9DQZ: Western equine encephalitis virus McMillan VLP

Structure of western equine encephalitis virus McMillan VLP in complex with human VLDLR. Determined by electron microscopy at 2.9 Å resolution. Released 26 Mar 2025.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Western equine encephalitis virus, Homo sapiens
Chains: 16
Atoms: 33,465
Mol. weight: 478.71 kDa
Ligands: CA, NAG
Released: 26 Mar 2025

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

Secondary structure: helices and β-sheets

9DQZ contains 105 α-helices and 400 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: 12 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	95
β-strand	11-19	9	96
β-strand	24	1	97
β-strand	27-48	22	96
β-strand	51	1	98
α-helix	57-58	2
β-strand	59-62	4	99
β-strand	74-81	8	99
β-strand	83	1	99
β-strand	87-88	2	100
β-strand	91-92	2	100
β-strand	100-108	9	99
β-strand	110	1	98
β-strand	119-137	19	96
β-strand	140-147	8	96
α-helix	152	1
β-strand	153	1	95
α-helix	154	1
β-strand	160-163	4	95
α-helix	164-166	3
β-strand	176-180	5	96
β-strand	183-185	3	96
α-helix	189-191	3
β-strand	203-204	2	101
β-strand	205	1	96
β-strand	214-215	2	101
β-strand	220-221	2	102
β-strand	233-234	2	102
α-helix	236-238	3
α-helix	239-245	7
α-helix	256-258	3
β-strand	260-262	3	96
β-strand	267-269	3	96
β-strand	275-281	7	95
β-strand	289	1	97
β-strand	296-304	9	103
β-strand	307	1	104
β-strand	315-322	8	103
β-strand	326-329	4	105
β-strand	330-332	3	106
β-strand	338-339	2	107
β-strand	343-346	4	105
β-strand	349-355	7	103
β-strand	356-357	2	107
β-strand	362	1	108
β-strand	365-369	5	106
β-strand	374-376	3	106
β-strand	379	1	108
α-helix	380	1
β-strand	381	1	104
α-helix	382-383	2
β-strand	387-388	2	109
α-helix	398-401	4
α-helix	404-437	34

Chain B: 8 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	110
β-strand	9	1	111
β-strand	14-16	3	112
β-strand	25-27	3	112
β-strand	31-35	5	113
β-strand	42-47	6	113
β-strand	51-53	3	114
β-strand	59-66	8	114
β-strand	76-79	4	114
β-strand	83-86	4	115
β-strand	90	1	115
β-strand	92-96	5	113
β-strand	98	1	114
β-strand	101-104	4	113
β-strand	108	1	116
β-strand	111-115	5	115
β-strand	123-126	4	115
β-strand	130	1	116
β-strand	138	1	117
β-strand	150-155	6	118
β-strand	165-169	5	110
β-strand	171	1	119
β-strand	180-183	4	120
β-strand	186-189	4	120
β-strand	197-202	6	121
β-strand	206-211	6	121
β-strand	216	1	120
α-helix	223-225	3
β-strand	229-230	2	121
β-strand	236	1	111
β-strand	237-238	2	110
α-helix	244	1
β-strand	245	1	119
α-helix	246	1
β-strand	253-256	4	110
β-strand	261-266	6	118
α-helix	271-275	5
β-strand	276-279	4	122
β-strand	282-285	4	122
β-strand	293-299	7	117
β-strand	307-311	5	117
β-strand	317-320	4	122
β-strand	326-330	5	117
α-helix	334-335	2
β-strand	336-338	3	117
β-strand	339-340	2	109
α-helix	352-362	11
α-helix	364-401	38
α-helix	407-408	2

Chain C: 3 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	8-11	4
β-strand	16-19	4	123
β-strand	24-28	5	123
β-strand	29-31	3	124
β-strand	34-38	5	124
β-strand	44-45	2	123
α-helix	48-51	4
β-strand	56-57	2	124
β-strand	63-67	5	124
α-helix	68-69	2
β-strand	79	1	125
β-strand	88-90	3	126
β-strand	93-95	3	126
β-strand	96-98	3	127
β-strand	101-105	5	127
β-strand	117-118	2	127
β-strand	119	1	126
β-strand	125	1	125
β-strand	127-133	7	127
β-strand	138-146	9	127
β-strand	152-155	4	127
β-strand	161	1	127

Chain D: 13 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	11-19	9	2
β-strand	24	1	3
β-strand	27-48	22	2
β-strand	51	1	4
α-helix	56-58	3
β-strand	59-62	4	5
β-strand	74-81	8	5
β-strand	87-88	2	6
β-strand	91-92	2	6
β-strand	100-108	9	5
β-strand	110	1	4
α-helix	112-115	4
β-strand	119-137	19	2
β-strand	140-147	8	2
α-helix	153	1
β-strand	154-155	2	1
β-strand	160-163	4	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	7
β-strand	205	1	2
β-strand	214-215	2	7
β-strand	220-221	2	8
α-helix	222-224	3
β-strand	228	1	6
β-strand	233-234	2	8
α-helix	236-238	3
α-helix	239-245	7
α-helix	251-253	3
α-helix	256-258	3
β-strand	260-262	3	2
β-strand	267-269	3	2
β-strand	276-281	6	1
β-strand	289	1	3
β-strand	296-304	9	9
β-strand	307	1	10
β-strand	315-322	8	9
β-strand	326-329	4	11
β-strand	330-332	3	12
β-strand	338-339	2	13
β-strand	343-346	4	11
β-strand	350-355	6	9
β-strand	356-357	2	13
β-strand	362	1	14
β-strand	366-369	4	12
β-strand	374-375	2	12
β-strand	379	1	14
β-strand	381	1	10
α-helix	382-383	2
β-strand	387-388	2	15
α-helix	398-401	4
α-helix	404-437	34

Chain E: 9 helices, 40 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	42-49	8	19
β-strand	50	1	20
β-strand	51	1	19
β-strand	53	1	21
β-strand	59	1	21
β-strand	63-66	4	20
β-strand	76-79	4	20
α-helix	80-82	3
β-strand	83-86	4	22
β-strand	90	1	22
β-strand	92-96	5	19
β-strand	98-104	7	19
β-strand	108-115	8	22
β-strand	123-130	8	22
β-strand	138	1	23
β-strand	150-155	6	24
β-strand	165-169	5	16
β-strand	171	1	25
α-helix	177-179	3
β-strand	180-183	4	26
β-strand	186-189	4	26
β-strand	197-202	6	27
β-strand	206-211	6	27
α-helix	223-225	3
β-strand	226-230	5	27
β-strand	236	1	17
β-strand	237-238	2	16
α-helix	244	1
β-strand	245	1	25
α-helix	246	1
β-strand	253-256	4	16
β-strand	261-266	6	24
α-helix	269-275	7
β-strand	276-279	4	28
β-strand	282-285	4	28
β-strand	293-299	7	23
β-strand	307-311	5	23
β-strand	317-320	4	28
β-strand	326-330	5	23
α-helix	334-335	2
β-strand	336-338	3	23
β-strand	339-340	2	15
α-helix	352-362	11
α-helix	364-401	38

Chain F: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
β-strand	15-19	5	29
β-strand	24-31	8	29
β-strand	34-36	3	29
β-strand	37-38	2	30
β-strand	44-45	2	29
α-helix	54-55	2
β-strand	56-57	2	30
β-strand	63-65	3	30
α-helix	71-73	3
β-strand	79	1	31
β-strand	88-89	2	32
β-strand	94-95	2	32
β-strand	96	1	31
α-helix	98-100	3
β-strand	103	1	31
β-strand	117-119	3	31
β-strand	125-133	9	31
β-strand	140-146	7	31
β-strand	152-155	4	31

Chain G: 11 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	33
β-strand	11	1	34
β-strand	15-19	5	34
β-strand	24	1	35
β-strand	27-48	22	34
β-strand	51	1	36
α-helix	56-58	3
β-strand	59-62	4	37
β-strand	74-81	8	37
β-strand	87-88	2	38
β-strand	91-92	2	38
β-strand	100-108	9	37
β-strand	110	1	36
β-strand	119-137	19	34
β-strand	140-147	8	34
β-strand	153	1	33
β-strand	160-163	4	33
β-strand	176-180	5	34
β-strand	183-185	3	34
α-helix	189-191	3
β-strand	203-205	3	34
β-strand	213-215	3	34
β-strand	220-221	2	39
α-helix	222-224	3
β-strand	228	1	38
β-strand	233-234	2	39
α-helix	236-238	3
α-helix	239-245	7
α-helix	251-253	3
α-helix	256-258	3
β-strand	260-262	3	34
β-strand	267-269	3	34
β-strand	275-281	7	33
β-strand	289	1	35
β-strand	296-303	8	40
β-strand	307	1	41
β-strand	316-322	7	40
β-strand	326-329	4	42
β-strand	330-332	3	43
β-strand	337-339	3	44
β-strand	343-346	4	42
β-strand	349-354	6	40
β-strand	356-358	3	44
β-strand	366-369	4	43
β-strand	372-375	4	43
α-helix	380	1
β-strand	381	1	41
α-helix	382-383	2
β-strand	387-388	2	45
α-helix	398-401	4
α-helix	404-437	34

Chain H: 11 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	42-53	12	49
β-strand	59-67	9	49
β-strand	75-79	5	49
α-helix	80-82	3
β-strand	83-86	4	48
β-strand	90	1	48
α-helix	91	1
β-strand	92-104	13	49
β-strand	108-115	8	48
β-strand	123-130	8	48
β-strand	138	1	50
β-strand	150-155	6	51
β-strand	162-169	8	52
β-strand	171	1	53
α-helix	177-179	3
β-strand	180-183	4	54
β-strand	186-189	4	54
β-strand	197-202	6	55
β-strand	206-211	6	55
β-strand	215-216	2	54
α-helix	223-225	3
β-strand	226	1	55
β-strand	229-230	2	55
β-strand	236	1	46
β-strand	237-238	2	52
α-helix	244	1
β-strand	245	1	53
α-helix	246	1
β-strand	253-258	6	52
β-strand	261-266	6	51
α-helix	271-274	4
β-strand	276-279	4	56
β-strand	282-285	4	56
β-strand	293-299	7	50
β-strand	307-311	5	50
β-strand	317-319	3	56
β-strand	326-330	5	50
α-helix	334-335	2
β-strand	336-338	3	50
β-strand	339-340	2	45
α-helix	352-362	11
α-helix	364-401	38
α-helix	407-408	2

7 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	438	Western equine encephalitis virus	P13897
Structural polyprotein	B, E, H, K	protein	409	Western equine encephalitis virus	P13897
Capsid protein	C, F, I, L	protein	158	Western equine encephalitis virus	P13897
Very low-density lipoprotein receptor	M, N, O, P	protein	78	Homo sapiens	P98155 (AlphaFold model)

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

>9DQZ_1 Structural polyprotein (chains A, D, G, J)
FEHATTVPNVPGIPYKALVERAGYAPLNLEITVVSSELTPSTNKEYVTCKFHTVIPSPQV
KCCGSLECKASSKADYTCRVFGGVYPFMWGGAQCFCDSENTQLSEAYVEFAPDCTIDHAV
ALKVHTAALKVGLRIVYGNTTAHLDTFVNGVTPGSSRDLKVIAGPISAAFSPFDHKVVIR
KGLVYNYDFPEYGAMKPGAFGDIQASSLDATDIVARTDIRLLKPSVKNIHVPYTQAVSGY
EMWKNNSGRPLQETAPFGCKIEVEPLRASNCAYGHIPISIDIPDAAFVRSSESPTILEVS
CTVADCIYSADFGGSLTLQYKADREGHCPVHSHSTTAVLKEATTHVTATGSITLHFSTSS
PQANFIVSLCGKKTTCNAECKPPADHIIGEPHKVDQEFQAAVSKTSWNWLLALFGGASSL
IVVGLIVLVCSSMLINTR

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

>9DQZ_2 Structural polyprotein (chains B, E, H, K)
SITDDFTLTSPYLGFCPYCRHSAPCFSPIKIENVWDESDDGSIRIQVSAQFGYNQAGTAD
VTKFRYMSYDHDHDIKEDSMEKIAISTSGPCRRLGHKGYFLLAQCPPGDSVTVSITSGAS
ENSCTVEKKIRRKFVGREEYLFPPVQGKLVKCHVYDRLKETSAGYITMHRPGPHAYKSYL
KEASGEVYIKPPSGKNVTYECKCGDYSTGIVSTQTKMNGCTKARQCIAYKLDQTKWVFNS
PDLIRHTDHSVQGKLHIPFRLTPTVCPVPLAHTPTVTKWFKGITLHLTATRPTLLTTRKL
GLRADATAEWITGTTSRNFSVGREGLEYVWGNHEPVRVWAQESAPGDPHGWPHEIIIHYY
HRHPVYTVIVLCGVALAILVGTASSAACIAKARRDCLTPYALAPNATVP

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

>9DQZ_3 Capsid protein (chains C, F, I, L)
MCMKLESDKTFPIMLNGQVNGYACVVGGRLMKPLHVEGKIDNEQLAAVKLKKASMYDLEY
GDVPQNMKSDTLQYTSDKPPGFYNWHHGAVQYENGRFTVPRGVGGKGDSGRPILDNRGRV
VAIVLGGANEGTRTALSVVTWNQKGVTIKDTPEGSEPW

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

>9DQZ_4 Very low-density lipoprotein receptor (chains M, N, O, P)
CEPSQFQCTNGRCITLLWKCDGDEDCVDGSDEKNCVKKTCAESDFVCNNGQCVPSRWKCD
GDPDCEDGSDESPEQCHM

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	8
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…
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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