9UIO: Western equine encephalitis virus California VLP

CryoEM structure of Western equine encephalitis virus California VLP in complex with VLDLR-LA1-3. Determined by electron microscopy at 3.03 Å resolution. Released 26 Nov 2025.

Method: Electron microscopy
Resolution: 3.03 Å
Organisms: Western equine encephalitis virus, Homo sapiens
Chains: 9
Atoms: 21,591
Mol. weight: 308.37 kDa
Ligands: CA
Released: 26 Nov 2025

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

Secondary structure: helices and β-sheets

9UIO contains 68 α-helices and 238 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: 10 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	1
β-strand	15-19	5	2
β-strand	24	1	3
β-strand	27-31	5	2
β-strand	33-48	16	2
β-strand	51-54	4	4
α-helix	56-58	3
β-strand	59-61	3	4
β-strand	74-81	8	4
β-strand	87-88	2	5
β-strand	91-92	2	5
β-strand	101-110	10	4
α-helix	112-115	4
β-strand	119-137	19	2
β-strand	140-148	9	2
β-strand	154	1	6
β-strand	161	1	6
β-strand	162-163	2	1
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	5
β-strand	233-234	2	8
α-helix	236-238	3
α-helix	239-245	7
α-helix	251-254	4
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	296-302	7	9
β-strand	306	1	10
β-strand	307	1	11
β-strand	314	1	10
β-strand	315-322	8	9
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	9
β-strand	356-358	3	14
β-strand	366-369	4	13
β-strand	374-375	2	13
β-strand	381	1	11
α-helix	382-383	2
β-strand	387-388	2	15
α-helix	404-438	35

Chain B: 9 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	16
α-helix	6-8	3
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	122-130	9	20
β-strand	138	1	21
β-strand	148-155	8	22
β-strand	165-169	5	16
β-strand	175	1	23
α-helix	177-179	3
β-strand	180	1	24
β-strand	189	1	24
β-strand	197-203	7	23
β-strand	205-211	7	23
β-strand	215	1	24
α-helix	223-225	3
β-strand	226-230	5	23
β-strand	236	1	17
β-strand	237-238	2	16
α-helix	244-246	3
β-strand	251-256	6	16
β-strand	261-268	8	22
α-helix	272-274	3
β-strand	275-279	5	21
β-strand	282-299	18	21
β-strand	307-320	14	21
β-strand	326-330	5	21
β-strand	336-338	3	21
β-strand	339-340	2	15
α-helix	352-362	11
α-helix	364-396	33
α-helix	397-401	5

Chain C: 8 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	27
β-strand	14-21	8	28
β-strand	24-32	9	28
β-strand	33-48	16	29
β-strand	51-54	4	30
α-helix	56-58	3
β-strand	59-61	3	30
β-strand	74-81	8	30
β-strand	87-88	2	31
β-strand	91-92	2	31
β-strand	101-110	10	30
α-helix	112-115	4
β-strand	119-133	15	29
β-strand	136-137	2	28
β-strand	140-141	2	28
β-strand	144-147	4	29
β-strand	153-154	2	27
β-strand	161-163	3	27
β-strand	176-180	5	29
β-strand	183-186	4	29
β-strand	203-204	2	32
β-strand	205	1	29
β-strand	214-215	2	32
β-strand	220-221	2	33
α-helix	222-224	3
β-strand	228	1	31
β-strand	233-234	2	33
α-helix	236-238	3
α-helix	239-245	7
α-helix	251-254	4
β-strand	260-262	3	29
β-strand	267-269	3	29
β-strand	275-281	7	27
β-strand	289	1	28
β-strand	296	1	34
β-strand	300-303	4	35
β-strand	307	1	36
β-strand	315-321	7	35
β-strand	322	1	34
β-strand	326-329	4	37
β-strand	330-332	3	38
β-strand	337-339	3	39
β-strand	343-346	4	37
β-strand	349-355	7	35
β-strand	356-358	3	39
β-strand	366-369	4	38
β-strand	373-375	3	38
β-strand	381	1	36
α-helix	382-383	2
β-strand	387-388	2	40
α-helix	404-438	35

Chain D: 9 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	41
α-helix	6-8	3
β-strand	9	1	42
β-strand	14-16	3	43
β-strand	25-27	3	43
β-strand	31-35	5	44
β-strand	42-53	12	44
β-strand	59-67	9	44
β-strand	75-79	5	44
α-helix	80-82	3
β-strand	83-86	4	45
β-strand	90	1	45
β-strand	92-104	13	44
β-strand	108-115	8	45
β-strand	122-130	9	45
β-strand	138	1	46
β-strand	148-155	8	47
β-strand	165-169	5	41
β-strand	175	1	48
α-helix	177-179	3
β-strand	180	1	49
β-strand	189	1	49
β-strand	197-203	7	48
β-strand	205-211	7	48
β-strand	215	1	49
α-helix	223-225	3
β-strand	226-229	4	48
β-strand	236	1	42
β-strand	237-238	2	41
α-helix	244-246	3
β-strand	251-256	6	41
β-strand	261-268	8	47
α-helix	271-274	4
β-strand	275-279	5	46
β-strand	282-299	18	46
β-strand	307-319	13	46
β-strand	326-330	5	46
β-strand	336-338	3	46
β-strand	339-340	2	40
α-helix	352-362	11
α-helix	364-397	34
α-helix	410-413	4

Chain E: 10 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	52
β-strand	15-19	5	53
β-strand	24	1	54
β-strand	27-31	5	53
β-strand	33-48	16	55
β-strand	51-54	4	56
α-helix	56-58	3
β-strand	59-61	3	56
β-strand	74-82	9	56
β-strand	87-88	2	57
β-strand	91-92	2	57
β-strand	101-110	10	56
α-helix	112-115	4
β-strand	119-133	15	55
β-strand	136-137	2	53
β-strand	140-141	2	53
β-strand	144-147	4	55
β-strand	162-163	2	52
α-helix	164-166	3
β-strand	176-180	5	55
β-strand	183-185	3	55
α-helix	189-191	3
β-strand	203-204	2	58
β-strand	205	1	55
β-strand	214-215	2	58
β-strand	220-221	2	59
β-strand	228	1	57
β-strand	233-234	2	59
α-helix	236-238	3
α-helix	239-245	7
α-helix	251-254	4
β-strand	260-262	3	55
β-strand	267-269	3	55
β-strand	275-281	7	52
β-strand	289	1	54
β-strand	296-306	11	60
β-strand	307	1	61
β-strand	314-322	9	60
β-strand	326-329	4	62
β-strand	330-332	3	63
β-strand	337-339	3	60
β-strand	343-346	4	62
β-strand	349-358	10	60
β-strand	366-369	4	63
β-strand	374-375	2	63
α-helix	380	1
β-strand	381	1	61
α-helix	382-383	2
β-strand	387-388	2	64
α-helix	404-438	35

Chain F: 11 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	65
β-strand	9	1	66
β-strand	14-16	3	67
β-strand	25-27	3	67
β-strand	31-35	5	68
β-strand	42-53	12	68
β-strand	59-67	9	68
β-strand	75-79	5	68
α-helix	80-82	3
β-strand	83-86	4	69
β-strand	90	1	69
β-strand	92-104	13	68
β-strand	108-115	8	69
β-strand	123-130	8	69
β-strand	138	1	70
β-strand	148-155	8	71
β-strand	165-169	5	65
α-helix	170-173	4
α-helix	177-179	3
β-strand	180	1	72
β-strand	189	1	72
β-strand	197-203	7	73
β-strand	205-211	7	73
β-strand	215	1	72
α-helix	223-225	3
β-strand	226-229	4	73
β-strand	236	1	66
β-strand	237-238	2	65
α-helix	244-246	3
β-strand	253-256	4	65
β-strand	261-268	8	71
α-helix	271-274	4
β-strand	275-279	5	74
β-strand	282-287	6	74
β-strand	293-299	7	70
β-strand	307-311	5	70
β-strand	315-319	5	74
β-strand	326-330	5	70
β-strand	336-338	3	70
β-strand	339-340	2	64
α-helix	352-362	11
α-helix	364-382	19
α-helix	384-396	13
α-helix	397-401	5
α-helix	410-412	3

Chain R: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	37-39	3	25
β-strand	45-47	3	25
α-helix	48-50	3
β-strand	76-78	3	26
β-strand	84-86	3	26
α-helix	87-89	3

Chain S: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	37-39	3	50
α-helix	40	1
β-strand	45-47	3	50
α-helix	48-50	3
α-helix	71-73	3
β-strand	76-78	3	51
β-strand	84-86	3	51
α-helix	87-89	3
α-helix	101-103	3

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	439	Western equine encephalitis virus	P13897
Spike glycoprotein E2	B, D, F	protein	418	Western equine encephalitis virus	P13897
Very low-density lipoprotein receptor	R, S, T	protein	79	Homo sapiens	P98155 (AlphaFold model)

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

>9UIO_1 Spike glycoprotein E1 (chains A, C, E)
FEHATTVPNVPGIPYKALVERAGYAPLNLEITVVSSELTPSTNKEYVTCKFHTVIPSPQV
KCCGSLECKASSKADYTCRVFGGVYPFMWGGAQCFCDSENTQLSEAYVEFAPDCTIDHAV
ALKVHTAALKVGLRIVYGNTTAHLDTFVNGVTPGSSRDLKVIAGPISAAFSPFDHKVVIR
KGLVYNYDFPEYGAMKPGAFGDIQASSLYATDIVARTDIRLLKPSVKNIHVPYTQAVSGY
EMWKNNSGRPLQETAPFGCKIEVEPLRASNCAYGHIPISIDIPDAAFVRSSESPTILEVS
CTVADCIYSADFGGSLTLQYKADREGHCPVHSHSTTAVLKEATTHVTATGSITLHFSTSS
PQANFIVSLCGKKTTCNAECKPPADHIIGEPHKVDQEFQAAVSKTSWNWLLALFGGASSL
IVVGLIVLVCSSMLINTRR

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

>9UIO_2 Spike glycoprotein E2 (chains B, D, F)
SITDDFTLTSPYLGFCPYCRHSAPCFSPIKIENVWDESDDGSIRIQVSAQFGYNQAGTAD
VTKFRYMSYDHDHDIKEDSMEKIAISTSGPCRRLGHKGYFLLAQCPPGDSVTVSITSGAS
ENSCTVEKKIRRKFVGREEYLFPPVHGKLLKCHIYDHLKETSAGYITMHRPGPHAYKSYL
KEASGEVYIKPPSGKNVTYECKCGDYSTGIVSTQTKMNGCTKARQCIAYTRDQTKWVFNS
PDLIRHTDHSVQGKLHIPFRLTPTVCRVPLAHTPTVTKWFKGITLHLTATRPTLLTTRKL
GLRADATAEWITGTTSRNFSVGREGLEYVWGNHEPVRVWAQESAPGDPHGWPHEIIIHYY
HRHPVYTVIVLCGVALAILVGTASSAACIAKARRDCLTPYALAPNATVPTALAVLCCI

Sequence of entity 3 (R, S, T), FASTA

>9UIO_3 Very low-density lipoprotein receptor (chains R, S, T)
KCEPSQFQCTNGRCITLLWKCDGDEDCVDGSDEKNCVKKTCAESDFVCNNGQCVPSRWKC
DGDPDCEDGSDESPEQCHM

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	6

Primary citation

Structural insights into VLDLR recognition by Western Equine Encephalitis Virus. Liang, S.J., Lou, Z.Y. To be published.

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…
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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