9L3V: Structural polyprotein

structure of WEEV strain 71V1658 virus-like particle(3-fold region). Determined by electron microscopy at 2.53 Å resolution. Released 27 Aug 2025.

Method: Electron microscopy
Resolution: 2.53 Å
Organism: Western equine encephalitis virus
Chains: 6
Atoms: 19,743
Mol. weight: 281.29 kDa
Released: 27 Aug 2025

Explore 9L3V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9L3V contains 66 α-helices and 244 β-strands across 6 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, 46 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
α-helix	57-58	2
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
α-helix	112-115	4
β-strand	119-137	19	2
β-strand	140-147	8	2
β-strand	148	1	1
β-strand	154	1	1
β-strand	161-163	3	1
β-strand	176-180	5	2
β-strand	183-186	4	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
β-strand	228	1	6
β-strand	233-234	2	8
α-helix	236-238	3
α-helix	239-245	7
α-helix	256-258	3
α-helix	259	1
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	296-303	8	9
β-strand	307	1	10
β-strand	308	1	9
β-strand	314-322	9	9
β-strand	326	1	11
β-strand	329	1	12
β-strand	330-332	3	13
β-strand	334	1	9
β-strand	337-339	3	9
β-strand	343	1	12
β-strand	346	1	11
β-strand	349-358	10	9
β-strand	362-363	2	14
β-strand	366-369	4	13
β-strand	372-375	4	13
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	404-438	35

Chain B: 10 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	16
β-strand	13	1	17
β-strand	18-20	3	18
β-strand	29-31	3	18
β-strand	35-39	5	19
β-strand	46-57	12	19
β-strand	63-71	9	19
β-strand	79-83	5	19
α-helix	84-86	3
β-strand	87-90	4	20
β-strand	94	1	20
β-strand	96-108	13	19
β-strand	112-119	8	20
β-strand	127-134	8	20
β-strand	142	1	21
β-strand	152-159	8	22
β-strand	166-173	8	16
β-strand	175	1	23
β-strand	179	1	24
α-helix	181-183	3
β-strand	184-186	3	25
β-strand	191-193	3	25
β-strand	201-207	7	24
β-strand	209-215	7	24
β-strand	219-221	3	25
α-helix	227-229	3
β-strand	230-234	5	24
β-strand	240	1	17
β-strand	241-242	2	16
β-strand	249	1	23
β-strand	257-262	6	16
β-strand	265-272	8	22
α-helix	275-278	4
β-strand	279-280	2	21
β-strand	283	1	21
β-strand	286-303	18	21
β-strand	311-324	14	21
β-strand	330-334	5	21
α-helix	338-339	2
β-strand	340-342	3	21
β-strand	343-344	2	15
α-helix	356-365	10
α-helix	368-371	4
α-helix	372-377	6
α-helix	378-401	24
α-helix	414-420	7

Chain C: 11 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	26
β-strand	15-19	5	27
β-strand	24	1	28
β-strand	27-48	22	27
β-strand	51-54	4	29
α-helix	57-58	2
β-strand	59-60	2	30
β-strand	77-81	5	30
β-strand	87-88	2	31
β-strand	91-92	2	31
β-strand	102-106	5	30
β-strand	107-110	4	29
α-helix	112-115	4
β-strand	119-137	19	27
β-strand	140-147	8	27
β-strand	148	1	26
β-strand	154	1	26
β-strand	161-163	3	26
β-strand	176-180	5	27
β-strand	183-186	4	27
α-helix	189-191	3
β-strand	203-204	2	32
β-strand	205	1	27
β-strand	214-215	2	32
β-strand	220-221	2	33
β-strand	228	1	31
β-strand	233-234	2	33
α-helix	236-238	3
α-helix	239-245	7
α-helix	256-258	3
α-helix	259	1
β-strand	260-262	3	27
β-strand	267-269	3	27
β-strand	275-281	7	26
α-helix	284-286	3
β-strand	289	1	28
β-strand	296-303	8	34
β-strand	307	1	35
β-strand	314-322	9	34
β-strand	326	1	36
β-strand	329	1	37
β-strand	330-332	3	38
β-strand	337-339	3	34
β-strand	343	1	37
β-strand	346	1	36
β-strand	349-358	10	34
β-strand	362-363	2	39
β-strand	366-369	4	38
β-strand	372-375	4	38
β-strand	378-379	2	39
β-strand	381	1	35
α-helix	382-383	2
β-strand	387-388	2	40
α-helix	399-401	3
α-helix	404-438	35

Chain D: 10 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	41
β-strand	13	1	42
β-strand	18-20	3	43
β-strand	29-31	3	43
β-strand	35-39	5	44
β-strand	46-57	12	44
β-strand	63-71	9	44
β-strand	79-83	5	44
α-helix	84-86	3
β-strand	87-90	4	45
β-strand	94	1	45
β-strand	96-108	13	44
β-strand	112-119	8	45
β-strand	127-134	8	45
β-strand	142	1	46
β-strand	152-159	8	47
β-strand	166-173	8	41
β-strand	175	1	48
β-strand	179	1	49
α-helix	181-183	3
β-strand	184-186	3	50
β-strand	191-193	3	50
β-strand	201-207	7	49
β-strand	209-215	7	49
β-strand	219-221	3	50
α-helix	227-229	3
β-strand	230-234	5	49
β-strand	240	1	42
β-strand	241-242	2	41
β-strand	249	1	48
β-strand	257-262	6	41
β-strand	265-272	8	47
α-helix	275-278	4
β-strand	279-280	2	46
β-strand	283	1	46
β-strand	286-303	18	46
β-strand	311-324	14	46
β-strand	330-334	5	46
α-helix	338-339	2
β-strand	340-342	3	46
β-strand	343-344	2	40
α-helix	356-365	10
α-helix	368-371	4
α-helix	372-377	6
α-helix	378-401	24
α-helix	414-420	7

Chain E: 12 helices, 46 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	51
β-strand	15-19	5	52
β-strand	24	1	53
β-strand	27-39	13	52
β-strand	42-48	7	54
β-strand	51-54	4	55
α-helix	57-58	2
β-strand	59-60	2	56
β-strand	77-81	5	56
β-strand	87-88	2	57
β-strand	91-92	2	57
β-strand	102-106	5	56
β-strand	107-110	4	55
α-helix	112-115	4
β-strand	119-124	6	54
β-strand	128-137	10	52
β-strand	140-147	8	52
β-strand	148	1	51
β-strand	154	1	51
β-strand	161-163	3	51
β-strand	176-180	5	54
β-strand	183-186	4	54
α-helix	189-191	3
β-strand	203-204	2	58
β-strand	205	1	54
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	256-258	3
α-helix	259	1
β-strand	260-262	3	52
β-strand	267-269	3	52
β-strand	275-281	7	51
α-helix	284-286	3
β-strand	289	1	53
β-strand	296-303	8	60
β-strand	307	1	61
β-strand	314-322	9	60
β-strand	326	1	62
β-strand	329	1	63
β-strand	330-332	3	64
β-strand	337-339	3	60
β-strand	343	1	63
β-strand	346	1	62
β-strand	349-358	10	60
β-strand	362-363	2	65
β-strand	366-369	4	64
β-strand	372-375	4	64
β-strand	378-379	2	65
α-helix	380	1
β-strand	381	1	61
α-helix	382-383	2
β-strand	387-388	2	66
α-helix	399-401	3
α-helix	404-438	35

Chain F: 12 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	67
β-strand	13	1	68
β-strand	18-20	3	69
β-strand	29-31	3	69
β-strand	35-39	5	70
β-strand	46-57	12	70
β-strand	63-71	9	70
β-strand	79-83	5	70
α-helix	84-86	3
β-strand	87-90	4	71
β-strand	94	1	71
β-strand	96-108	13	70
β-strand	112-119	8	71
β-strand	127-134	8	71
β-strand	142	1	72
β-strand	152-159	8	73
β-strand	166-173	8	67
β-strand	175	1	74
β-strand	179	1	75
α-helix	181-183	3
β-strand	184-186	3	76
β-strand	191-193	3	76
β-strand	201-207	7	75
β-strand	209-215	7	75
β-strand	219-221	3	76
α-helix	227-229	3
β-strand	230-234	5	75
β-strand	240	1	68
β-strand	241-242	2	67
α-helix	248	1
β-strand	249	1	74
α-helix	250	1
β-strand	257-262	6	67
β-strand	265-272	8	73
α-helix	275-278	4
β-strand	279-280	2	72
β-strand	283	1	72
β-strand	286-303	18	72
β-strand	311-324	14	72
β-strand	330-334	5	72
α-helix	338-339	2
β-strand	340-342	3	72
β-strand	343-344	2	66
α-helix	356-365	10
α-helix	368-371	4
α-helix	372-377	6
α-helix	378-401	24
α-helix	414-420	7

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

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

>9L3V_1 Structural polyprotein (chains A, C, E)
FEHATTVPNVPGIPYKALVERAGYAPLNLEITVVSSELTPSTNKEYVTCKFHTVIPSPQV
KCCGSLECKASSKADYTCRVFGGVYPFMWGGAQCFCDSENTQLSEAYVEFAPDCTIDHAV
ALKVHTAALKVGLRIVYGNTTAHLDTFVNGVTPGSSRDLKVIAGPISAAFSPFDHKVVIR
KGLVYNYDFPEYGAMKPGAFGDIQASSLDATDIVARTDIRLLKPSVKNIHVPYTQAVSGY
EMWKNNSGRPLQETAPFGCKIEVEPLRASNCAYGHIPISIDIPDAAFVRSSESPTILEVS
CTVADCIYSADFGGSLTLQYKADREGHCPVHSHSTTAVLKEATTHVTAVGSITLHFSTSS
PQANFIVSLCGKKSTCNAECKPPADHIIGEPHKVDQEFQAAVSKTSWNWLLALFGGASSL
IVVGLIVLVCSSMLINTRR

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

>9L3V_2 Structural polyprotein (chains B, D, F)
SITDDFTLTSPYLGFCPYCRHSTPCFSPIKIENVWDESDDGSIRIQVSAQFGYNQAGTAD
VTKFRYMSFDHDHDIKEDSMEKIAISTSGPCRRLGHKGYFLLAQCPPGDSVTVSITSGAS
ENSCTVEKKIRRKFVGREEYLFPPVHGKLVKCHVYDHLKETSAGYITMHRPGPHAYKSYL
EEASGEVYIKPPSGKNVTYECKCGDYSTGIVSTRTKMNGCTKAKQCIAYKSDQTKWVFNS
PDLIRHTDHSVQGKLHIPFRLTPTVCPVPLAHTPTVTKWFKGITLHLTAMRPTLLTTRKL
GLRADATAEWITGSTSRNFSVGREGLEYVWGNHEPVRVWAQESAPGDPHGWPHEIIIHYY
HRHPVYTVIVLCGVALAILVGTASSAACIAKARRDCLTPYALAPNATVPTALAVLCCI

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:

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
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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