9E96: WEEV CBA87 VLP

WEEV CBA87 VLP in complex with human PCDH10-EC1. Determined by electron microscopy at 4.05 Å resolution. Released 23 Apr 2025.

Method: Electron microscopy
Resolution: 4.05 Å
Organisms: Western equine encephalitis virus, Homo sapiens
Chains: 16
Atoms: 33,952
Mol. weight: 485.27 kDa
Released: 23 Apr 2025

Explore 9E96 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9E96 contains 115 α-helices and 396 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: 8 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	1
β-strand	14-19	6	2
β-strand	24	1	3
β-strand	27-48	22	2
β-strand	51-54	4	4
α-helix	56-58	3
β-strand	59-60	2	4
β-strand	74-81	8	4
β-strand	87	1	5
β-strand	92	1	5
β-strand	102-110	9	4
β-strand	119-137	19	2
β-strand	140	1	2
β-strand	143-148	6	2
β-strand	153	1	1
β-strand	160-163	4	1
β-strand	176-180	5	2
β-strand	183-185	3	2
α-helix	189-191	3
β-strand	203-204	2	6
β-strand	205	1	2
β-strand	214-215	2	6
β-strand	220-221	2	7
β-strand	228	1	5
β-strand	233-234	2	7
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
β-strand	289	1	3
β-strand	298-306	9	8
β-strand	307	1	9
β-strand	308	1	8
β-strand	314-321	8	8
β-strand	326-329	4	10
β-strand	330-332	3	11
β-strand	337-339	3	8
β-strand	343-346	4	10
β-strand	349-358	10	8
β-strand	366-369	4	11
β-strand	372-375	4	11
α-helix	380	1
β-strand	381	1	9
α-helix	382-383	2
β-strand	387-388	2	12
α-helix	399-401	3
α-helix	404-437	34

Chain B: 11 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	14-16	3	13
β-strand	25-27	3	13
β-strand	31-35	5	14
β-strand	42-49	8	14
β-strand	50	1	15
β-strand	51	1	14
β-strand	53	1	16
β-strand	59	1	16
β-strand	63-67	5	15
β-strand	75-79	5	15
α-helix	80-82	3
β-strand	83-86	4	17
β-strand	90	1	17
α-helix	91	1
β-strand	92-104	13	14
β-strand	108-117	10	17
β-strand	120-130	11	17
β-strand	138	1	18
β-strand	147-155	9	19
β-strand	164-167	4	20
β-strand	168-169	2	21
β-strand	171	1	22
β-strand	180-183	4	23
β-strand	186-189	4	23
α-helix	191-192	2
β-strand	197-202	6	24
β-strand	206-211	6	24
β-strand	215-216	2	23
α-helix	223-225	3
β-strand	226-230	5	24
β-strand	237-238	2	21
α-helix	244	1
β-strand	245	1	22
α-helix	246	1
β-strand	254-257	4	20
β-strand	261-269	9	19
α-helix	271-274	4
β-strand	275-279	5	18
β-strand	282-299	18	18
β-strand	307-320	14	18
β-strand	326-330	5	18
α-helix	334-335	2
β-strand	336-338	3	18
β-strand	339-340	2	12
α-helix	352-362	11
α-helix	364-401	38
α-helix	410-416	7

Chain E: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	111-116	6	25
β-strand	119-127	9	25
β-strand	130-134	5	25
β-strand	140-141	2	25
α-helix	144-147	4
β-strand	152-154	3	25
α-helix	155-157	3
β-strand	159-163	5	25
β-strand	173	1	25
α-helix	174	1
β-strand	175	1	26
β-strand	182-186	5	26
β-strand	189-194	6	26
β-strand	197-201	5	26
β-strand	213-215	3	26
β-strand	221-230	10	26
β-strand	234-242	9	26
β-strand	248-251	4	26
β-strand	257-258	2	26

Chain F: 11 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	27
β-strand	14-19	6	28
β-strand	24	1	29
β-strand	27-39	13	28
β-strand	42-48	7	30
α-helix	50	1
β-strand	51-54	4	31
α-helix	56-58	3
β-strand	59-60	2	31
β-strand	74-81	8	31
β-strand	87	1	32
β-strand	102-110	9	31
α-helix	112-115	4
β-strand	119-124	6	30
β-strand	128-137	10	28
β-strand	140-147	8	28
β-strand	148	1	27
α-helix	152	1
β-strand	153-156	4	27
β-strand	159-163	5	27
β-strand	176-180	5	30
β-strand	183-185	3	30
α-helix	189-191	3
β-strand	203-204	2	33
β-strand	205	1	30
β-strand	214-215	2	33
β-strand	220-221	2	34
β-strand	228	1	32
β-strand	233-234	2	34
α-helix	239-245	7
α-helix	251-253	3
α-helix	256-258	3
β-strand	260-262	3	28
β-strand	267-269	3	28
β-strand	275-281	7	27
α-helix	284-286	3
β-strand	289	1	29
β-strand	296-303	8	35
β-strand	306-307	2	36
β-strand	314-322	9	35
β-strand	326	1	37
β-strand	329	1	38
β-strand	330-332	3	39
β-strand	337-339	3	35
β-strand	343	1	38
β-strand	346	1	37
β-strand	349-358	10	35
β-strand	362-369	8	39
β-strand	372-379	8	39
β-strand	380-381	2	36
α-helix	382-383	2
β-strand	387-388	2	40
α-helix	404-438	35

Chain G: 10 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	14-16	3	41
β-strand	19	1	42
β-strand	25-27	3	41
β-strand	31-35	5	43
β-strand	42-53	12	43
β-strand	59-65	7	43
β-strand	67	1	44
β-strand	75	1	44
β-strand	78	1	43
α-helix	80-82	3
β-strand	83-86	4	42
β-strand	90	1	42
α-helix	91	1
β-strand	92-104	13	43
β-strand	108-115	8	42
β-strand	117	1	45
β-strand	119	1	45
β-strand	123-130	8	42
β-strand	138	1	46
β-strand	148-155	8	47
β-strand	165-169	5	48
β-strand	171	1	49
β-strand	180-183	4	50
β-strand	186-189	4	50
β-strand	197-202	6	51
β-strand	206-211	6	51
β-strand	215-216	2	50
α-helix	223-225	3
β-strand	226-230	5	51
β-strand	237-238	2	48
α-helix	244	1
β-strand	245	1	49
α-helix	246	1
β-strand	253-256	4	48
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
α-helix	334-335	2
β-strand	336-338	3	46
β-strand	339-340	2	40
α-helix	352-362	11
α-helix	364-401	38
α-helix	411-416	6

Chain H: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	20-25	6	52
α-helix	28-29	2
β-strand	33-36	4	53
α-helix	37-40	4
α-helix	47-50	4
β-strand	54-55	2	52
β-strand	64-67	4	53
β-strand	72-75	4	53
β-strand	92-99	8	52
β-strand	104-113	10	52
α-helix	114-115	2

Chain I: 6 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	111-116	6	54
β-strand	119-127	9	54
β-strand	130-134	5	54
β-strand	140-141	2	54
α-helix	146-148	3
β-strand	152-154	3	54
α-helix	155-157	3
β-strand	159-163	5	54
α-helix	164-165	2
α-helix	167-170	4
β-strand	173	1	54
β-strand	174	1	55
α-helix	175	1
β-strand	182-186	5	56
β-strand	189-194	6	56
β-strand	197-201	5	56
β-strand	210	1	54
α-helix	212	1
β-strand	213-215	3	56
β-strand	220	1	55
β-strand	221-230	10	56
β-strand	234-241	8	56
β-strand	249-251	3	56
β-strand	257-258	2	56

Chain J: 10 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	57
β-strand	15-19	5	58
β-strand	24	1	59
β-strand	27-39	13	58
β-strand	42-48	7	60
α-helix	50	1
β-strand	51-54	4	61
α-helix	56-58	3
β-strand	59-60	2	61
α-helix	68-70	3
β-strand	74-81	8	61
β-strand	87	1	62
β-strand	102-110	9	61
α-helix	112-115	4
β-strand	119-124	6	60
α-helix	126-127	2
β-strand	128-137	10	58
β-strand	140-148	9	58
β-strand	153-156	4	57
β-strand	159-163	5	57
β-strand	176-180	5	60
β-strand	183-185	3	60
α-helix	190-191	2
β-strand	203-204	2	63
β-strand	205	1	60
β-strand	214-215	2	63
β-strand	219-221	3	64
β-strand	228	1	62
β-strand	233-235	3	64
α-helix	239-245	7
α-helix	251-253	3
β-strand	260-262	3	58
β-strand	267-269	3	58
β-strand	275-281	7	57
β-strand	289	1	59
β-strand	298-306	9	65
β-strand	307	1	66
β-strand	314-321	8	65
β-strand	326	1	67
β-strand	329	1	68
β-strand	330-332	3	69
β-strand	337-339	3	65
β-strand	343	1	68
β-strand	346	1	67
β-strand	349-358	10	65
β-strand	362-369	8	69
β-strand	372-379	8	69
β-strand	381	1	66
α-helix	382-383	2
β-strand	387-388	2	70
α-helix	404-437	34

8 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, F, J, N	protein	439	Western equine encephalitis virus	Q1W679
Structural polyprotein	B, G, K, O	protein	408	Western equine encephalitis virus	Q1W679
Capsid protein	E, I, M, R	protein	153	Western equine encephalitis virus	P13897
Protocadherin-10	H, L, P, Q	protein	104	Homo sapiens	Q9P2E7 (AlphaFold model)

Sequence of entity 1 (A, F, J, N), FASTA

>9E96_1 Structural polyprotein (chains A, F, J, N)
FEHATTVPNVPGIPYKALVERAGYAPLNLEITVVSSELTPSTNKEYVTCKFHTVVPSPQV
KCCGSLECKASSKADYTCRVFGGVYPFMWGGAQCFCDSENTQLSEAYVEFAPDCTIDHAV
ALKVHTAALKVGLRIVYGNTTARLDTFVNGVTPGSSRDLKVIAGPISAAFSPFDHKVVIR
KGLVYNYDFPEYGAMNPGAFGDIQASSLDATDIVARTDIRLLKPSVKNIHVPYTQAVSGY
EMWKNNSGRPLQETAPFGCKIEVEPLRATNCAYGHIPISIDIPDAAFVRSSESPTILEVS
CTVADCIYSADFGGSLTLQYKANREGHCPVHSHSTTAVLKEATTHVTATGSITLHFSTSS
PQANFIVSLCGKKTTCNAECKPPADHIIGEPHKVDQEFQAAVSKTSWNWLLALFGGASSL
IVVGLIVLVCSSMLINTRR

Sequence of entity 2 (B, G, K, O), FASTA

>9E96_2 Structural polyprotein (chains B, G, K, O)
PYLGFCPYCRHSAPCFSPIKIENVWDESDDGSIRIQVSAQFGYNQAGTADVTKFRYMSYD
HDHDIKEDSMEKLAISTSGPCRRLGHKGYFLLAQCPPGDSVTVSITSGASENSCTVEKKI
RRKFVGREEYLFPPVHGKLVKCHVYDHLKETSAGYITMHRPGPHAYKSYLEEASGEVYIK
PPSGKNVTYECKCGDYSTGIVSTRTKMNGCTKAKQCIAYKRDQTKWVFNSPDLIRHTDHS
VQGKLHIPFRLTPTVCPVPLAHTPTVTKWFKGITLHLTATRPTLLTTRKLGLRADATAEW
ITGTTSRNFSVGREGLEYVWGNHEPVRVWAQESAPGDPHGWPHEIIIHYYHRHPVYTVIV
LCGVALAILVGTASSAACIAKARRDCLTPYALAPNATVPTALAVLCCI

Sequence of entity 3 (E, I, M, R), FASTA

>9E96_3 Capsid protein (chains E, I, M, R)
ESDKTFPIMLNGQVNGYACVVGGRLMKPLHVEGKIDNEQLAAVKLKKASMYDLEYGDVPQ
NMKSDTLQYTSDKPPGFYNWHHGAVQYENGRFTVPRGVGGKGDSGRPILDNRGRVVAIVL
GGANEGTRTALSVVTWNQKGVTIKDTPEGSEPW

Sequence of entity 4 (H, L, P, Q), FASTA

>9E96_4 Protocadherin-10 (chains H, L, P, Q)
QLHYTVQEEQEHGTFVGNIAEDLGLDITKLSARGFQTVPNSRTPYLDLNLETGVLYVNEK
IDREQICKQSPSCVLHLEVFLENPLELFQVEIEVLDINDNPPSF

Primary citation

Structural basis for plasticity in receptor engagement by an encephalitic alphavirus. Raju, S., Palakurty, S., Sariol, A. et al. Cell (2025) 188:2943. DOI 10.1016/j.cell.2025.02.036 · PubMed

Other PDB entries of the same protein (UniProt Q1W679), best resolution first:

8DAQ 4.35 Å, CryoEM structure of Western equine encephalitis virus VLP
8DAN 4.74 Å, CryoEM structure of Western equine encephalitis virus VLP in complex with the avian…

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