8EWF: Western equine encephalitis virus VLP

CryoEM structure of Western equine encephalitis virus VLP in complex with the avian MXRA8 receptor. Determined by electron microscopy at 3.92 Å resolution. Released 25 Oct 2023.

Method: Electron microscopy
Resolution: 3.92 Å
Organisms: Chikungunya virus, Anas platyrhynchos
Chains: 9
Atoms: 28,665
Mol. weight: 409.35 kDa
Ligands: NAG
Released: 25 Oct 2023

Explore 8EWF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8EWF contains 81 α-helices and 315 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, G, K and O: 11 helices, 37 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	27-40	14	2
β-strand	44-48	5	4
β-strand	51-54	4	5
α-helix	57-58	2
β-strand	59-61	3	6
β-strand	77-82	6	6
β-strand	87-88	2	7
β-strand	91-92	2	7
β-strand	101-106	6	6
β-strand	107-110	4	5
α-helix	112-115	4
β-strand	119-122	4	4
β-strand	127-137	11	2
β-strand	140-147	8	2
β-strand	153-156	4	1
β-strand	159-163	5	1
β-strand	177-179	3	4
β-strand	184-186	3	4
α-helix	189-191	3
α-helix	195-196	2
β-strand	203-205	3	4
β-strand	213-215	3	4
β-strand	220-221	2	8
α-helix	223-225	3
β-strand	233-234	2	8
α-helix	235-238	4
α-helix	239-245	7
α-helix	251-254	4
α-helix	256-258	3
β-strand	260-261	2	2
β-strand	268-269	2	2
β-strand	275-281	7	1
β-strand	289	1	3
β-strand	296-305	10	9
β-strand	314-322	9	9
β-strand	326-329	4	10
β-strand	330-331	2	11
β-strand	337-339	3	9
β-strand	343-346	4	10
β-strand	350-358	9	9
β-strand	362-369	8	11
β-strand	372-379	8	11
β-strand	387-388	2	12
α-helix	405-413	9
α-helix	418-433	16

Chains C, I, M and Q: 7 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	17-18	2	13
β-strand	29-30	2	13
β-strand	37-38	2	14
β-strand	46-49	4	14
β-strand	66-71	6	15
β-strand	74-79	6	15
β-strand	84-86	3	16
β-strand	90	1	16
β-strand	92-93	2	14
β-strand	97	1	14
β-strand	100-104	5	14
β-strand	108	1	17
β-strand	111-116	6	16
β-strand	122-127	6	16
β-strand	131	1	17
β-strand	149-156	8	18
β-strand	166-168	3	19
β-strand	169-170	2	20
β-strand	175	1	21
β-strand	183-184	2	22
β-strand	187-190	4	22
β-strand	197-200	4	21
β-strand	208-211	4	21
β-strand	215-217	3	22
α-helix	222-224	3
β-strand	226-229	4	21
β-strand	236-237	2	20
α-helix	243-244	2
β-strand	254-256	3	19
β-strand	261-268	8	18
α-helix	272-274	3
β-strand	275-279	5	23
β-strand	282-286	5	23
β-strand	293-299	7	24
β-strand	307-311	5	24
β-strand	316-320	5	23
β-strand	326-330	5	24
α-helix	334-335	2
β-strand	336-338	3	24
β-strand	339-340	2	12
α-helix	355-361	7
α-helix	369-400	32
α-helix	412-415	4

Chain E: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	34-44	11	25
β-strand	49-51	3	26
β-strand	54	1	27
α-helix	56-58	3
β-strand	70-77	8	28
β-strand	87-93	7	28
α-helix	98	1
β-strand	99-100	2	28
β-strand	109-110	2	29
α-helix	115-118	4
β-strand	123-125	3	29
α-helix	130-132	3
β-strand	134-142	9	28
β-strand	148-158	11	28
α-helix	161-163	3
β-strand	166-168	3	28
β-strand	173-178	6	28
β-strand	183-185	3	29
β-strand	205-211	7	25
β-strand	213	1	30
β-strand	215	1	30
β-strand	221-227	7	25
β-strand	232-234	3	25
α-helix	240-243	4
β-strand	244-246	3	26
α-helix	250-253	4
β-strand	255	1	27
α-helix	257	1
β-strand	258-260	3	26
α-helix	265-267	3
β-strand	269-277	9	25
β-strand	282-293	12	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E1 envelope protein	A, G, K, O	protein	439	Chikungunya virus	Q5XXP3
Spike glycoprotein E2	C, I, M, Q	protein	419	Chikungunya virus	Q5XXP3
Chimeric MXRA8 receptor: D1 from Duck MXRA8 and D2 from Mouse MXRA8	E	protein	265	Anas platyrhynchos	Q9DBV4 (AlphaFold model), R0KGK0 (AlphaFold model)

Sequence of entity 1 (A, G, K, O), FASTA

>8EWF_1 E1 envelope protein (chains A, G, K, O)
YEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELQSVTLEPTLSLDYITCEYKTVIPSPYV
KCCGTAECKDKSLPDYSCKVFTGVYPFMWGGAYCFCDAENTQLSEAHVEKSESCKTEFAS
AYRAHTASASAKLRVLYQGNNITVAAYANGDHAVTVKDAKFVVGPMSSAWTPFDNKIVVY
KGDVYNMDYPPFGAGRPGQFGDIQSRTPESKDVYANTQLVLQRPAAGTVHVPYSQAPSGF
KYWLKERGASLQHTAPFGCQIATNPVRAVNCAVGNIPISIDIPDAAFTRVVDAPSVTDMS
CEVPACTHSSDFGGVAIIKYTASKKGKCAVHSMTNAVTIREADVEVEGNSQLQISFSTAL
ASAEFRVQVCSTQVHCAAACHPPKDHIVNYPASHTTLGVQDISTTAMSWVQKITGGVGLI
VAVAALILIVVLCVSFSRH

Sequence of entity 2 (C, I, M, Q), FASTA

>8EWF_2 Spike glycoprotein E2 (chains C, I, M, Q)
NFNVYKATRPYLAHCPDCGEGHSCHSPIALERIRNEATDGTLKIQVSLQIGIKTDDSHDW
TKLRYMDSHTPADAERAGLLVRTSAPCTITGTMGHFILARCPKGETLTVGFTDSRKISHT
CTHPFHHEPPVIGRERFHSRPQHGKELPCSTYVQSTAATAEEIEVHMPPDTPDRTLMTQQ
SGNVKITVNGQTVRYKCNCGGSNEGLTTTDKVINNCKIDQCHAAVTNHKNWQYNSPLVPR
NAELGDRKGKIHIPFPLANVTCRVPKARNPTVTYGKNQVTMLLYPDHPTLLSYRNMGQEP
NYHEEWVTHKKEVTLTVPTEGLEVTWGNNEPYKYWPQMSTNGTAHGHPHEIILYYYELYP
TMTVVIVSVASFVLLSMVGTAVGMCVCARRRCITPYELTPGATVPFLLSLLCCVRTTKA

Sequence of entity 3 (E), FASTA

>8EWF_3 Chimeric MXRA8 receptor: D1 from Duck MXRA8 and D2 from Mouse MXRA8 (chains E)
SSSLVSESVVSLAAGTQAVLRCQSPRMVWTQDRLNDRQRVVHWDVYSTYYGDNKMERLCD
MYSAGDQRVYSSYNQGRIFMPQNAFTDGNFSLVIKDVAESDGGIYSCNLHHHYCHLYETV
KIQLDVTKKAKAAKEYWDGEKAVIVALEGSTVMLPCVNRNQIWTERHLEEAQQVVHWDRQ
LPGVSHDRADRLLDLYASGERRAYGPPFLRDRVSVNTNAFARGDFSLRIDELERADEGIY
SCHLHHHYCGLHERRVFHLQVTEPA

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	9

Primary citation

Vertebrate-class-specific binding modes of the alphavirus receptor MXRA8. Zimmerman, O., Zimmerman, M.I., Raju, S. et al. Cell (2023) 186:4818-4833.e25. DOI 10.1016/j.cell.2023.09.007 · PubMed

Other PDB entries of the same protein (UniProt Q5XXP3), best resolution first:

9W89 2.89 Å, Chikungunya virus E protein complexed with 10D5
9W8A 2.95 Å, Chikungunya virus E protein complexed with 7H9
9W7J 2.97 Å, Chikungunya virus E protein complexed with 8D1-H-10D5
8DWW 3.13 Å, Chikungunya VLP in complex with neutralizing Fab 506.A08 (asymmetric unit)
8DWY 3.18 Å, Chikungunya VLP in complex with neutralizing Fab CHK-265 (asymmetric unit)
8DWX 3.27 Å, Chikungunya VLP in complex with neutralizing Fab 506.C01 (asymmetric unit)
6NK6 4.06 Å, Electron Cryo-Microscopy Of Chikungunya VLP in complex with mouse Mxra8 receptor
6NK5 4.16 Å, Electron Cryo-Microscopy Of Chikungunya VLP
3J2W 5.0 Å, Electron cryo-microscopy of Chikungunya virus
5VU2 6.8 Å, Electron cryo-microscopy of "immature" Chikungunya VLP

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