8WLU: Bat RsSHC014 spike glycoprotein

Cryo-EM structure of bat RsSHC014 spike glycoprotein. Determined by electron microscopy at 2.87 Å resolution. Released 17 Jul 2024.

Method: Electron microscopy
Resolution: 2.87 Å
Organisms: Bat SARS-like coronavirus RsSHC014, Enterobacteria phage T6
Chains: 3
Atoms: 27,438
Mol. weight: 446.21 kDa
Ligands: NAG
Released: 17 Jul 2024

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

Secondary structure: helices and β-sheets

8WLU contains 117 α-helices and 233 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, 76 β-strands

Element	Residues	Length	Sheet
α-helix	27-29	3
β-strand	33-36	4	1
β-strand	41-42	2	2
β-strand	52-60	9	3
α-helix	61-62	2
β-strand	65-71	7	1
β-strand	82-83	2	4
β-strand	88-93	6	1
β-strand	99-105	7	4
β-strand	114-119	6	4
β-strand	124-133	10	4
β-strand	138-142	5	4
β-strand	147-149	3	4
α-helix	150	1
β-strand	154-165	12	4
β-strand	180-191	12	1
β-strand	194-206	13	1
α-helix	210-212	3
β-strand	216-217	2	2
β-strand	218-223	6	1
β-strand	231-238	8	4
β-strand	252-257	6	1
β-strand	259-267	9	3
β-strand	273-278	6	3
α-helix	283-290	8
β-strand	299-303	5	5
β-strand	313-316	4	6
β-strand	323	1	7
α-helix	324	1
α-helix	326-330	5
β-strand	342-346	5	8
β-strand	349-350	2	7
α-helix	353-356	4
β-strand	364-367	4	8
α-helix	372-377	6
β-strand	379-380	2	7
β-strand	382-391	10	8
α-helix	392-397	6
α-helix	405-409	5
β-strand	419-425	7	8
α-helix	427-430	4
β-strand	432	1	9
β-strand	436	1	10
β-strand	440-442	3	11
α-helix	448-450	3
β-strand	461	1	12
β-strand	472	1	13
β-strand	475	1	13
β-strand	476	1	12
β-strand	479-481	3	11
β-strand	484	1	10
β-strand	485	1	9
α-helix	490-492	3
β-strand	494-503	10	8
β-strand	511-512	2	7
α-helix	515-517	3
β-strand	525-530	6	6
β-strand	533-541	9	6
β-strand	552-554	3	6
β-strand	560-564	5	6
β-strand	571-575	5	6
β-strand	582-586	5	5
β-strand	596-600	5	5
α-helix	607-610	4
α-helix	613-615	3
α-helix	618-624	7
β-strand	629-632	4	5
β-strand	635-638	4	5
β-strand	641-642	2	14
β-strand	647	1	15
β-strand	651-654	4	14
β-strand	657-660	4	14
α-helix	662	1
β-strand	663	1	16
α-helix	664	1
β-strand	673	1	16
β-strand	676-679	4	14
β-strand	680	1	15
α-helix	681	1
β-strand	684-686	3	17
β-strand	694-711	18	18
β-strand	716-719	4	19
α-helix	721-724	4
α-helix	730-739	10
α-helix	742-765	24
β-strand	770-772	3	20
α-helix	773-775	3
β-strand	779-780	2	21
β-strand	783-784	2	21
α-helix	790-791	2
α-helix	800-808	9
α-helix	832-838	7
β-strand	841-844	4	19
α-helix	845-846	2
α-helix	850-866	17
α-helix	870-872	3
α-helix	881-892	12
α-helix	896-901	6
α-helix	903-922	20
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	18
β-strand	1042-1061	20	18
β-strand	1064-1066	3	22
β-strand	1069-1073	5	22
β-strand	1077-1080	4	18
β-strand	1085-1088	4	18
β-strand	1096	1	18
β-strand	1099	1	23
β-strand	1103-1108	6	22
β-strand	1116-1117	2	22
β-strand	1121	1	23

Chain B: 39 helices, 79 β-strands

Element	Residues	Length	Sheet
α-helix	27-29	3
β-strand	33-36	4	47
β-strand	41-42	2	48
β-strand	52-60	9	49
β-strand	65-71	7	47
β-strand	82-83	2	50
β-strand	88-93	6	47
β-strand	99-105	7	50
β-strand	114-119	6	50
β-strand	124-133	10	50
β-strand	138-142	5	50
β-strand	147-149	3	50
α-helix	150	1
β-strand	154-165	12	50
β-strand	180-191	12	47
β-strand	194-206	13	47
α-helix	210-212	3
β-strand	216-217	2	48
β-strand	218-223	6	47
β-strand	231-238	8	50
β-strand	252-257	6	47
β-strand	259-267	9	49
β-strand	273-278	6	49
α-helix	283-290	8
β-strand	299-303	5	51
β-strand	313-316	4	52
β-strand	323	1	53
α-helix	324	1
α-helix	326-330	5
β-strand	342-346	5	54
β-strand	349-350	2	53
α-helix	353-356	4
β-strand	364-367	4	54
α-helix	372-377	6
β-strand	379-380	2	53
β-strand	382-391	10	54
α-helix	392-397	6
α-helix	405-409	5
β-strand	419-425	7	54
α-helix	427-430	4
β-strand	432	1	55
β-strand	436	1	56
β-strand	440-442	3	57
α-helix	448-450	3
α-helix	459-460	2
β-strand	461	1	58
β-strand	472	1	59
β-strand	475	1	59
β-strand	476	1	58
β-strand	479-481	3	57
β-strand	484	1	56
β-strand	485	1	55
α-helix	490-492	3
β-strand	494-503	10	54
β-strand	511-512	2	53
α-helix	515-517	3
β-strand	525-530	6	52
β-strand	533-541	9	52
β-strand	552-554	3	52
β-strand	560-564	5	52
β-strand	571-575	5	52
β-strand	582-586	5	51
β-strand	596-599	4	51
α-helix	607-610	4
α-helix	613-615	3
α-helix	618-624	7
β-strand	629-632	4	51
β-strand	635-638	4	51
β-strand	641-642	2	60
β-strand	647	1	61
β-strand	651-654	4	60
β-strand	657-660	4	60
α-helix	662	1
β-strand	663	1	62
α-helix	664	1
β-strand	673	1	62
β-strand	676-679	4	60
β-strand	680	1	61
α-helix	681	1
β-strand	684-686	3	42
β-strand	695-711	17	63
β-strand	716-719	4	64
α-helix	721-724	4
α-helix	730-739	10
α-helix	742-765	24
β-strand	770-772	3	17
α-helix	773-775	3
β-strand	779-780	2	65
β-strand	783-784	2	65
β-strand	790	1	66
α-helix	791	1
β-strand	799	1	66
α-helix	800-808	9
α-helix	832-838	7
β-strand	841-844	4	64
α-helix	845-846	2
α-helix	850-866	17
α-helix	870-872	3
α-helix	881-892	12
α-helix	896-901	6
α-helix	903-922	20
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	63
β-strand	1042-1058	17	63
β-strand	1059-1061	3	67
β-strand	1064-1066	3	68
β-strand	1069-1073	5	68
β-strand	1077-1080	4	67
β-strand	1085-1088	4	67
β-strand	1096	1	67
β-strand	1099	1	69
β-strand	1103-1108	6	68
β-strand	1116-1117	2	68
β-strand	1121	1	69

Chain C: 39 helices, 78 β-strands

Element	Residues	Length	Sheet
α-helix	27-29	3
β-strand	33-36	4	24
β-strand	41-42	2	25
β-strand	52-60	9	26
β-strand	65-71	7	24
β-strand	82-83	2	27
β-strand	88-93	6	24
β-strand	99-105	7	27
β-strand	114-119	6	27
β-strand	124-133	10	27
β-strand	138-142	5	27
β-strand	147-149	3	27
α-helix	150	1
β-strand	154-165	12	27
β-strand	180-191	12	24
β-strand	194-206	13	24
α-helix	210-212	3
β-strand	216-217	2	25
β-strand	218-223	6	24
β-strand	231-238	8	27
β-strand	252-257	6	24
β-strand	259-267	9	26
β-strand	273-278	6	26
α-helix	283-290	8
β-strand	299-303	5	28
β-strand	313-316	4	29
β-strand	323	1	30
α-helix	324	1
α-helix	326-330	5
β-strand	342-346	5	31
β-strand	349-350	2	30
α-helix	353-356	4
β-strand	364-367	4	31
α-helix	372-377	6
β-strand	379-380	2	30
β-strand	382-391	10	31
α-helix	392-397	6
α-helix	405-409	5
β-strand	419-425	7	31
α-helix	427-430	4
β-strand	432	1	32
β-strand	436	1	33
β-strand	440-442	3	34
α-helix	448-450	3
α-helix	459-460	2
β-strand	461	1	35
β-strand	472	1	36
β-strand	475	1	36
β-strand	476	1	35
β-strand	479-481	3	34
β-strand	484	1	33
β-strand	485	1	32
α-helix	490-492	3
β-strand	494-503	10	31
β-strand	511-512	2	30
α-helix	515-517	3
β-strand	525-530	6	29
β-strand	533-541	9	29
β-strand	552-554	3	29
β-strand	560-564	5	29
β-strand	571-575	5	29
β-strand	582-586	5	28
β-strand	596-600	5	28
α-helix	607-610	4
α-helix	613-615	3
α-helix	618-624	7
β-strand	629-632	4	28
β-strand	635-638	4	28
β-strand	641-642	2	37
β-strand	647	1	38
β-strand	651-654	4	37
β-strand	657-660	4	37
α-helix	662	1
β-strand	663	1	39
α-helix	664	1
β-strand	673	1	39
β-strand	676-679	4	37
β-strand	680	1	38
α-helix	681	1
β-strand	684-686	3	20
β-strand	694-711	18	40
β-strand	716-719	4	41
α-helix	721-724	4
α-helix	730-739	10
α-helix	742-765	24
β-strand	770-772	3	42
α-helix	773-775	3
β-strand	779-780	2	43
β-strand	783-784	2	43
β-strand	790	1	44
α-helix	791	1
β-strand	799	1	44
α-helix	800-808	9
α-helix	832-838	7
β-strand	841-844	4	41
α-helix	845-846	2
α-helix	850-866	17
α-helix	870-872	3
α-helix	881-892	12
α-helix	896-901	6
α-helix	903-922	20
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	40
β-strand	1042-1061	20	40
β-strand	1064-1066	3	45
β-strand	1069-1073	5	45
β-strand	1077-1080	4	40
β-strand	1085-1088	4	40
β-strand	1096	1	40
β-strand	1099	1	46
β-strand	1103-1108	6	45
β-strand	1116-1117	2	45
β-strand	1121	1	46

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein,Fibritin	A, B, C	protein	1271	Bat SARS-like coronavirus RsSHC014, Enterobacteria phage T6	A0A346FJN8, U5WLK5

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

>8WLU_1 Spike glycoprotein,Fibritin (chains A, B, C)
MKLLVLVFATLVSSYTIEKCLDFDDRTPPANTQFLSSHRGVYYPDDIFRSNVLHLVQDHF
LPFDSNVTRFITFGLNFDNPIIPFRDGIYFAATEKSNVIRGWVFGSTMNNKSQSVIIMNN
STNLVIRACNFELCDNPFFVVLKSNNTQIPSYIFNNAFNCTFEYVSKDFNLDLGEKPGNF
KDLREFVFRNKDGFLHVYSGYQPISAASGLPTGFNALKPIFKLPLGINITNFRTLLTAFP
PRPDYWGTSAAAYFVGYLKPTTFMLKYDENGTITDAVDCSQNPLAELKCSVKSFEIDKGI
YQTSNFRVAPSKEVVRFPNITNLCPFGEVFNATTFPSVYAWERKRISNCVADYSVLYNST
SFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFLGC
VLAWNTNSKDSSTSGNYNYLYRWVRRSKLNPYERDLSNDIYSPGGQSCSAVGPNCYNPLR
PYGFFTTAGVGHQPYRVVVLSFELLNAPATVCGPKLSTDLIKNQCVNFNFNGLTGTGVLT
PSSKRFQPFQQFGRDVSDFTDSVRDPKTSEILDISPCSFGGVSVITPGTNTSSEVAVLYQ
DVNCTDVPVAIHADQLTPSWRVYSTGNNVFQTQAGCLIGAEHVDTSYECDIPIGAGICAS
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	6

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
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…
8WLY 3.96 Å, Cryo-EM structure of bat WIV1 spike glycoprotein
8ZHL 3.96 Å, SARS-CoV-2 spike trimer (6P) in complex with two H18 and two R1-32 Fabs

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