9DQV: Western equine encephalitis virus CBA87 VLP

Structure of western equine encephalitis virus CBA87 VLP in complex with human PCDH10 EC1. Determined by electron microscopy at 3.3 Å resolution. Released 26 Mar 2025.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: Western equine encephalitis virus, Homo sapiens
Chains: 16
Atoms: 33,701
Mol. weight: 489.05 kDa
Ligands: NAG
Released: 26 Mar 2025

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

Secondary structure: helices and β-sheets

9DQV contains 91 α-helices and 416 β-strands across 16 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: 11 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	106
β-strand	12-19	8	107
β-strand	27-48	22	107
β-strand	51	1	108
α-helix	56-58	3
β-strand	59-62	4	109
β-strand	77-82	6	109
β-strand	87	1	110
β-strand	92	1	110
β-strand	100-106	7	109
β-strand	110	1	108
α-helix	112-114	3
β-strand	119-137	19	107
β-strand	140-147	8	107
β-strand	148	1	106
β-strand	160-163	4	106
α-helix	164-166	3
β-strand	176-180	5	107
β-strand	183-185	3	107
α-helix	189-191	3
β-strand	203-205	3	107
β-strand	213-215	3	107
β-strand	219-221	3	111
β-strand	233-235	3	111
α-helix	236-238	3
α-helix	239-245	7
α-helix	251-253	3
α-helix	256-258	3
α-helix	259	1
β-strand	260-262	3	107
β-strand	267-269	3	107
β-strand	275-281	7	106
β-strand	296-304	9	112
β-strand	307	1	113
β-strand	315-322	8	112
β-strand	328-329	2	114
β-strand	332	1	115
β-strand	337-339	3	116
β-strand	343-344	2	114
β-strand	351-355	5	112
β-strand	356-358	3	116
β-strand	362	1	117
β-strand	365-369	5	115
β-strand	372-376	5	115
β-strand	379	1	117
β-strand	381	1	113
α-helix	382-383	2
β-strand	387-388	2	118
α-helix	404-433	30

Chain B: 9 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	119
α-helix	6-8	3
β-strand	9	1	120
β-strand	14-16	3	121
β-strand	18	1	122
β-strand	25-27	3	121
β-strand	31-35	5	123
β-strand	42-50	9	123
β-strand	51	1	124
β-strand	63-67	5	124
β-strand	75-79	5	124
α-helix	80-82	3
β-strand	83-86	4	122
β-strand	90	1	122
β-strand	92-104	13	123
β-strand	108-115	8	122
β-strand	124-130	7	122
β-strand	138	1	125
β-strand	150-155	6	126
β-strand	164-169	6	119
β-strand	171	1	127
α-helix	177-179	3
β-strand	180-183	4	128
β-strand	186-189	4	128
β-strand	198-202	5	129
β-strand	206-210	5	129
β-strand	216	1	128
β-strand	226-229	4	129
β-strand	236	1	120
β-strand	237-238	2	119
α-helix	244	1
β-strand	245	1	127
α-helix	246	1
β-strand	253-257	5	119
β-strand	261-266	6	126
α-helix	271-274	4
β-strand	275-278	4	130
β-strand	282-286	5	130
β-strand	293-299	7	125
β-strand	307-311	5	125
β-strand	316-320	5	130
β-strand	326-330	5	125
α-helix	334-335	2
β-strand	336-338	3	125
β-strand	339-340	2	118
α-helix	352-362	11
α-helix	364-397	34

Chain C: 2 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
β-strand	15-19	5	131
β-strand	24-25	2	131
β-strand	26	1	132
β-strand	27-29	3	131
β-strand	31	1	133
β-strand	34	1	133
β-strand	36-38	3	134
β-strand	44-45	2	131
β-strand	56-58	3	134
β-strand	63-65	3	134
α-helix	77-79	3
β-strand	88-90	3	135
β-strand	93-95	3	135
β-strand	96-97	2	136
β-strand	102-103	2	136
β-strand	104	1	137
β-strand	114	1	132
β-strand	117-119	3	138
β-strand	125-132	8	138
β-strand	139	1	137
β-strand	141-146	6	138
β-strand	152-155	4	138
β-strand	161	1	138

Chain D: 7 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	1
α-helix	14	1
β-strand	15-20	6	2
β-strand	26-48	23	2
β-strand	51	1	3
β-strand	59-62	4	4
β-strand	77-82	6	4
β-strand	87-88	2	5
β-strand	91-92	2	5
β-strand	100-106	7	4
β-strand	110	1	3
β-strand	119-137	19	2
β-strand	140-147	8	2
β-strand	154-155	2	1
β-strand	160-163	4	1
β-strand	176-180	5	2
β-strand	183-185	3	2
β-strand	203-204	2	6
β-strand	205	1	2
β-strand	214-215	2	6
β-strand	219-221	3	7
β-strand	233-235	3	7
α-helix	236-238	3
α-helix	239-245	7
β-strand	260-262	3	2
β-strand	267-269	3	2
β-strand	275-281	7	1
β-strand	296-304	9	8
β-strand	307	1	9
β-strand	315-322	8	8
β-strand	326-329	4	10
β-strand	332	1	11
β-strand	337-339	3	12
β-strand	343-346	4	10
β-strand	351-355	5	8
β-strand	356-358	3	12
β-strand	362	1	13
β-strand	365-367	3	11
β-strand	374-376	3	11
β-strand	379	1	13
α-helix	380	1
β-strand	381	1	9
α-helix	382-383	2
β-strand	387-388	2	14
α-helix	398-401	4
α-helix	404-432	29

Chain E: 8 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	15
β-strand	9	1	16
β-strand	14-16	3	17
β-strand	25-27	3	17
β-strand	31-35	5	18
β-strand	42-53	12	18
β-strand	59-67	9	18
β-strand	75-79	5	18
α-helix	80-82	3
β-strand	83-86	4	19
β-strand	90	1	19
β-strand	95-104	10	18
β-strand	108-115	8	19
β-strand	124-130	7	19
β-strand	138	1	20
β-strand	150-155	6	21
β-strand	165-169	5	15
β-strand	171	1	22
α-helix	177-179	3
β-strand	183	1	23
β-strand	186	1	23
β-strand	197-202	6	24
β-strand	206-211	6	24
β-strand	226-230	5	24
β-strand	236	1	16
β-strand	237-238	2	15
α-helix	244	1
β-strand	245	1	22
α-helix	246	1
β-strand	253-256	4	15
β-strand	261-266	6	21
α-helix	271-274	4
β-strand	275-278	4	20
β-strand	282-299	18	20
β-strand	307-320	14	20
β-strand	326-330	5	20
α-helix	334-335	2
β-strand	336-338	3	20
β-strand	339-340	2	14
α-helix	352-362	11
α-helix	364-401	38

Chain F: 3 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
β-strand	15-16	2	25
α-helix	17	1
β-strand	18-20	3	26
β-strand	23-24	2	26
β-strand	28-29	2	25
β-strand	30-31	2	27
β-strand	34-35	2	27
β-strand	44-45	2	26
α-helix	48-50	3
β-strand	56-58	3	28
β-strand	63-65	3	28
β-strand	88-90	3	29
β-strand	93-95	3	29
β-strand	96-97	2	30
β-strand	102-105	4	30
β-strand	116-119	4	29
β-strand	125-129	5	29
β-strand	131-132	2	31
β-strand	138-140	3	30
β-strand	143-145	3	29
β-strand	153-155	3	29
β-strand	161-162	2	31

Chain G: 9 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	32
β-strand	15-19	5	33
β-strand	24	1	34
β-strand	27-48	22	33
β-strand	51	1	35
α-helix	56-58	3
β-strand	59-61	3	36
α-helix	68-70	3
β-strand	77-84	8	36
β-strand	87-88	2	37
β-strand	91-92	2	37
α-helix	97-99	3
β-strand	100-106	7	36
β-strand	110	1	35
β-strand	119-137	19	33
β-strand	140-147	8	33
β-strand	160-163	4	32
α-helix	164-166	3
β-strand	176-180	5	33
β-strand	183-185	3	33
α-helix	189-191	3
β-strand	203-205	3	33
β-strand	213-215	3	33
β-strand	220-221	2	38
β-strand	233-234	2	38
α-helix	236-238	3
α-helix	239-245	7
α-helix	256-258	3
β-strand	260-262	3	33
β-strand	267-269	3	33
β-strand	275-281	7	32
β-strand	289	1	34
β-strand	301-303	3	39
β-strand	307	1	40
β-strand	316-319	4	39
β-strand	326-327	2	41
β-strand	332	1	42
β-strand	337-339	3	43
β-strand	345-346	2	41
β-strand	351-354	4	39
β-strand	356-358	3	43
β-strand	362	1	44
β-strand	365-369	5	42
β-strand	372-376	5	42
β-strand	379	1	44
β-strand	381	1	40
β-strand	387-388	2	45
α-helix	404-432	29

Chain H: 10 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	9	1	46
β-strand	14-16	3	47
β-strand	18	1	48
β-strand	25-27	3	47
β-strand	31-35	5	49
β-strand	42-50	9	49
β-strand	53	1	50
β-strand	59	1	50
β-strand	63-67	5	49
β-strand	75-79	5	49
α-helix	80-82	3
β-strand	83-86	4	48
β-strand	90	1	48
β-strand	92-104	13	49
β-strand	108-115	8	48
β-strand	124-130	7	48
β-strand	138	1	51
β-strand	150-155	6	52
β-strand	165-169	5	53
β-strand	171	1	54
α-helix	177-179	3
β-strand	180-183	4	55
β-strand	186-189	4	55
β-strand	197-202	6	56
β-strand	206-211	6	56
α-helix	223-225	3
β-strand	226-230	5	56
β-strand	236	1	46
β-strand	237-238	2	53
α-helix	244	1
β-strand	245	1	54
α-helix	246	1
β-strand	253-256	4	53
β-strand	261-266	6	52
α-helix	271-274	4
β-strand	275-279	5	57
β-strand	282-287	6	57
β-strand	293-299	7	51
β-strand	307-311	5	51
β-strand	315-319	5	57
β-strand	326-330	5	51
α-helix	334-335	2
β-strand	336-338	3	51
β-strand	339-340	2	45
α-helix	352-362	11
α-helix	364-397	34
α-helix	399-402	4

8 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
Structural polyprotein	A, D, G, J	protein	434	Western equine encephalitis virus	P13897
Structural polyprotein	B, E, H, K	protein	403	Western equine encephalitis virus	P13897
Capsid protein	C, F, I, L	protein	163	Western equine encephalitis virus	P13897
Protocadherin-10	M, N, O, P	protein	103	Homo sapiens	Q9P2E7 (AlphaFold model)

Sequence of entity 1 (A, D, G, J), FASTA

>9DQV_1 Structural polyprotein (chains A, D, G, J)
FEHATTVPNVPGIPYKALVERAGYAPLNLEITVVSSELTPSTNKEYVTCKFHTVVPSPQV
KCCGSLECKASSKADYTCRVFGGVYPFMWGGAQCFCDSENTQLSEAYVEFAPDCTIDHAV
ALKVHTAALKVGLRIVYGNTTARLDTFVNGVTPGSSRDLKVIAGPISAAFSPFDHKVVIR
KGLVYNYDFPEYGAMNPGAFGDIQASSLDATDIVARTDIRLLKPSVKNIHVPYTQAVSGY
EMWKNNSGRPLQETAPFGCKIEVEPLRATNCAYGHIPISIDIPDAAFVRSSESPTILEVS
CTVADCIYSADFGGSLTLQYKANREGHCPVHSHSTTAVLKEATTHVTATGSITLHFSTSS
PQANFIVSLCGKKTTCNAECKPPADHIIGEPHKVDQEFQAAVSKTSWNWLLALFGGASSL
IVVGLIVLVCSSML

Sequence of entity 2 (B, E, H, K), FASTA

>9DQV_2 Structural polyprotein (chains B, E, H, K)
SITDDFTLTSPYLGFCPYCRHSAPCFSPIKIENVWDESDDGSIRIQVSAQFGYNQAGTAD
VTKFRYMSYDHDHDIKEDSMEKLAISTSGPCRRLGHKGYFLLAQCPPGDSVTVSITSGAS
ENSCTVEKKIRRKFVGREEYLFPPVHGKLVKCHVYDHLKETSAGYITMHRPGPHAYKSYL
EEASGEVYIKPPSGKNVTYECKCGDYSTGIVSTRTKMNGCTKAKQCIAYKRDQTKWVFNS
PDLIRHTDHSVQGKLHIPFRLTPTVCPVPLAHTPTVTKWFKGITLHLTATRPTLLTTRKL
GLRADATAEWITGTTSRNFSVGREGLEYVWGNHEPVRVWAQESAPGDPHGWPHEIIIHYY
HRHPVYTVIVLCGVALAILVGTASSAACIAKARRDCLTPYALA

Sequence of entity 3 (C, F, I, L), FASTA

>9DQV_3 Capsid protein (chains C, F, I, L)
GKRQRMCMKLESDKTFPIMLNGQVNGYACVVGGRLMKPLHVEGKIDNEQLAAVKLKKASM
YDLEYGDVPQNMKSDTLQYTSDKPPGFYNWHHGAVQYENGRFTVPRGVGGKGDSGRPILD
NRGRVVAIVLGGANEGTRTALSVVTWNQKGVTIKDTPEGSEPW

Sequence of entity 4 (M, N, O, P), FASTA

>9DQV_4 Protocadherin-10 (chains M, N, O, P)
QLHYTVQEEQEHGTFVGNIAEDLGLDITKLSARGFQTVPNSRTPYLDLNLETGVLYVNEK
IDREQICKQSPSCVLHLEVFLENPLELFQVEIEVLDINDNPPS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	16

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)
9DQY 2.8 Å, Structure of western equine encephalitis virus Imperial 181 VLP in complex with house…
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…
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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