9W7J: Chikungunya virus E protein

Chikungunya virus E protein complexed with 8D1-H-10D5. Determined by electron microscopy at 2.97 Å resolution. Released 12 Aug 2026.

Method: Electron microscopy
Resolution: 2.97 Å
Organisms: Homo sapiens, Chikungunya virus (strain 37997), Camelus bactrianus
Chains: 4
Atoms: 5,733
Mol. weight: 108.65 kDa
Released: 12 Aug 2026

Explore 9W7J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9W7J contains 14 α-helices and 78 β-strands across 4 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: 0 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	34-38	5	2
β-strand	45-49	5	2
β-strand	53-54	2	2
β-strand	62-67	6	1
β-strand	70-75	6	1
β-strand	85-89	5	2
β-strand	90	1	3
β-strand	93	1	3
β-strand	98-102	5	2

Chain B: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	4
β-strand	11-12	2	5
β-strand	18-25	8	4
β-strand	32-39	8	6
β-strand	45-51	7	6
β-strand	58-60	3	6
β-strand	68-73	6	4
β-strand	78-83	6	4
α-helix	88-90	3
β-strand	92-100	9	6
β-strand	107-110	4	6
β-strand	114-116	3	6
β-strand	117-118	2	5

Chain C: 9 helices, 42 β-strands

Element	Residues	Length	Sheet
α-helix	69-74	6
β-strand	77-78	2	7
β-strand	82-84	3	8
β-strand	86	1	9
β-strand	93-95	3	8
β-strand	99-103	5	10
β-strand	110-121	12	10
β-strand	127-136	10	10
β-strand	139-144	6	10
α-helix	145-147	3
β-strand	149-151	3	9
β-strand	155	1	9
β-strand	157-169	13	10
β-strand	173-181	9	9
β-strand	187-196	10	9
β-strand	217-221	5	11
β-strand	231-235	5	7
α-helix	236-239	4
β-strand	240-241	2	12
β-strand	246-247	2	13
β-strand	253-255	3	13
β-strand	262-265	4	12
β-strand	274-276	3	12
β-strand	280-282	3	13
β-strand	291-294	4	12
β-strand	300-302	3	7
α-helix	308-309	2
β-strand	316-321	6	7
β-strand	326-330	5	11
β-strand	472-475	4	14
β-strand	477-480	4	15
β-strand	485-487	3	16
β-strand	490	1	17
β-strand	504-507	4	16
β-strand	513-514	2	18
β-strand	517-518	2	18
β-strand	526	1	17
β-strand	527-531	5	16
β-strand	533-536	4	15
α-helix	538-541	4
β-strand	544-547	4	14
β-strand	605-606	2	14
β-strand	609-610	2	14
α-helix	616-617	2
β-strand	629-630	2	19
β-strand	640-641	2	19
β-strand	646-647	2	20
α-helix	648-651	4
β-strand	659-660	2	20
α-helix	662-664	3
α-helix	665-672	8

Chain D: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	21
β-strand	12-13	2	22
β-strand	17-26	10	21
β-strand	33-39	7	23
β-strand	45-52	8	23
β-strand	57-59	3	23
α-helix	61-63	3
β-strand	67-71	5	21
β-strand	78-83	6	21
α-helix	87-89	3
β-strand	91-98	8	23
α-helix	99	1
α-helix	100-103	4
β-strand	110-112	3	23
β-strand	117-119	3	23
β-strand	121-122	2	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
10D5 Light Chain	A	protein	103	Homo sapiens
10D5 Heavy Chain	B	protein	120	Homo sapiens
Spike glycoprotein E2,Spike glycoprotein E1	C	protein	649	Chikungunya virus (strain 37997)	Q5XXP3
10D5 Heavy Chain	D	protein	123	Camelus bactrianus

Sequence of entity 1 (A), FASTA

>9W7J_1 10D5 Light Chain (chains A)
DIVMTQSPATLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQSYFFGPGTKVDIK

Sequence of entity 2 (B), FASTA

>9W7J_2 10D5 Heavy Chain (chains B)
QVQLVESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCANKEDGDYVPFDYWGQGTLVTVSS

Sequence of entity 3 (C), FASTA

>9W7J_3 Spike glycoprotein E2,Spike glycoprotein E1 (chains C)
TKDNFNVYKATRPYLAHCPDCGEGHSCHSPIALERIRNEATDGTLKIQVSLQIGIKTDDS
HDWTKLRYMDSHTPADAERAGLLVRTSAPCTITGTMGHFILARCPKGETLTVGFTDSRKI
SHTCTHPFHHEPPVIGRERFHSRPQHGKELPCSTYVQSTAATAEEIEVHMPPDTPDRTLM
TQQSGNVKITVNGQTVRYKCNCGGSNEGLTTTDKVINNCKIDQCHAAVTNHKNWQYNSPL
VPRNAELGDRKGKIHIPFPLANVTCRVPKARNPTVTYGKNQVTMLLYPDHPTLLSYRNMG
QEPNYHEEWVTHKKEVTLTVPTEGLEVTWGNNEPYKYWPQGGGGSGGGGSGGGGSGGGGS
YEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELQSVTLEPTLSLDYITCEYKTVIPSPYV
KCCGTAECKDKSLPDYSCKVFTGVYPFMWGGAYCFCDAENTQLSEAHVEKSESCKTEFAS
AYRAHTASASAKLRVLYQGNNITVAAYANGDHAVTVKDAKFVVGPMSSAWTPFDNKIVVY
KGDVYNMDYPPFGAGRPGQFGDIQSRTPESKDVYANTQLVLQRPAAGTVHVPYSQAPSGF
KYWLKERGASLQHTAPFGCQIATNPVRAVNCAVGNIPISIDIPDAAFTR

Sequence of entity 4 (D), FASTA

>9W7J_4 10D5 Heavy Chain (chains D)
QVQLQESGGGSVQSGGSLRLSCAVSGYTYSSYCRGWFRQAPGKEREGVAGIDSDGSTRYA
DSVKGRFTISQDNAKNTLYLQMNSLKPEDTAMYYCAEVFCDSFHQGKYEAFYWGQGTQVT
VSS

Primary citation

Chikungunya virus E protein complexed with 8D1-H-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:

9W89 2.89 Å, Chikungunya virus E protein complexed with 10D5
9W8A 2.95 Å, Chikungunya virus E protein complexed with 7H9
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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