9DQX: Western equine encephalitis virus CBA87 VLP

Structure of western equine encephalitis virus CBA87 VLP. Determined by electron microscopy at 3.4 Å resolution. Released 26 Mar 2025.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Western equine encephalitis virus
Chains: 12
Atoms: 30,900
Mol. weight: 443.74 kDa
Ligands: NAG
Released: 26 Mar 2025

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

Secondary structure: helices and β-sheets

9DQX contains 70 α-helices and 383 β-strands across 12 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: 8 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	60
β-strand	12-19	8	61
β-strand	24	1	62
β-strand	27-48	22	61
β-strand	51	1	63
α-helix	56-58	3
β-strand	59-62	4	64
α-helix	67-70	4
β-strand	77-82	6	64
β-strand	87-88	2	65
β-strand	91-92	2	65
β-strand	100-106	7	64
β-strand	110	1	63
β-strand	119-137	19	61
β-strand	140-147	8	61
β-strand	160-163	4	60
β-strand	176-180	5	61
β-strand	183-185	3	61
β-strand	203-205	3	61
β-strand	213-215	3	61
β-strand	219-221	3	66
β-strand	233-235	3	66
α-helix	236-238	3
α-helix	239-245	7
α-helix	256-258	3
β-strand	260-262	3	67
β-strand	267-269	3	67
β-strand	275-281	7	60
β-strand	289	1	62
β-strand	296-303	8	68
β-strand	307	1	69
β-strand	314-322	9	68
β-strand	326-329	4	70
β-strand	330-332	3	71
β-strand	338-339	2	68
β-strand	343-346	4	70
β-strand	351-357	7	68
β-strand	362-366	5	72
β-strand	367-369	3	71
β-strand	375-379	5	72
β-strand	381	1	69
α-helix	382-383	2
β-strand	387-388	2	73
α-helix	398-401	4
α-helix	404-436	33

Chain B: 6 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	14-16	3	97
β-strand	25-27	3	97
β-strand	31-35	5	98
β-strand	42-47	6	98
β-strand	50-53	4	99
β-strand	59-66	8	99
β-strand	76-79	4	99
β-strand	83-86	4	100
β-strand	90	1	100
β-strand	92-97	6	98
β-strand	100-104	5	98
β-strand	108-115	8	100
β-strand	124-130	7	100
β-strand	138	1	101
β-strand	147	1	102
β-strand	150-155	6	103
β-strand	162-169	8	104
β-strand	175	1	105
β-strand	180-183	4	106
β-strand	186-189	4	106
α-helix	192-194	3
β-strand	197-201	5	105
β-strand	207-211	5	105
β-strand	228-230	3	105
β-strand	237-238	2	104
α-helix	244-246	3
β-strand	253-258	6	104
β-strand	261-266	6	103
β-strand	269	1	102
α-helix	271-274	4
β-strand	275-279	5	107
β-strand	282-287	6	107
β-strand	293-299	7	101
β-strand	307-311	5	101
β-strand	315-319	5	107
β-strand	326-330	5	101
α-helix	334-335	2
β-strand	336-338	3	101
β-strand	339-340	2	73
α-helix	352-362	11
α-helix	364-402	39

Chain C: 1 helix, 24 β-strands

Element	Residues	Length	Sheet
β-strand	17-19	3	124
β-strand	24-27	4	124
β-strand	29-31	3	125
β-strand	34-36	3	125
β-strand	44-45	2	124
β-strand	56-58	3	126
β-strand	63-65	3	126
β-strand	67	1	125
β-strand	88	1	127
β-strand	89	1	128
β-strand	95	1	127
β-strand	96-97	2	129
β-strand	102-103	2	129
β-strand	104-105	2	130
α-helix	116	1
β-strand	117-118	2	131
β-strand	119	1	128
β-strand	127-129	3	131
β-strand	132	1	132
β-strand	133	1	133
β-strand	138-139	2	130
β-strand	140	1	133
β-strand	143-146	4	131
β-strand	152-155	4	131
β-strand	161	1	132

Chain D: 9 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	32
β-strand	12-19	8	33
β-strand	27-40	14	33
β-strand	44-49	6	34
β-strand	51	1	35
β-strand	59-62	4	36
β-strand	74-82	9	36
β-strand	87-88	2	37
β-strand	91-92	2	37
β-strand	100-108	9	36
β-strand	110	1	35
β-strand	118-122	5	34
β-strand	127-137	11	33
β-strand	140-147	8	33
β-strand	161-163	3	32
β-strand	177-180	4	34
β-strand	183-185	3	34
β-strand	203-204	2	38
β-strand	205	1	34
β-strand	214-215	2	38
β-strand	220-221	2	39
β-strand	228	1	37
β-strand	233-234	2	39
α-helix	236-238	3
α-helix	239-245	7
α-helix	256-258	3
α-helix	259	1
β-strand	260-262	3	40
β-strand	267-269	3	40
β-strand	275-281	7	32
α-helix	287-289	3
β-strand	302-304	3	41
β-strand	307	1	42
β-strand	314-329	16	41
β-strand	331-332	2	43
β-strand	337-339	3	41
β-strand	343-358	16	41
β-strand	362-368	7	43
β-strand	374-379	6	43
α-helix	380	1
β-strand	381	1	42
α-helix	382-383	2
β-strand	387-388	2	44
α-helix	395-397	3
α-helix	404-436	33

Chain E: 8 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	9	1	74
β-strand	14-16	3	75
β-strand	25-27	3	75
β-strand	31-35	5	76
β-strand	42-47	6	76
β-strand	63-67	5	77
β-strand	75-79	5	77
α-helix	80-82	3
β-strand	83-86	4	78
β-strand	90	1	78
β-strand	92-97	6	76
β-strand	100-104	5	76
β-strand	108-115	8	78
β-strand	117	1	79
β-strand	120	1	79
β-strand	124-130	7	78
β-strand	138	1	80
β-strand	150-155	6	81
β-strand	162-169	8	82
β-strand	175	1	83
β-strand	180-183	4	84
β-strand	186-189	4	84
α-helix	192-194	3
β-strand	197-201	5	83
β-strand	207-211	5	83
β-strand	216	1	84
α-helix	223-225	3
β-strand	227-230	4	83
β-strand	236	1	74
β-strand	237-238	2	82
α-helix	244-246	3
β-strand	253-258	6	82
β-strand	261-266	6	81
α-helix	271-274	4
β-strand	275-279	5	85
β-strand	282-287	6	85
β-strand	293-299	7	80
β-strand	307-311	5	80
β-strand	315-320	6	85
β-strand	326-330	5	80
α-helix	334-335	2
β-strand	336-338	3	80
β-strand	339-340	2	44
α-helix	352-362	11
α-helix	364-401	38

Chain F: 1 helix, 22 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
β-strand	17-19	3	108
β-strand	24-27	4	108
β-strand	29-31	3	109
β-strand	34-36	3	109
β-strand	44-45	2	108
β-strand	56-58	3	110
β-strand	63-65	3	110
β-strand	79	1	111
β-strand	89	1	112
β-strand	97	1	113
β-strand	102	1	113
β-strand	103-105	3	114
β-strand	117-118	2	115
β-strand	119	1	112
β-strand	125	1	111
β-strand	127-129	3	115
β-strand	132	1	116
β-strand	133	1	114
β-strand	138-140	3	114
β-strand	143-146	4	115
β-strand	152-155	4	115
β-strand	161	1	116

Chain G: 10 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	45
β-strand	11-19	9	46
β-strand	24	1	47
β-strand	27-35	9	46
β-strand	37-48	12	48
β-strand	51	1	49
α-helix	57-58	2
β-strand	59-62	4	50
α-helix	68-70	3
β-strand	77-82	6	50
β-strand	87-88	2	51
β-strand	91-92	2	51
β-strand	100-106	7	50
β-strand	110	1	49
α-helix	112-115	4
β-strand	119-129	11	48
β-strand	130-137	8	46
β-strand	140-147	8	46
β-strand	160-163	4	45
β-strand	176-180	5	48
β-strand	183-185	3	48
β-strand	203-204	2	52
β-strand	205	1	48
β-strand	214-215	2	52
β-strand	219-221	3	53
β-strand	233-235	3	53
α-helix	236-238	3
α-helix	239-245	7
α-helix	256-258	3
β-strand	260-262	3	48
β-strand	267-269	3	48
β-strand	275-281	7	45
β-strand	289	1	47
α-helix	290-292	3
β-strand	296-303	8	54
β-strand	307	1	55
β-strand	316-322	7	54
β-strand	326-329	4	56
β-strand	330-332	3	57
β-strand	337-339	3	58
β-strand	343-346	4	56
β-strand	351-354	4	54
β-strand	356-358	3	58
β-strand	362-369	8	57
β-strand	372-379	8	57
β-strand	381	1	55
α-helix	382-383	2
β-strand	387-388	2	59
α-helix	398-401	4
α-helix	404-436	33

Chain H: 8 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	86
β-strand	9	1	87
β-strand	14-16	3	88
β-strand	25-27	3	88
β-strand	31-35	5	89
β-strand	42-47	6	89
β-strand	50-53	4	90
β-strand	59-67	9	90
β-strand	75-79	5	90
α-helix	80-82	3
β-strand	83-86	4	91
β-strand	90	1	91
α-helix	91	1
β-strand	92-97	6	89
β-strand	100-104	5	89
β-strand	108-115	8	91
β-strand	123-130	8	91
β-strand	138	1	92
β-strand	150-155	6	93
β-strand	165-169	5	86
β-strand	171	1	94
β-strand	180-183	4	95
β-strand	186-189	4	95
α-helix	192-194	3
β-strand	197-201	5	96
β-strand	207-211	5	96
α-helix	223-225	3
β-strand	226-230	5	96
β-strand	236	1	87
β-strand	237-238	2	86
β-strand	245	1	94
β-strand	253-256	4	86
β-strand	261-266	6	93
α-helix	271-274	4
β-strand	275-278	4	92
β-strand	283-299	17	92
β-strand	307-319	13	92
β-strand	326-330	5	92
α-helix	334-335	2
β-strand	336-338	3	92
β-strand	339-340	2	59
α-helix	352-362	11
α-helix	364-401	38

4 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	437	Western equine encephalitis virus	P13897
Structural polyprotein	B, E, H, K	protein	406	Western equine encephalitis virus	P13897
Capsid protein	C, F, I, L	protein	163	Western equine encephalitis virus	P13897

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

>9DQX_1 Structural polyprotein (chains A, D, G, J)
FEHATTVPNVPGIPYKALVERAGYAPLNLEITVVSSELTPSTNKEYVTCKFHTVVPSPQV
KCCGSLECKASSKADYTCRVFGGVYPFMWGGAQCFCDSENTQLSEAYVEFAPDCTIDHAV
ALKVHTAALKVGLRIVYGNTTARLDTFVNGVTPGSSRDLKVIAGPISAAFSPFDHKVVIR
KGLVYNYDFPEYGAMNPGAFGDIQASSLDATDIVARTDIRLLKPSVKNIHVPYTQAVSGY
EMWKNNSGRPLQETAPFGCKIEVEPLRATNCAYGHIPISIDIPDAAFVRSSESPTILEVS
CTVADCIYSADFGGSLTLQYKANREGHCPVHSHSTTAVLKEATTHVTATGSITLHFSTSS
PQANFIVSLCGKKTTCNAECKPPADHIIGEPHKVDQEFQAAVSKTSWNWLLALFGGASSL
IVVGLIVLVCSSMLINT

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

>9DQX_2 Structural polyprotein (chains B, E, H, K)
SITDDFTLTSPYLGFCPYCRHSAPCFSPIKIENVWDESDDGSIRIQVSAQFGYNQAGTAD
VTKFRYMSYDHDHDIKEDSMEKLAISTSGPCRRLGHKGYFLLAQCPPGDSVTVSITSGAS
ENSCTVEKKIRRKFVGREEYLFPPVHGKLVKCHVYDHLKETSAGYITMHRPGPHAYKSYL
EEASGEVYIKPPSGKNVTYECKCGDYSTGIVSTRTKMNGCTKAKQCIAYKRDQTKWVFNS
PDLIRHTDHSVQGKLHIPFRLTPTVCPVPLAHTPTVTKWFKGITLHLTATRPTLLTTRKL
GLRADATAEWITGTTSRNFSVGREGLEYVWGNHEPVRVWAQESAPGDPHGWPHEIIIHYY
HRHPVYTVIVLCGVALAILVGTASSAACIAKARRDCLTPYALAPNA

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

>9DQX_3 Capsid protein (chains C, F, I, L)
GKRQRMCMKLESDKTFPIMLNGQVNGYACVVGGRLMKPLHVEGKIDNEQLAAVKLKKASM
YDLEYGDVPQNMKSDTLQYTSDKPPGFYNWHHGAVQYENGRFTVPRGVGGKGDSGRPILD
NRGRVVAIVLGGANEGTRTALSVVTWNQKGVTIKDTPEGSEPW

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)
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…
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
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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