8WLY: Bat WIV1 spike glycoprotein

Cryo-EM structure of bat WIV1 spike glycoprotein. Determined by electron microscopy at 3.96 Å resolution. Released 17 Jul 2024.

Method: Electron microscopy
Resolution: 3.96 Å
Organisms: Bat SARS-like coronavirus WIV1, Enterobacteria phage T6
Chains: 3
Atoms: 22,598
Mol. weight: 433.72 kDa
Ligands: NAG
Released: 17 Jul 2024

Explore 8WLY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8WLY contains 76 α-helices and 193 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: 23 helices, 60 β-strands

Element	Residues	Length	Sheet
β-strand	32-35	4	1
β-strand	41-42	2	2
β-strand	47-49	3	3
β-strand	52-60	9	4
α-helix	61-62	2
β-strand	66-72	7	1
β-strand	81-83	3	5
β-strand	88-94	7	1
β-strand	99-105	7	5
β-strand	114-118	5	5
β-strand	120	1	6
β-strand	123	1	6
β-strand	125-129	5	5
β-strand	139-140	2	7
β-strand	141	1	8
α-helix	142	1
β-strand	148	1	8
α-helix	149-150	2
β-strand	162-165	4	5
α-helix	166-168	3
β-strand	182-191	10	1
β-strand	194-202	9	1
α-helix	211	1
β-strand	216-217	2	2
β-strand	218-224	7	1
β-strand	231-236	6	5
β-strand	237-238	2	7
β-strand	251-257	7	1
β-strand	259-267	9	4
β-strand	273-275	3	4
β-strand	278	1	4
α-helix	283-291	9
β-strand	299-302	4	9
β-strand	526-530	5	10
β-strand	533-537	5	10
β-strand	538-541	4	11
β-strand	552-554	3	11
β-strand	560-564	5	11
α-helix	565	1
β-strand	571-575	5	11
α-helix	576-578	3
β-strand	583-586	4	9
β-strand	596-597	2	9
β-strand	630-631	2	12
β-strand	636-637	2	12
β-strand	638	1	9
β-strand	641-642	2	13
β-strand	651-654	4	13
β-strand	657-662	6	13
β-strand	674-679	6	13
β-strand	684-686	3	14
β-strand	694-711	18	15
β-strand	716-719	4	16
α-helix	721-725	5
α-helix	735-737	3
α-helix	742-765	24
β-strand	770-772	3	17
α-helix	773-775	3
β-strand	779-780	2	18
β-strand	783-784	2	18
α-helix	790-791	2
α-helix	800-808	9
β-strand	841-844	4	16
α-helix	845-846	2
α-helix	850-867	18
α-helix	881-891	11
α-helix	896-922	27
α-helix	929-947	19
α-helix	948-950	3
α-helix	960-966	7
α-helix	969-1011	43
α-helix	1012-1016	5
β-strand	1030-1039	10	15
β-strand	1042-1059	18	15
β-strand	1064-1065	2	19
β-strand	1070-1073	4	19
β-strand	1077-1080	4	20
β-strand	1085-1088	4	20
β-strand	1096	1	20
β-strand	1099	1	21
β-strand	1103-1105	3	19
β-strand	1116-1117	2	19
β-strand	1121	1	21

Chain B: 30 helices, 73 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
β-strand	32-35	4	22
β-strand	38-42	5	23
β-strand	47-48	2	11
β-strand	53-60	8	24
β-strand	66-71	6	22
β-strand	73	1	25
β-strand	76	1	25
β-strand	82-83	2	26
β-strand	88-94	7	22
β-strand	99-105	7	26
β-strand	109-119	11	26
β-strand	123-132	10	26
β-strand	138-141	4	26
β-strand	148-149	2	26
β-strand	162-168	7	26
β-strand	182-191	10	22
β-strand	194-203	10	22
α-helix	210-212	3
β-strand	214-217	4	23
β-strand	218-223	6	22
β-strand	231-238	8	26
β-strand	251-257	7	22
β-strand	259-267	9	24
α-helix	269-271	3
β-strand	273-278	6	24
α-helix	279-281	3
α-helix	283-291	9
β-strand	299-306	8	27
β-strand	313	1	28
α-helix	322	1
β-strand	323	1	29
α-helix	324	1
α-helix	326-330	5
β-strand	342-346	5	30
β-strand	350	1	29
α-helix	353-359	7
β-strand	364-367	4	30
α-helix	373-376	4
β-strand	379-380	2	31
β-strand	381-391	11	30
α-helix	392-395	4
α-helix	405-409	5
β-strand	419-425	7	30
α-helix	427-430	4
β-strand	436	1	32
β-strand	441-442	2	33
α-helix	449-450	2
β-strand	461	1	34
β-strand	476	1	34
β-strand	479-480	2	33
β-strand	484	1	32
β-strand	494-503	10	30
β-strand	511-512	2	31
β-strand	526-530	5	28
β-strand	533-537	5	28
β-strand	538-541	4	35
β-strand	552	1	35
β-strand	553	1	36
β-strand	562-564	3	35
β-strand	571-575	5	35
β-strand	580-586	7	27
β-strand	596-599	4	27
β-strand	629-632	4	27
β-strand	635-638	4	27
β-strand	641-642	2	37
β-strand	651-654	4	37
β-strand	657-660	4	37
β-strand	676-679	4	37
β-strand	684-686	3	38
β-strand	694-711	18	39
β-strand	717-719	3	40
α-helix	720	1
α-helix	734-738	5
α-helix	742-765	24
β-strand	770-772	3	14
α-helix	773-775	3
β-strand	779-780	2	41
β-strand	783-784	2	41
α-helix	790-791	2
α-helix	800-808	9
β-strand	841-843	3	40
α-helix	844-846	3
α-helix	850-867	18
α-helix	868-872	5
α-helix	881-891	11
α-helix	896-901	6
α-helix	903-922	20
α-helix	929-949	21
α-helix	960-966	7
α-helix	969-1011	43
α-helix	1012-1016	5
β-strand	1030-1039	10	39
β-strand	1042-1059	18	39
β-strand	1064-1065	2	42
β-strand	1069-1073	5	42
β-strand	1077-1080	4	39
β-strand	1085-1088	4	39
β-strand	1097	1	39
β-strand	1099	1	43
β-strand	1103-1108	6	42
β-strand	1116-1117	2	42
β-strand	1121	1	43

Chain C: 23 helices, 60 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
β-strand	32-35	4	44
β-strand	41-42	2	45
β-strand	48	1	36
β-strand	52-57	6	46
β-strand	60	1	47
β-strand	66-71	6	44
β-strand	82	1	48
β-strand	88-94	7	44
β-strand	99-105	7	48
β-strand	114-119	6	48
β-strand	123-133	11	48
β-strand	138-141	4	48
β-strand	148-149	2	48
β-strand	154-168	15	48
β-strand	180	1	49
β-strand	182-191	10	44
β-strand	194-202	9	44
β-strand	206	1	49
α-helix	210-212	3
β-strand	216-217	2	45
β-strand	218-223	6	44
β-strand	231-238	8	48
β-strand	252-257	6	44
β-strand	259	1	47
β-strand	262-267	6	46
β-strand	273-278	6	46
α-helix	283-291	9
β-strand	299-300	2	50
α-helix	308-310	3
β-strand	312-315	4	3
β-strand	518	1	3
β-strand	525-530	6	3
β-strand	533-541	9	3
α-helix	545-547	3
β-strand	552-554	3	3
β-strand	560-564	5	3
β-strand	571-575	5	3
α-helix	576-578	3
β-strand	582-586	5	50
β-strand	596-599	4	50
β-strand	629-631	3	50
β-strand	636-638	3	50
β-strand	641-642	2	51
β-strand	651-654	4	51
β-strand	657-661	5	51
β-strand	675-679	5	51
α-helix	680-681	2
β-strand	684-686	3	17
β-strand	694-711	18	52
β-strand	717-719	3	53
α-helix	721-725	5
α-helix	734-738	5
α-helix	742-765	24
β-strand	770-772	3	38
α-helix	773-775	3
β-strand	779-780	2	54
β-strand	783-784	2	54
α-helix	800-809	10
β-strand	841-843	3	53
α-helix	844-846	3
α-helix	850-866	17
α-helix	868-872	5
α-helix	881-892	12
α-helix	896-901	6
α-helix	903-922	20
α-helix	929-947	19
α-helix	960-966	7
α-helix	969-1011	43
α-helix	1012-1016	5
β-strand	1030-1039	10	52
β-strand	1042-1061	20	52
β-strand	1064-1065	2	55
β-strand	1070-1071	2	55
β-strand	1072-1073	2	56
β-strand	1077-1080	4	52
β-strand	1085-1088	4	52
β-strand	1096-1097	2	52
β-strand	1099	1	57
β-strand	1103-1104	2	56
β-strand	1116-1117	2	55
α-helix	1119-1120	2
β-strand	1121	1	57

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein,Fibritin	A, B, C	protein	1271	Bat SARS-like coronavirus WIV1, Enterobacteria phage T6	A0A346FJN8, U5WLK5

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

>8WLY_1 Spike glycoprotein,Fibritin (chains A, B, C)
MKLLVLVFATLVSSYTIEKCLDFDDRTPPANTQFLSSHRGVYYPDDIFRSNVLHLVQDHF
LPFDSNVTRFITFGLNFDNPIIPFKDGIYFAATEKSNVIRGWVFGSTMNNKSQSVIIMNN
STNLVIRACNFELCDNPFFVVLKSNNTQIPSYIFNNAFNCTFEYVSKDFNLDLGEKPGNF
KDLREFVFRNKDGFLHVYSGYQPISAASGLPTGFNALKPIFKLPLGINITNFRTLLTAFP
PRPDYWGTSAAAYFVGYLKPTTFMLKYDENGTITDAVDCSQNPLAELKCSVKSFEIDKGI
YQTSNFRVAPSKEVVRFPNITNLCPFGEVFNATTFPSVYAWERKRISNCVADYSVLYNST
SFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFTGC
VLAWNTRNIDATQTGNYNYKYRSLRHGKLRPFERDISNVPFSPDGKPCTPPAFNCYWPLN
DYGFYITNGIGYQPYRVVVLSFELLNAPATVCGPKLSTDLIKNQCVNFNFNGLTGTGVLT
PSSKRFQPFQQFGRDVSDFTDSVRDPKTSEILDISPCSFGGVSVITPGTNTSSEVAVLYQ
DVNCTDVPVAIHADQLTPSWRVHSTGNNVFQTQAGCLIGAEHVDTSYECDIPIGAGICAS
YHTVSSLRSTSQKSIVAYTMSLGADSSIAYSNNTIAIPTNFSISITTEVMPVSMAKTSVD
CNMYICGDSTECANLLLQYGSFCTQLNRALSGIAVEQDRNTREVFAQVKQMYKTPTLKDF
GGFNFSQILPDPLKPTKRSFIEDLLFNKVTLADAGFMKQYGECLGDINARDLICAQKFNG
LTVLPPLLTDDMIAAYTAALVSGTATAGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLY
ENQKQIANQFNKAISQIQESLTTTSTALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVL
NDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQS
KRVDFCGKGYHLMSFPQAAPHGVVFLHVTYVPSQERNFTTAPAICHEGKAYFPREGVFVF
NGTSWFITQRNFFSPQIITTDNTFVSGSCDVVIGIINNTVYDPLQPELDSFKEELDKYFK
NHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEAP
RDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHSAWSHPQFEKGGGSGGGGSG
GSAWSHPQFEK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	19

Primary citation

Structural determinants of spike infectivity in bat SARS-like coronaviruses RsSHC014 and WIV1. Qiao, S., Wang, X. J Virol (2024) 98:e0034224-e0034224. DOI 10.1128/jvi.00342-24 · PubMed

Other PDB entries of the same protein (UniProt A0A346FJN8), best resolution first:

9VWE 2.06 Å, Cryo-EM structure of RSV pre-F (strain A2) in complex with Fabs 1A2 and 2D10
8ZQ6 2.77 Å, preF6P of RSV glycoprotein
8ZQ7 2.77 Å, Crystal structure of prefusion RSV F protein
9UE3 2.78 Å, The structure of FIPV spike glycoprotein
8WLU 2.87 Å, Cryo-EM structure of bat RsSHC014 spike glycoprotein
8ZPY 2.92 Å, Crystal structure of prefusion F of RSV
9VWF 3.14 Å, Cryo-EM structure of RSV pre-F (strain A2) in complex with Fab 3G12
8ZHE 3.16 Å, SARS-CoV-2 spike trimer (6P) in complex with three R1-26 Fabs
8ZHM 3.39 Å, SARS-CoV-2 spike trimer (6P) in complex with three H18 and three R1-32 Fabs
8ZHD 3.41 Å, SARS-CoV-2 spike trimer (6P) in complex with two R1-26 Fabs
8ZHG 3.51 Å, SARS-CoV-2 spike trimer (6P) in complex with R1-26 Fab, focused refinement of RBD-Fab…
8ZHL 3.96 Å, SARS-CoV-2 spike trimer (6P) in complex with two H18 and two R1-32 Fabs

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