9W89: Chikungunya virus E protein

Chikungunya virus E protein complexed with 10D5. Determined by electron microscopy at 2.89 Å resolution. Released 12 Aug 2026.

Method: Electron microscopy
Resolution: 2.89 Å
Organisms: Chikungunya virus (strain 37997), Camelus bactrianus
Chains: 2
Atoms: 5,862
Mol. weight: 84.66 kDa
Released: 12 Aug 2026

Explore 9W89 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9W89 contains 18 α-helices and 71 β-strands across 2 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: 16 helices, 59 β-strands

Element	Residues	Length	Sheet
α-helix	70-74	5
β-strand	77	1	1
β-strand	82-84	3	2
β-strand	86	1	3
β-strand	93-95	3	2
β-strand	99-103	5	4
β-strand	110-121	12	4
β-strand	127-136	10	4
β-strand	139-144	6	4
α-helix	145-147	3
β-strand	149-151	3	3
β-strand	155	1	3
β-strand	157-169	13	4
β-strand	173-181	9	3
β-strand	187-196	10	3
α-helix	198-201	4
β-strand	204	1	5
β-strand	214-221	8	6
β-strand	231-235	5	7
α-helix	236-239	4
β-strand	240-241	2	8
α-helix	243-245	3
β-strand	246-249	4	9
β-strand	252-255	4	9
β-strand	262-266	5	8
β-strand	274-276	3	8
β-strand	280-282	3	9
α-helix	287-289	3
β-strand	290-294	5	8
β-strand	300	1	1
β-strand	301-302	2	7
β-strand	316-321	6	7
β-strand	326-333	8	6
α-helix	336-339	4
β-strand	340-343	4	10
β-strand	347-352	6	10
β-strand	358-364	7	5
β-strand	372-376	5	5
β-strand	380-385	6	10
β-strand	391-395	5	5
α-helix	399-400	2
β-strand	401-403	3	5
β-strand	426-434	9	11
β-strand	441-445	5	12
α-helix	451-452	2
β-strand	453-465	13	12
β-strand	468-474	7	13
β-strand	477-480	4	14
β-strand	485-487	3	15
β-strand	503-508	6	15
β-strand	513-514	2	16
β-strand	517-518	2	16
β-strand	527-532	6	15
β-strand	533-536	4	14
α-helix	538-541	4
β-strand	545-550	6	13
β-strand	554-563	10	12
β-strand	566-573	8	12
β-strand	579-582	4	11
β-strand	585-589	5	11
β-strand	602-606	5	13
β-strand	609-611	3	13
α-helix	615-617	3
β-strand	629-631	3	13
β-strand	639-641	3	13
β-strand	646-647	2	17
α-helix	649-651	3
β-strand	659-660	2	17
α-helix	662-664	3
α-helix	665-672	8
α-helix	677-680	4
α-helix	682-684	3
β-strand	686-688	3	12
β-strand	693-695	3	12
β-strand	701-709	9	11

Chain B: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	18
β-strand	11-13	3	19
β-strand	18-26	9	18
β-strand	33-39	7	20
β-strand	46-52	7	20
β-strand	57-59	3	20
β-strand	68-72	5	18
β-strand	77-82	6	18
α-helix	87-89	3
β-strand	91-98	8	20
α-helix	100-104	5
β-strand	110-113	4	20
β-strand	117-119	3	20
β-strand	120-122	3	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein E2,Spike glycoprotein E1	A	protein	649	Chikungunya virus (strain 37997)	Q5XXP3
10D5 heavy chain	B	protein	123	Camelus bactrianus

Sequence of entity 1 (A), FASTA

>9W89_1 Spike glycoprotein E2,Spike glycoprotein E1 (chains A)
TKDNFNVYKATRPYLAHCPDCGEGHSCHSPIALERIRNEATDGTLKIQVSLQIGIKTDDS
HDWTKLRYMDSHTPADAERAGLLVRTSAPCTITGTMGHFILARCPKGETLTVGFTDSRKI
SHTCTHPFHHEPPVIGRERFHSRPQHGKELPCSTYVQSTAATAEEIEVHMPPDTPDRTLM
TQQSGNVKITVNGQTVRYKCNCGGSNEGLTTTDKVINNCKIDQCHAAVTNHKNWQYNSPL
VPRNAELGDRKGKIHIPFPLANVTCRVPKARNPTVTYGKNQVTMLLYPDHPTLLSYRNMG
QEPNYHEEWVTHKKEVTLTVPTEGLEVTWGNNEPYKYWPQGGGGSGGGGSGGGGSGGGGS
YEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELQSVTLEPTLSLDYITCEYKTVIPSPYV
KCCGTAECKDKSLPDYSCKVFTGVYPFMWGGAYCFCDAENTQLSEAHVEKSESCKTEFAS
AYRAHTASASAKLRVLYQGNNITVAAYANGDHAVTVKDAKFVVGPMSSAWTPFDNKIVVY
KGDVYNMDYPPFGAGRPGQFGDIQSRTPESKDVYANTQLVLQRPAAGTVHVPYSQAPSGF
KYWLKERGASLQHTAPFGCQIATNPVRAVNCAVGNIPISIDIPDAAFTR

Sequence of entity 2 (B), FASTA

>9W89_2 10D5 heavy chain (chains B)
QVQLQESGGGSVQSGGSLRLSCAVSGYTYSSYCRGWFRQAPGKEREGVAGIDSDGSTRYA
DSVKGRFTISQDNAKNTLYLQMNSLKPEDTAMYYCAEVFCDSFHQGKYEAFYWGQGTQVT
VSS

Primary citation

Chikungunya virus E protein complexed with 10D5. Yuan, H.Y., Song, L.Y., Li, J.M. To be published.

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

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)
8EWF 3.92 Å, CryoEM structure of Western equine encephalitis virus VLP in complex with the avian…
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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