9DQY: Spike glycoprotein E1

Structure of western equine encephalitis virus Imperial 181 VLP in complex with house sparrow PCDH10 EC1. Determined by electron microscopy at 2.8 Å resolution. Released 26 Mar 2025.

Method: Electron microscopy
Resolution: 2.8 Å
Organisms: Western equine encephalitis virus, Passer domesticus
Chains: 9
Atoms: 21,667
Mol. weight: 312.81 kDa
Ligands: NAG
Released: 26 Mar 2025

Explore 9DQY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9DQY contains 69 α-helices and 258 β-strands across 9 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: 9 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	1
β-strand	15-17	3	2
β-strand	24	1	3
β-strand	29-48	20	2
β-strand	51	1	4
β-strand	54	1	5
β-strand	59-62	4	6
β-strand	77-82	6	6
β-strand	87-88	2	7
β-strand	91-92	2	7
β-strand	100-106	7	6
β-strand	107	1	5
β-strand	110	1	4
α-helix	112-115	4
β-strand	119-137	19	2
β-strand	140-147	8	2
β-strand	153-156	4	1
β-strand	159-163	5	1
α-helix	164-166	3
β-strand	176-180	5	2
β-strand	183-185	3	2
α-helix	189-191	3
β-strand	203-204	2	8
β-strand	205	1	2
β-strand	214-215	2	8
β-strand	220-221	2	9
β-strand	233-234	2	9
α-helix	236-238	3
α-helix	239-245	7
α-helix	256-258	3
β-strand	260-262	3	2
β-strand	267-269	3	2
β-strand	275-281	7	1
β-strand	289	1	3
β-strand	296-304	9	10
β-strand	307	1	11
β-strand	315-322	8	10
β-strand	326-329	4	12
β-strand	330-332	3	13
β-strand	337-339	3	14
β-strand	343-346	4	12
β-strand	349-355	7	10
β-strand	356-358	3	14
β-strand	362-369	8	13
β-strand	372-379	8	13
β-strand	381	1	11
α-helix	382-383	2
β-strand	387-388	2	15
α-helix	398-401	4
α-helix	404-433	30

Chain B: 9 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	16
β-strand	9	1	17
β-strand	14-16	3	18
β-strand	25-27	3	18
β-strand	31-35	5	19
β-strand	42-53	12	19
β-strand	59-67	9	19
β-strand	75-79	5	19
α-helix	80-82	3
β-strand	83-86	4	20
β-strand	90	1	20
β-strand	92-104	13	19
β-strand	108-115	8	20
β-strand	123-130	8	20
β-strand	138	1	21
β-strand	150-155	6	22
β-strand	162-169	8	16
β-strand	171	1	23
α-helix	177-179	3
β-strand	180-183	4	24
β-strand	186-189	4	24
β-strand	197-201	5	25
β-strand	202	1	26
β-strand	206	1	26
β-strand	209-211	3	25
β-strand	216	1	24
α-helix	223-225	3
β-strand	226-230	5	25
β-strand	236	1	17
β-strand	237-238	2	16
α-helix	244	1
β-strand	245	1	23
α-helix	246	1
β-strand	253-258	6	16
β-strand	261-266	6	22
α-helix	271-274	4
β-strand	275-279	5	21
β-strand	282-299	18	21
β-strand	307-320	14	21
β-strand	326-330	5	21
α-helix	334-335	2
β-strand	336-338	3	21
β-strand	339-340	2	15
α-helix	352-362	11
α-helix	364-397	34

Chain C: 10 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	27
β-strand	15-19	5	28
β-strand	24	1	29
β-strand	27-48	22	28
β-strand	51	1	30
β-strand	59-61	3	31
β-strand	77-84	8	31
β-strand	87-88	2	32
β-strand	91-92	2	32
β-strand	100-106	7	31
β-strand	110	1	30
α-helix	112-115	4
β-strand	119-137	19	28
β-strand	140-148	9	28
β-strand	153-154	2	27
β-strand	160-163	4	27
α-helix	164-166	3
β-strand	176-180	5	28
β-strand	183-185	3	28
α-helix	189-191	3
β-strand	203-204	2	33
β-strand	205	1	28
β-strand	214-215	2	33
β-strand	220-221	2	34
α-helix	222-224	3
β-strand	233-234	2	34
α-helix	236-238	3
α-helix	239-245	7
α-helix	256-258	3
β-strand	260-262	3	28
β-strand	267-269	3	28
β-strand	275-281	7	27
β-strand	289	1	29
β-strand	296-304	9	35
β-strand	307	1	36
β-strand	314-322	9	35
β-strand	326-329	4	37
β-strand	330-332	3	38
β-strand	334	1	35
β-strand	337-339	3	35
β-strand	343-346	4	37
β-strand	349-358	10	35
β-strand	365-369	5	38
β-strand	372-376	5	38
α-helix	380	1
β-strand	381	1	36
α-helix	382-383	2
β-strand	387-388	2	39
α-helix	404-432	29

Chain D: 9 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	40
β-strand	9	1	41
β-strand	14-16	3	42
β-strand	25-27	3	42
β-strand	31-35	5	43
β-strand	42-47	6	43
β-strand	50-53	4	44
β-strand	59-67	9	44
β-strand	75-79	5	44
α-helix	80-82	3
β-strand	84-86	3	45
β-strand	90	1	45
β-strand	92-97	6	43
β-strand	100-104	5	43
β-strand	108-114	7	45
β-strand	123-130	8	45
β-strand	138	1	46
β-strand	150-155	6	47
β-strand	165-169	5	40
β-strand	171	1	48
α-helix	177-179	3
β-strand	180-183	4	49
β-strand	186-189	4	49
β-strand	197-202	6	50
β-strand	206-211	6	50
β-strand	215-216	2	49
α-helix	223-225	3
β-strand	226-230	5	50
β-strand	236	1	41
β-strand	237-238	2	40
α-helix	244	1
β-strand	245	1	48
α-helix	246	1
β-strand	253-256	4	40
β-strand	261-266	6	47
α-helix	271-274	4
β-strand	275-276	2	51
β-strand	279	1	52
β-strand	282	1	52
β-strand	283-287	5	51
β-strand	293-299	7	46
β-strand	307-311	5	46
β-strand	315-319	5	51
β-strand	326-330	5	46
α-helix	334-335	2
β-strand	336-338	3	46
β-strand	339-340	2	39
α-helix	352-362	11
α-helix	364-397	34

Chain E: 12 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	53
β-strand	12-19	8	54
β-strand	24	1	55
β-strand	27-48	22	54
β-strand	51-54	4	56
α-helix	56-58	3
β-strand	59-61	3	57
β-strand	77-84	8	57
β-strand	87-88	2	58
β-strand	91-92	2	58
β-strand	100-106	7	57
β-strand	107-110	4	56
α-helix	112-115	4
β-strand	119-137	19	54
β-strand	140-148	9	54
α-helix	152	1
β-strand	153	1	53
α-helix	154	1
β-strand	161-163	3	53
β-strand	176-180	5	54
β-strand	183-185	3	54
α-helix	189-191	3
β-strand	203-204	2	59
β-strand	205	1	54
β-strand	214-215	2	59
β-strand	220-221	2	60
α-helix	222-224	3
β-strand	233-234	2	60
α-helix	236-238	3
α-helix	239-245	7
α-helix	256-258	3
β-strand	260-262	3	54
β-strand	267-269	3	54
β-strand	275-281	7	53
β-strand	289	1	55
α-helix	294	1
β-strand	295	1	61
β-strand	299-304	6	62
β-strand	306-307	2	63
β-strand	315-320	6	62
β-strand	323	1	61
β-strand	326-329	4	64
β-strand	330-333	4	65
β-strand	337-339	3	66
β-strand	343-346	4	64
β-strand	350-355	6	62
β-strand	356-358	3	66
β-strand	362-365	4	67
β-strand	366-369	4	65
β-strand	372-373	2	65
β-strand	376-379	4	67
β-strand	380-381	2	63
β-strand	387-388	2	68
α-helix	403	1
α-helix	407-433	27

Chain F: 10 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	69
α-helix	6-8	3
β-strand	9	1	70
β-strand	14-16	3	71
β-strand	25-27	3	71
β-strand	31-35	5	72
β-strand	42-47	6	72
β-strand	50-53	4	73
β-strand	59-67	9	73
β-strand	75-79	5	73
α-helix	80-82	3
β-strand	83-86	4	74
β-strand	90-91	2	74
β-strand	92-97	6	72
β-strand	100-104	5	72
β-strand	108-115	8	74
β-strand	122-130	9	74
β-strand	138	1	75
β-strand	147	1	76
β-strand	150-155	6	77
β-strand	162-169	8	69
β-strand	171	1	78
α-helix	177-179	3
β-strand	180-182	3	79
β-strand	187-189	3	79
β-strand	197-202	6	80
β-strand	206-211	6	80
β-strand	215-217	3	79
α-helix	223-225	3
β-strand	226-230	5	80
β-strand	236	1	70
β-strand	237-238	2	69
α-helix	244	1
β-strand	245	1	78
α-helix	246	1
β-strand	253-258	6	69
β-strand	261-266	6	77
β-strand	269	1	76
α-helix	271-274	4
β-strand	275-279	5	75
β-strand	282-299	18	75
β-strand	307-320	14	75
β-strand	326-330	5	75
α-helix	334-335	2
β-strand	336-338	3	75
β-strand	339-340	2	68
α-helix	352-362	11
α-helix	364-397	34

Chain G: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	81
α-helix	10-11	2
β-strand	15-18	4	82
α-helix	19-23	5
α-helix	27-32	6
β-strand	36-37	2	81
β-strand	46-49	4	82
β-strand	54-57	4	82
α-helix	63-66	4
β-strand	76-81	6	81
β-strand	86-94	9	81

Chain H: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	83
α-helix	10-11	2
β-strand	15-18	4	84
α-helix	19-22	4
β-strand	36-37	2	83
β-strand	46-48	3	84
β-strand	54-57	4	84
α-helix	63-66	4
β-strand	74-81	8	83
β-strand	86-94	9	83

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein E1	A, C, E	protein	434	Western equine encephalitis virus	P13897
Structural polyprotein	B, D, F	protein	401	Western equine encephalitis virus	P13897
Cadherin domain-containing protein	G, H, I	protein	103	Passer domesticus	A0A8C0UQJ6 (AlphaFold model)

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

>9DQY_1 Spike glycoprotein E1 (chains A, C, E)
FEHATTVPNVPGIPYKALVERAGYAPLNLEITVVSSELTPSTNKEYVTCKFHTVIPSPQV
KCCGSLECKASSRADYTCRVFGGVYPFMWGGAQCFCDSENTQLSEAYVEFAPDCTIDHAV
ALKVHTAALKVGLRIVYGNTTAHLDTFVNGVTPGSSRDLKVIAGPISAAFSPFDHKVVIR
KGFVYNYDFPEYGAMKPGAFGDIQASSLDATDIVARTDIRLLKPSVKNIHVPYTQAVSGY
EMWKNNSGRPLQETAPFGCKIEVEPLRASNCAYGHIPISIDIPDAAFVRSSESPTILEVS
CTVADCIYSADFGGSLTLQYKADREGHCPVHSHSTTAVLKEATTHVTAVGSITLHFSTSS
PQANFIVSLCGKKSTCNAECKPPADHIIGEPHKVDQEFQAAVSTTSWNWLLALFGGASSL
IVVGLIVLVCSSML

Sequence of entity 2 (B, D, F), FASTA

>9DQY_2 Structural polyprotein (chains B, D, F)
SITDDFTLTSPYLGFCPYCRHSTPCFSPIKIENVWDESDDGSIRIQVSAQFGYNQAGTAD
VTKFRYMSFDHDHDIKEDSMEKIAISTSGPCRRLGHKGYFLLAQCPPGDSVTVSITSGTA
ENSCTVERKIRRKFVGREEYLLPPIHGKQVKCHVYDHLKETSAGYITMHRPGPHAYKSYL
EEASGEVYIKPPSGKNVTYECKCGDYSTGIVSTRTKINGCTKAKQCIAYKSDQTKWVFNS
PDLIRHTDHSVQGKLHIPFRLTPTVCPVPLAHTPTVMKWFKGITLHLTATRPTLLTTRKL
GLRADATAEWITGTTSRNFSVGREGLEYVWGNHEPVRVWAQESAPGDPHGWPHEIIIHYY
HRHPVYTVIVLCGVALAILVGTASSAACISKARRDCLTPYA

Sequence of entity 3 (G, H, I), FASTA

>9DQY_3 Cadherin domain-containing protein (chains G, H, I)
QLHYTVQEEQEHGTFVGNIAEDLGLDITKLSARRFQTAPNSRSPYLELNLETGVLYVNEK
IDREQICKQSPSCLLHLEVFLENPLELFRVEIEVLDINDNPPS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	12

Primary citation

Molecular basis for shifted receptor recognition by an encephalitic arbovirus. Fan, X., Li, W., Oros, J. et al. Cell (2025) 188:2957-2973.e28. DOI 10.1016/j.cell.2025.03.029 · PubMed

Other PDB entries of the same protein (UniProt P13897), best resolution first:

9L3V 2.53 Å, structure of WEEV strain 71V1658 virus-like particle(3-fold region)
9DQZ 2.9 Å, Structure of western equine encephalitis virus McMillan VLP in complex with human VLDLR
9L41 2.99 Å, Structure of WEEV strain 71V1658 virus-like particles (VLPs) in complex with human…
9UIO 3.03 Å, CryoEM structure of Western equine encephalitis virus California VLP in complex with…
9UIH 3.05 Å, CryoEM structure of Western equine encephalitis virus California VLP
9WSL 3.27 Å, CryoEM structure of Western equine encephalitis virus California VLP in complex with…
9DQV 3.3 Å, Structure of western equine encephalitis virus CBA87 VLP in complex with human PCDH10 EC1
9L1N 3.3 Å, Structure of Western equine encephalitis virus 71V1658 strain VLP in complex with human…
8DEE 3.4 Å, Asymmetric Unit of Western Equine Encephalitis Virus
9DQX 3.4 Å, Structure of western equine encephalitis virus CBA87 VLP
9L99 3.6 Å, Structure of Western equine encephalitis virus McMillan strain in complex with VLDLR LA1-2
8SQN 3.89 Å, CryoEM structure of Western equine encephalitis virus VLP in complex with the chimeric…

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