-helix	971-977	7
α-helix	980-1022	43
α-helix	1023-1027	5
β-strand	1041-1050	10	46
β-strand	1053-1063	11	46
β-strand	1066-1072	7	45
β-strand	1075-1076	2	49
β-strand	1080-1084	5	49
β-strand	1088-1091	4	45
β-strand	1096-1099	4	45
β-strand	1107-1108	2	45
β-strand	1110	1	50
β-strand	1114-1119	6	49
α-helix	1120-1122	3
β-strand	1127-1128	2	49
α-helix	1130-1131	2
β-strand	1132	1	50

Chain C: 40 helices, 80 β-strands

Element	Residues	Length	Sheet
α-helix	25-26	2
β-strand	27-31	5	51
β-strand	36-37	2	52
β-strand	43	1	36
β-strand	48-55	8	53
α-helix	56-57	2
β-strand	60-67	8	51
β-strand	81-83	3	54
β-strand	88-94	7	51
β-strand	99-105	7	54
β-strand	109	1	55
β-strand	114-119	6	54
β-strand	124-129	6	54
β-strand	132	1	55
β-strand	133-142	10	54
β-strand	143-144	2	56
β-strand	149-150	2	56
β-strand	156-158	3	54
β-strand	166-169	4	54
α-helix	170-172	3
β-strand	188-195	8	51
β-strand	198-205	8	51
β-strand	220-221	2	52
β-strand	222-227	6	51
β-strand	235-244	10	54
β-strand	261-267	7	51
β-strand	269-277	9	53
α-helix	278	1
β-strand	283-288	6	53
α-helix	293-301	9
β-strand	309	1	57
β-strand	312	1	58
β-strand	322-326	5	3
β-strand	333	1	59
α-helix	334	1
α-helix	336-340	5
β-strand	347	1	60
β-strand	352-356	5	60
β-strand	359-360	2	59
α-helix	366-369	4
β-strand	374-377	4	60
α-helix	382-387	6
β-strand	389-390	2	59
β-strand	393-401	9	60
α-helix	402-404	3
α-helix	415-419	5
β-strand	429-435	7	60
α-helix	437-440	4
β-strand	446	1	61
β-strand	450-452	3	62
α-helix	458-460	3
α-helix	469-470	2
β-strand	471-472	2	63
β-strand	486-487	2	63
β-strand	490-492	3	62
β-strand	495	1	61
α-helix	501-503	3
β-strand	505-512	8	60
β-strand	522-523	2	59
β-strand	536-541	6	3
β-strand	544-552	9	3
β-strand	563-564	2	3
β-strand	573-575	3	3
β-strand	582-586	5	3
β-strand	594-596	3	58
β-strand	597	1	57
β-strand	607-610	4	58
α-helix	615-617	3
α-helix	618-622	5
α-helix	624-626	3
α-helix	629-635	7
β-strand	641-642	2	58
β-strand	647-649	3	58
β-strand	652-653	2	64
β-strand	658	1	65
β-strand	662-665	4	64
β-strand	668-673	6	64
α-helix	677-679	3
β-strand	685-690	6	64
β-strand	691	1	65
α-helix	692	1
β-strand	696-698	3	22
β-strand	705-709	5	66
β-strand	712-722	11	67
β-strand	727-730	4	68
α-helix	732-737	6
α-helix	747-776	30
β-strand	782-784	3	44
α-helix	785-786	2
α-helix	788	1
β-strand	801	1	69
β-strand	810	1	69
α-helix	811-819	9
α-helix	831-836	6
α-helix	843-849	7
β-strand	852-855	4	68
α-helix	856-857	2
α-helix	861-878	18
α-helix	879-882	4
α-helix	892-902	11
α-helix	907-912	6
α-helix	914-934	21
α-helix	940-959	20
α-helix	971-977	7
α-helix	980-1022	43
α-helix	1023-1027	5
β-strand	1041-1050	10	67
β-strand	1053-1063	11	67
β-strand	1066-1072	7	66
β-strand	1075-1076	2	70
β-strand	1080-1084	5	70
β-strand	1088-1091	4	66
β-strand	1096-1099	4	66
β-strand	1107-1108	2	66
β-strand	1110	1	71
β-strand	1114-1119	6	70
α-helix	1120-1122	3
β-strand	1127-1128	2	70
α-helix	1130-1131	2
β-strand	1132	1	71

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycoprotein	A, B, C	protein	1295	Pangolin coronavirus	A0A7T8KZF1

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

>7CN8_1 Glycoprotein (chains A, B, C)
MFVFLFVLPLVSSQCVNLTTRTGIPPGYTNSSTRGVYYPDKVFRSSILHLTQDLFLPFFS
NVTWFNTINYQGGFKKFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDARTQSLLIVNN
ATNVVIKVCEFQFCTDPFLGVYYHNNNKTWVENEFRVYSSANNCTFEYISQPFLMDLEGK
QGNFKNLREFVFKNVDGYFKIYSKHTPIDLVRDLPRGFAALEPLVDLPIGINITRFQTLL
ALHRSYLTPGNLESGWTTGAAAYYVGYLQQRTFLLSYNQNGTITDAVDCSLDPLSETKCT
LKSLTVEKGIYQTSNFRVQPTISIVRFPNITNLCPFGEVFNASKFASVYAWNRKRISNCV
ADYSVLYNSTSFSTFKCYGVSPTKLNDLCFTNVYADSFVVKGDEVRQIAPGQTGVIADYN
YKLPDDFTGCVIAWNSVKQDALTGGNYGYLYRLFRKSKLKPFERDISTEIYQAGSTPCNG
QVGLNCYYPLERYGFHPTTGVNYQPFRVVVLSFELLNGPATVCGPKLSTTLVKDKCVNFN
FNGLTGTGVLTTSKKQFLPFQQFGRDISDTTDAVRDPQTLEILDITPCSFGGVSVITPGT
NTSNQVAVLYQDVNCTEVPMAIHAEQLTPAWRVYSAGANVFQTRAGCLVGAEHVNNSYEC
DIPVGAGICASYHSMSSLRSVNQRSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEI
LPVSMTKTSVDCTMYICGDSIECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVK
QIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAA
RDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRF
NGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQL
SSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAA
TKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHEGK
AHFPREGVFVSNGTHWFITQRNFYEPQIITTDNTFVSGSCDVVIGIVNNTVYDPLQPELD
SFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESPIDLQELGKY
EQYIKGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHSAWSHP
QFEKGGGSGGGGSGGSAWSHPQFEKGSDYKDDDDK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	27
EIC	Linoleic acid	C18 H32 O2	3

Primary citation

Bat and pangolin coronavirus spike glycoprotein structures provide insights into SARS-CoV-2 evolution. Zhang, S., Qiao, S., Yu, J. et al. Nat Commun (2021) 12:1607-1607. DOI 10.1038/s41467-021-21767-3 · PubMed

Other PDB entries of the same protein (UniProt A0A7T8KZF1), best resolution first:

8HFX 2.98 Å, Cryo-EM structure of SARS-CoV-2 Omicron BA.1 spike protein in complex with white-tailed…
8UPX 3.4 Å, Omicron-S-MERS-RBD

Browse structure collections

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