9L1N: E1 glycoprotein

Structure of Western equine encephalitis virus 71V1658 strain VLP in complex with human PCDH10 EC1. Determined by electron microscopy at 3.3 Å resolution. Released 4 Jun 2025.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: Western equine encephalitis virus, Homo sapiens
Chains: 13
Atoms: 31,688
Mol. weight: 452.46 kDa
Ligands: NAG
Released: 4 Jun 2025

Explore 9L1N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9L1N contains 70 α-helices and 393 β-strands across 13 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: 7 helices, 41 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	35-41	7	2
β-strand	46-48	3	4
β-strand	51-54	4	5
α-helix	57-58	2
β-strand	59-61	3	5
β-strand	74-82	9	5
β-strand	87	1	6
β-strand	101-110	10	5
β-strand	119-121	3	4
β-strand	125-137	13	2
β-strand	140-147	8	2
β-strand	155	1	7
β-strand	160	1	7
β-strand	161	1	1
β-strand	178-180	3	4
β-strand	183-185	3	4
α-helix	189-191	3
β-strand	203-204	2	8
β-strand	205	1	4
β-strand	214-215	2	8
β-strand	220-221	2	9
β-strand	228	1	6
β-strand	233-234	2	9
α-helix	236-238	3
α-helix	239-245	7
α-helix	256-258	3
β-strand	275-281	7	1
β-strand	289	1	3
α-helix	290-292	3
β-strand	296-303	8	10
β-strand	307	1	11
β-strand	314-322	9	10
β-strand	326-329	4	12
β-strand	332	1	13
β-strand	337-339	3	10
β-strand	343-346	4	12
β-strand	351-358	8	10
β-strand	362	1	14
β-strand	365-369	5	13
β-strand	372-376	5	13
β-strand	379	1	14
β-strand	381	1	11
β-strand	388	1	15
α-helix	404-436	33

Chain B: 9 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
β-strand	9	1	16
β-strand	14-16	3	17
β-strand	25-27	3	17
β-strand	33-35	3	18
β-strand	42-51	10	18
β-strand	63	1	19
β-strand	64-65	2	18
β-strand	79	1	19
α-helix	80-82	3
β-strand	83-86	4	20
β-strand	90	1	20
α-helix	91	1
β-strand	92-104	13	18
β-strand	108-116	9	20
β-strand	121-130	10	20
β-strand	148-155	8	21
β-strand	162	1	22
β-strand	166-169	4	23
β-strand	176	1	24
β-strand	189	1	25
β-strand	197-203	7	24
β-strand	205-207	3	24
β-strand	210-211	2	24
β-strand	216	1	25
α-helix	223-225	3
β-strand	226-230	5	24
β-strand	236	1	16
β-strand	237-238	2	23
β-strand	253-255	3	23
β-strand	258	1	22
β-strand	261-268	8	21
α-helix	271-273	3
β-strand	275-279	5	26
β-strand	282-286	5	26
β-strand	293-298	6	27
β-strand	307-311	5	27
β-strand	316-319	4	26
β-strand	326-330	5	27
α-helix	334-335	2
β-strand	336-338	3	27
β-strand	339	1	15
α-helix	352-361	10
α-helix	364-394	31
α-helix	410-415	6

Chain C: 3 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	112-116	5	28
β-strand	119-124	6	28
β-strand	125-127	3	29
β-strand	130-134	5	29
β-strand	140-141	2	28
β-strand	152-154	3	29
β-strand	159-163	5	29
α-helix	166-168	3
β-strand	173	1	29
β-strand	175	1	30
β-strand	185-186	2	30
β-strand	189-190	2	30
β-strand	194	1	31
β-strand	197	1	31
β-strand	199-200	2	32
α-helix	212-213	2
β-strand	214-215	2	30
β-strand	221	1	30
β-strand	224-226	3	32
β-strand	227	1	33
β-strand	228-231	4	32
β-strand	234-242	9	32
β-strand	248-251	4	32
α-helix	252-253	2
β-strand	258	1	33

Chain D: 5 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	34
β-strand	16-19	4	35
β-strand	24	1	36
β-strand	27-42	16	35
β-strand	46-48	3	37
β-strand	51-54	4	38
α-helix	56-59	4
β-strand	60-61	2	39
β-strand	77-78	2	40
β-strand	87	1	41
β-strand	101-102	2	39
β-strand	105-106	2	40
β-strand	107-110	4	38
β-strand	119-123	5	37
β-strand	124-136	13	35
β-strand	141-147	7	35
β-strand	153-155	3	34
β-strand	160-163	4	34
β-strand	176-180	5	37
β-strand	183-184	2	37
β-strand	203-204	2	42
β-strand	214-215	2	42
β-strand	220-221	2	43
β-strand	228	1	41
β-strand	233-234	2	43
α-helix	239-245	7
α-helix	251-253	3
β-strand	275-281	7	34
α-helix	284-286	3
β-strand	289	1	36
β-strand	296-302	7	44
β-strand	314-322	9	44
β-strand	326-329	4	45
β-strand	330-332	3	46
β-strand	338	1	47
β-strand	343-346	4	45
β-strand	353-356	4	44
β-strand	357	1	47
β-strand	364-369	6	46
β-strand	373-377	5	46
β-strand	387-388	2	48
α-helix	404-435	32

Chain E: 8 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	9	1	49
β-strand	14-16	3	50
β-strand	25-27	3	50
β-strand	31-35	5	51
β-strand	42-51	10	51
β-strand	63-65	3	51
β-strand	77-79	3	51
α-helix	80-82	3
β-strand	83-86	4	52
β-strand	90	1	52
β-strand	92-104	13	51
β-strand	110-115	6	52
β-strand	122-127	6	52
β-strand	138	1	53
β-strand	149-155	7	54
β-strand	166-169	4	55
β-strand	175-176	2	56
β-strand	180-181	2	57
β-strand	188-189	2	57
β-strand	197-199	3	58
β-strand	209-211	3	58
β-strand	228-229	2	56
β-strand	230	1	58
β-strand	236	1	49
β-strand	237-238	2	55
α-helix	244-246	3
β-strand	251-255	5	55
β-strand	261-267	7	54
α-helix	271-274	4
β-strand	275-279	5	59
β-strand	282-288	7	59
β-strand	293-299	7	53
β-strand	307-311	5	53
β-strand	314-319	6	59
β-strand	326-330	5	53
β-strand	336-338	3	53
β-strand	339-340	2	48
α-helix	352-355	4
α-helix	358-361	4
α-helix	366-396	31
α-helix	409-410	2
α-helix	411-415	5

Chain F: 5 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	112-113	2	60
β-strand	114-115	2	61
β-strand	116	1	62
β-strand	119	1	62
β-strand	123-124	2	60
β-strand	126-127	2	63
β-strand	130-131	2	63
β-strand	140-141	2	61
α-helix	144-147	4
β-strand	152-154	3	64
α-helix	155-157	3
β-strand	159-161	3	64
β-strand	163	1	63
α-helix	164-165	2
α-helix	166-168	3
β-strand	183-186	4	65
β-strand	189-194	6	65
β-strand	197-200	4	65
β-strand	213	1	66
β-strand	224-225	2	66
β-strand	230	1	65
β-strand	235-236	2	65
β-strand	239-242	4	66
β-strand	248-250	3	66
α-helix	252-253	2

Chain G: 7 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	67
β-strand	15-19	5	68
β-strand	24	1	69
β-strand	27-41	15	68
β-strand	44-48	5	70
β-strand	51-54	4	71
α-helix	56-59	4
β-strand	60-61	2	72
β-strand	77-82	6	72
β-strand	87	1	73
β-strand	101-106	6	72
β-strand	107-110	4	71
β-strand	119-123	5	70
β-strand	125-137	13	68
β-strand	140-147	8	68
β-strand	161-163	3	67
α-helix	164-166	3
β-strand	176-180	5	70
β-strand	183-184	2	70
α-helix	189-191	3
β-strand	203-204	2	74
β-strand	214-215	2	74
β-strand	220-221	2	75
β-strand	228	1	73
β-strand	233-234	2	75
α-helix	236-238	3
α-helix	239-244	6
α-helix	251-253	3
β-strand	260	1	68
β-strand	269	1	68
β-strand	275-281	7	67
β-strand	289	1	69
β-strand	300-305	6	76
β-strand	307	1	77
β-strand	314-319	6	76
β-strand	327-329	3	78
β-strand	330-332	3	79
β-strand	337-339	3	76
β-strand	343-345	3	78
β-strand	351	1	76
β-strand	354-358	5	76
β-strand	364-369	6	79
β-strand	372-377	6	79
β-strand	381	1	77
β-strand	388	1	80
α-helix	404-437	34

Chain H: 4 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	9	1	81
β-strand	14-16	3	82
β-strand	25-27	3	82
β-strand	31-35	5	83
β-strand	42-51	10	83
β-strand	63	1	84
β-strand	79	1	84
β-strand	85-86	2	85
β-strand	90-91	2	85
β-strand	92-104	13	83
β-strand	111-113	3	85
β-strand	116	1	86
β-strand	121	1	86
β-strand	124-126	3	85
β-strand	147-155	9	87
β-strand	166	1	88
β-strand	168-169	2	89
β-strand	180-181	2	90
β-strand	188-189	2	90
β-strand	196-202	7	91
β-strand	206-212	7	91
β-strand	216	1	90
α-helix	223-225	3
β-strand	226-227	2	91
β-strand	236	1	81
β-strand	237-238	2	89
β-strand	251	1	89
β-strand	255	1	88
β-strand	261-269	9	87
β-strand	276-279	4	92
β-strand	282-286	5	92
β-strand	293-299	7	93
β-strand	307-311	5	93
β-strand	316-318	3	92
β-strand	326-330	5	93
β-strand	336-338	3	93
β-strand	339	1	80
α-helix	353-355	3
α-helix	364-394	31
α-helix	409-415	7

5 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
E1 glycoprotein	A, D, G, J	protein	439	Western equine encephalitis virus	P13897
E2 glycoprotein	B, E, H, K	protein	416	Western equine encephalitis virus	P13897
Capsid glycoprotein	C, F, I, L	protein	150	Western equine encephalitis virus	P13897
Protocadherin-10	M	protein	95	Homo sapiens	Q9P2E7 (AlphaFold model)

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

>9L1N_1 E1 glycoprotein (chains A, D, G, J)
FEHATTVPNVPGIPYKALVERAGYAPLNLEITVVSSELTPSTNKEYVTCKFHTVIPSPQV
KCCGSLECKASSKADYTCRVFGGVYPFMWGGAQCFCDSENTQLSEAYVEFAPDCTIDHAV
ALKVHTAALKVGLRIVYGNTTAHLDTFVNGVTPGSSRDLKVIAGPISAAFSPFDHKVVIR
KGLVYNYDFPEYGAMKPGAFGDIQASSLDATDIVARTDIRLLKPSVKNIHVPYTQAVSGY
EMWKNNSGRPLQETAPFGCKIEVEPLRASNCAYGHIPISIDIPDAAFVRSSESPTILEVS
CTVADCIYSADFGGSLTLQYKADREGHCPVHSHSTTAVLKEATTHVTAVGSITLHFSTSS
PQANFIVSLCGKKSTCNAECKPPADHIIGEPHKVDQEFQAAVSKTSWNWLLALFGGASSL
IVVGLIVLVCSSMLINTRR

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

>9L1N_2 E2 glycoprotein (chains B, E, H, K)
SITDDFTLTSPYLGFCPYCRHSTPCFSPIKIENVWDESDDGSIRIQVSAQFGYNQAGTAD
VTKFRYMSFDHDHDIKEDSMEKIAISTSGPCRRLGHKGYFLLAQCPPGDSVTVSITSGAS
ENSCTVEKKIRRKFVGREEYLFPPVHGKLVKCHVYDHLKETSAGYITMHRPGPHAYKSYL
EEASGEVYIKPPSGKNVTYECKCGDYSTGIVSTRTKMNGCTKAKQCIAYKSDQTKWVFNS
PDLIRHTDHSVQGKLHIPFRLTPTVCPVPLAHTPTVTKWFKGITLHLTAMRPTLLTTRKL
GLRADATAEWITGSTSRNFSVGREGLEYVWGNHEPVRVWAQESAPGDPHGWPHEIIIHYY
HRHPVYTVIVLCGVALAILVGTASSAACIAKARRDCLTPYALAPNATVPTALAVLC

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

>9L1N_3 Capsid glycoprotein (chains C, F, I, L)
KTFPIMLNGQVNGYACVVGGRLMKPLHVEGKIDNEQLAAVKLKKASMYDLEYGDVPQNMK
SDTLQYTSDKPPGFYNWHHGAVQYENGRFTVPRGVGGKGDSGRPILDNRGRVVAIVLGGA
NEGTRTALSVVTWNQKGVTIRDTPEGSEPW

Sequence of entity 4 (M), FASTA

>9L1N_4 Protocadherin-10 (chains M)
QLHYTVQEEQEHGTFVGNIAEDLGLDITKLSARGFQTVPNSRTPYLDLNLETGVLYVNEK
IDREQICKQSPSCVLHLEVFLENPLELFQVEIEVL

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	8

Primary citation

Structural basis for the recognition of two different types of receptors by Western equine encephalitis virus. Ma, B., Cao, Z., Ding, W. et al. Cell Rep (2025) 44:115724-115724. DOI 10.1016/j.celrep.2025.115724 · 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
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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