9L41: WEEV strain 71V1658 virus-like particles

Structure of WEEV strain 71V1658 virus-like particles (VLPs) in complex with human PCDH10 extracellular cadherin repeats 1-2 (EC1-EC2)(3-fold region). Determined by electron microscopy at 2.99 Å resolution. Released 27 Aug 2025.

Method: Electron microscopy
Resolution: 2.99 Å
Organisms: Western equine encephalitis virus, Homo sapiens
Chains: 9
Atoms: 22,059
Mol. weight: 314.23 kDa
Released: 27 Aug 2025

Explore 9L41 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9L41 contains 60 α-helices and 246 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.

Chains A, C and E: 7 helices, 40 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	27-48	22	2
β-strand	51-54	4	4
β-strand	59-60	2	5
β-strand	77-81	5	5
β-strand	87-88	2	6
β-strand	91-92	2	6
β-strand	102-106	5	5
β-strand	107-110	4	4
β-strand	119-137	19	2
β-strand	140-147	8	2
β-strand	160-163	4	1
β-strand	176-180	5	2
β-strand	183-186	4	2
β-strand	203-204	2	7
β-strand	205	1	2
β-strand	214-215	2	7
β-strand	220-221	2	8
β-strand	233-234	2	8
α-helix	236-238	3
α-helix	239-245	7
α-helix	251-253	3
β-strand	260-262	3	2
β-strand	267-269	3	2
β-strand	275-281	7	1
α-helix	284-286	3
β-strand	289	1	3
β-strand	301-303	3	9
β-strand	307	1	10
β-strand	316-321	6	9
β-strand	329	1	11
β-strand	330-332	3	12
β-strand	337-339	3	13
β-strand	343	1	11
β-strand	349-354	6	9
β-strand	356-358	3	13
β-strand	362-363	2	14
β-strand	366-369	4	12
β-strand	372-375	4	12
β-strand	378-379	2	14
β-strand	381	1	10
α-helix	382-383	2
β-strand	387-388	2	15
α-helix	399-401	3
α-helix	404-437	34

Chains B, D and F: 9 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	16
α-helix	10-12	3
β-strand	13	1	17
β-strand	18-20	3	18
β-strand	22	1	19
β-strand	29-31	3	18
β-strand	35-39	5	20
β-strand	46-57	12	20
β-strand	63-71	9	20
β-strand	79-83	5	20
α-helix	84-86	3
β-strand	87-90	4	19
β-strand	94	1	19
β-strand	96-108	13	20
β-strand	112-119	8	19
β-strand	126	1	19
β-strand	129-134	6	19
β-strand	142	1	21
β-strand	152-159	8	22
β-strand	169-173	5	16
α-helix	181-183	3
β-strand	184-187	4	23
β-strand	190-193	4	23
α-helix	195	1
β-strand	201-206	6	24
β-strand	210-215	6	24
β-strand	219-221	3	23
β-strand	230-234	5	24
β-strand	240	1	17
β-strand	241-242	2	16
β-strand	257-260	4	16
β-strand	265-272	8	22
α-helix	276-278	3
β-strand	279-283	5	25
β-strand	286-290	5	25
β-strand	293-303	11	21
β-strand	313-317	5	21
β-strand	320-323	4	25
β-strand	330-334	5	21
β-strand	340-342	3	21
β-strand	343-344	2	15
α-helix	356-366	11
α-helix	368-371	4
α-helix	375-404	30
α-helix	414-417	4

Chains R, S and T: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	26
β-strand	18	1	27
α-helix	19-23	5
α-helix	25-26	2
α-helix	30-33	4
β-strand	36-37	2	26
β-strand	54	1	27
α-helix	63-66	4
β-strand	74-80	7	26
β-strand	88-94	7	26

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Structural polyprotein	A, C, E	protein	439	Western equine encephalitis virus	P13897
Structural polyprotein	B, D, F	protein	418	Western equine encephalitis virus	P13897
Protocadherin-10	R, S, T	protein	96	Homo sapiens	Q9P2E7 (AlphaFold model)

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

>9L41_1 Structural polyprotein (chains A, C, E)
FEHATTVPNVPGIPYKALVERAGYAPLNLEITVVSSELTPSTNKEYVTCKFHTVIPSPQV
KCCGSLECKASSKADYTCRVFGGVYPFMWGGAQCFCDSENTQLSEAYVEFAPDCTIDHAV
ALKVHTAALKVGLRIVYGNTTAHLDTFVNGVTPGSSRDLKVIAGPISAAFSPFDHKVVIR
KGLVYNYDFPEYGAMKPGAFGDIQASSLDATDIVARTDIRLLKPSVKNIHVPYTQAVSGY
EMWKNNSGRPLQETAPFGCKIEVEPLRASNCAYGHIPISIDIPDAAFVRSSESPTILEVS
CTVADCIYSADFGGSLTLQYKADREGHCPVHSHSTTAVLKEATTHVTAVGSITLHFSTSS
PQANFIVSLCGKKSTCNAECKPPADHIIGEPHKVDQEFQAAVSKTSWNWLLALFGGASSL
IVVGLIVLVCSSMLINTRR

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

>9L41_2 Structural polyprotein (chains B, D, F)
SITDDFTLTSPYLGFCPYCRHSTPCFSPIKIENVWDESDDGSIRIQVSAQFGYNQAGTAD
VTKFRYMSFDHDHDIKEDSMEKIAISTSGPCRRLGHKGYFLLAQCPPGDSVTVSITSGAS
ENSCTVEKKIRRKFVGREEYLFPPVHGKLVKCHVYDHLKETSAGYITMHRPGPHAYKSYL
EEASGEVYIKPPSGKNVTYECKCGDYSTGIVSTRTKMNGCTKAKQCIAYKSDQTKWVFNS
PDLIRHTDHSVQGKLHIPFRLTPTVCPVPLAHTPTVTKWFKGITLHLTAMRPTLLTTRKL
GLRADATAEWITGSTSRNFSVGREGLEYVWGNHEPVRVWAQESAPGDPHGWPHEIIIHYY
HRHPVYTVIVLCGVALAILVGTASSAACIAKARRDCLTPYALAPNATVPTALAVLCCI

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

>9L41_3 Protocadherin-10 (chains R, S, T)
QLHYTVQEEQEHGTFVGNIAEDLGLDITKLSARGFQTVPNSRTPYLDLNLETGVLYVNEK
IDREQICKQSPSCVLHLEVFLENPLELFQVEIEVLD

Primary citation

Structural basis for engagement of Western Equine Encephalitis Virus with the PCDH10 receptor. Liang, S., Yang, Y., Liu, Y. et al. Nat Commun (2025) 16:6290-6290. DOI 10.1038/s41467-025-61659-4 · 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
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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