8DWX: Chikungunya VLP

Chikungunya VLP in complex with neutralizing Fab 506.C01 (asymmetric unit). Determined by electron microscopy at 3.27 Å resolution. Released 31 May 2023.

Method: Electron microscopy
Resolution: 3.27 Å
Organisms: Chikungunya virus strain Senegal 37997, Homo sapiens
Chains: 20
Atoms: 38,228
Mol. weight: 547.59 kDa
Ligands: NAG
Released: 31 May 2023

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

Secondary structure: helices and β-sheets

8DWX contains 100 α-helices and 474 β-strands across 20 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: 9 helices, 42 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	27-39	13	2
β-strand	42-48	7	4
β-strand	51-54	4	5
α-helix	56-58	3
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	119-124	6	4
β-strand	128-137	10	2
β-strand	140-147	8	2
β-strand	154-155	2	1
β-strand	160-163	4	1
β-strand	176-180	5	4
β-strand	183-186	4	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	219-221	3	9
α-helix	223-225	3
β-strand	233-235	3	9
α-helix	236-238	3
α-helix	239-246	8
α-helix	251-254	4
β-strand	260-263	4	2
β-strand	266-269	4	2
β-strand	275-281	7	1
α-helix	284-286	3
β-strand	289	1	3
β-strand	296	1	10
β-strand	300-306	7	11
β-strand	307	1	12
β-strand	314-321	8	11
β-strand	322	1	10
β-strand	326-329	4	13
β-strand	330-332	3	14
β-strand	338-339	2	11
β-strand	343-346	4	13
β-strand	349-357	9	11
β-strand	362-369	8	14
β-strand	373-379	7	14
β-strand	381	1	12
β-strand	387-388	2	15
α-helix	404-438	35

Chain B: 8 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	16
β-strand	15-19	5	17
β-strand	24	1	18
β-strand	27-39	13	17
β-strand	42-48	7	19
β-strand	51-54	4	20
β-strand	59-61	3	21
β-strand	77-82	6	21
β-strand	87-88	2	22
β-strand	91-92	2	22
β-strand	101-106	6	21
β-strand	107-110	4	20
α-helix	112-115	4
β-strand	119-124	6	19
β-strand	128-137	10	17
β-strand	140-147	8	17
β-strand	154-156	3	16
β-strand	159-163	5	16
β-strand	176-180	5	19
β-strand	183-186	4	19
α-helix	189-191	3
β-strand	203-204	2	23
β-strand	205	1	19
β-strand	214-215	2	23
β-strand	219-221	3	24
α-helix	223-225	3
β-strand	233-235	3	24
α-helix	236-238	3
α-helix	239-244	6
α-helix	251-254	4
β-strand	260-263	4	17
β-strand	266-269	4	17
β-strand	275-281	7	16
α-helix	284-286	3
β-strand	289	1	18
β-strand	296	1	25
β-strand	300-306	7	26
β-strand	307	1	27
β-strand	314-321	8	26
β-strand	322	1	25
β-strand	326-329	4	28
β-strand	330-332	3	29
β-strand	338-339	2	26
β-strand	343-346	4	28
β-strand	349-357	9	26
β-strand	362-369	8	29
β-strand	373-379	7	29
β-strand	381	1	27
β-strand	387-388	2	30
α-helix	404-438	35

Chain C: 9 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	31
β-strand	15-19	5	32
β-strand	24	1	33
β-strand	27-39	13	32
β-strand	42-48	7	34
β-strand	51-54	4	35
β-strand	59-62	4	36
β-strand	77-82	6	36
β-strand	87-88	2	37
β-strand	91-92	2	37
β-strand	100-106	7	36
β-strand	107-110	4	35
α-helix	112-115	4
β-strand	119-124	6	34
β-strand	128-137	10	32
β-strand	140-147	8	32
β-strand	152	1	38
β-strand	154-156	3	31
β-strand	159-163	5	31
β-strand	176-180	5	34
β-strand	183-186	4	34
α-helix	189-191	3
β-strand	192	1	39
β-strand	203-204	2	40
β-strand	205	1	34
β-strand	214-215	2	40
β-strand	219-221	3	41
α-helix	223-225	3
β-strand	233-235	3	41
α-helix	236-238	3
α-helix	239-246	8
α-helix	251-254	4
α-helix	256-258	3
β-strand	260-263	4	32
β-strand	266-269	4	32
β-strand	275-281	7	31
α-helix	284-286	3
β-strand	289	1	33
β-strand	296	1	42
β-strand	300-306	7	43
β-strand	307	1	44
β-strand	314-321	8	43
β-strand	322	1	42
β-strand	326-329	4	45
β-strand	330-332	3	46
β-strand	337-339	3	43
β-strand	343-346	4	45
β-strand	349-358	10	43
β-strand	362-369	8	46
β-strand	373-379	7	46
β-strand	381	1	44
β-strand	387-388	2	47
α-helix	404-438	35

Chain D: 10 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	48
β-strand	15-19	5	49
β-strand	24	1	50
β-strand	27-39	13	49
β-strand	42-48	7	51
β-strand	51-54	4	52
α-helix	56-58	3
β-strand	59-61	3	53
β-strand	77-82	6	53
β-strand	87-88	2	54
β-strand	91-92	2	54
β-strand	101-106	6	53
β-strand	107-110	4	52
α-helix	112-115	4
β-strand	119-124	6	51
β-strand	128-137	10	49
β-strand	140-147	8	49
β-strand	152	1	39
β-strand	154-156	3	48
β-strand	159-163	5	48
β-strand	176-180	5	51
β-strand	183-186	4	51
α-helix	189-191	3
β-strand	192	1	38
β-strand	203-204	2	55
β-strand	205	1	51
β-strand	214-215	2	55
β-strand	219-221	3	56
α-helix	223-225	3
β-strand	233-235	3	56
α-helix	236-238	3
α-helix	239-245	7
α-helix	251-254	4
β-strand	260-263	4	49
β-strand	266-269	4	49
β-strand	275-281	7	48
α-helix	284-286	3
β-strand	289	1	50
β-strand	296-306	11	57
β-strand	307	1	58
β-strand	314-322	9	57
β-strand	326-329	4	59
β-strand	330-332	3	60
β-strand	337-339	3	61
β-strand	343-346	4	59
β-strand	349-354	6	57
β-strand	356-358	3	61
β-strand	362-369	8	60
β-strand	373-379	7	60
β-strand	381	1	58
β-strand	387-388	2	62
α-helix	395-397	3
α-helix	404-438	35

Chains H, V and X: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	115
β-strand	11-12	2	116
β-strand	18-25	8	115
β-strand	34-41	8	117
β-strand	48-53	6	117
β-strand	59-61	3	117
β-strand	69-71	3	115
β-strand	74	1	115
β-strand	79-84	6	115
α-helix	89-91	3
β-strand	94-101	8	117
β-strand	117-118	2	117
β-strand	122-123	2	117
β-strand	125-126	2	116

Chains L, W and Y: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	112
β-strand	10-13	4	113
β-strand	19-25	7	112
β-strand	30	1	114
β-strand	33-38	6	113
β-strand	44-49	6	113
β-strand	53-54	2	113
β-strand	62-67	6	112
β-strand	68	1	114
β-strand	70-75	6	112
α-helix	80-82	3
β-strand	85-90	6	113
α-helix	96	1
β-strand	98	1	113
β-strand	102-106	5	113

Chain M: 8 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
β-strand	12	1	63
β-strand	17-19	3	64
β-strand	28-30	3	64
β-strand	34	1	65
β-strand	38	1	66
β-strand	46-56	11	66
β-strand	62-71	10	66
β-strand	74-79	6	66
α-helix	80-82	3
β-strand	84-86	3	67
β-strand	90	1	67
β-strand	92-104	13	66
β-strand	108-116	9	67
β-strand	122-131	10	67
β-strand	139	1	68
β-strand	149-156	8	69
β-strand	166-170	5	70
β-strand	175-176	2	71
α-helix	178-180	3
β-strand	182-184	3	72
β-strand	187-190	4	72
β-strand	197-201	5	71
β-strand	208-211	4	71
β-strand	215-217	3	72
β-strand	225-229	5	71
β-strand	235	1	63
β-strand	236	1	70
β-strand	251-256	6	70
β-strand	261-268	8	69
α-helix	271-273	3
β-strand	275-279	5	73
β-strand	282-287	6	73
β-strand	293-299	7	68
β-strand	307-311	5	68
β-strand	315-320	6	73
β-strand	326-330	5	68
β-strand	336-338	3	68
β-strand	339-340	2	15
α-helix	352-362	11
α-helix	364-397	34
α-helix	398-401	4
α-helix	410-414	5

Chain N: 8 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
β-strand	12	1	74
β-strand	17-19	3	75
β-strand	28-30	3	75
β-strand	34-38	5	76
β-strand	46-56	11	76
β-strand	62-70	9	76
β-strand	75-79	5	76
α-helix	80-82	3
β-strand	84-87	4	77
β-strand	89-90	2	77
β-strand	92-104	13	76
β-strand	108-116	9	77
β-strand	122-131	10	77
β-strand	139	1	78
β-strand	148-156	9	79
β-strand	166-170	5	80
β-strand	175-176	2	81
α-helix	178-180	3
β-strand	181-184	4	82
β-strand	187-190	4	82
β-strand	197-201	5	81
β-strand	208-211	4	81
β-strand	215-217	3	82
β-strand	225-229	5	81
β-strand	235	1	74
β-strand	236-237	2	80
α-helix	249-251	3
β-strand	253-256	4	80
β-strand	261-269	9	79
α-helix	271-274	4
β-strand	275-279	5	83
β-strand	282-287	6	83
β-strand	293-299	7	78
β-strand	307-311	5	78
β-strand	315-320	6	83
β-strand	326-330	5	78
β-strand	336-338	3	78
β-strand	339-340	2	30
α-helix	352-360	9
α-helix	364-402	39
α-helix	410-414	5

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
E1 glycoprotein	A, B, C, D	protein	439	Chikungunya virus strain Senegal 37997	Q5XXP3
E2 glycoprotein	M, N, O, P	protein	419	Chikungunya virus strain Senegal 37997	Q5XXP3
Capsid protein	Q, R, S, T	protein	151	Chikungunya virus strain Senegal 37997	Q5XXP3
506.C01 light chain	L, U, W, Y	protein	107	Homo sapiens
506.C01 heavy chain	H, V, X, Z	protein	128	Homo sapiens

Sequence of entity 1 (A, B, C, D), FASTA

>8DWX_1 E1 glycoprotein (chains A, B, C, D)
YEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELQSVTLEPTLSLDYITCEYKTVIPSPYV
KCCGTAECKDKSLPDYSCKVFTGVYPFMWGGAYCFCDAENTQLSEAHVEKSESCKTEFAS
AYRAHTASASAKLRVLYQGNNITVAAYANGDHAVTVKDAKFVVGPMSSAWTPFDNKIVVY
KGDVYNMDYPPFGAGRPGQFGDIQSRTPESKDVYANTQLVLQRPAAGTVHVPYSQAPSGF
KYWLKERGASLQHTAPFGCQIATNPVRAVNCAVGNIPISIDIPDAAFTRVVDAPSVTDMS
CEVPACTHSSDFGGVAIIKYTASKKGKCAVHSMTNAVTIREADVEVEGNSQLQISFSTAL
ASAEFRVQVCSTQVHCAAACHPPKDHIVNYPASHTTLGVQDISTTAMSWVQKITGGVGLI
VAVAALILIVVLCVSFSRH

Sequence of entity 2 (M, N, O, P), FASTA

>8DWX_2 E2 glycoprotein (chains M, N, O, P)
NFNVYKATRPYLAHCPDCGEGHSCHSPIALERIRNEATDGTLKIQVSLQIGIKTDDSHDW
TKLRYMDSHTPADAERAGLLVRTSAPCTITGTMGHFILARCPKGETLTVGFTDSRKISHT
CTHPFHHEPPVIGRERFHSRPQHGKELPCSTYVQSTAATAEEIEVHMPPDTPDRTLMTQQ
SGNVKITVNGQTVRYKCNCGGSNEGLTTTDKVINNCKIDQCHAAVTNHKNWQYNSPLVPR
NAELGDRKGKIHIPFPLANVTCRVPKARNPTVTYGKNQVTMLLYPDHPTLLSYRNMGQEP
NYHEEWVTHKKEVTLTVPTEGLEVTWGNNEPYKYWPQMSTNGTAHGHPHEIILYYYELYP
TMTVVIVSVASFVLLSMVGTAVGMCVCARRRCITPYELTPGATVPFLLSLLCCVRTTKA

Sequence of entity 3 (Q, R, S, T), FASTA

>8DWX_3 Capsid protein (chains Q, R, S, T)
NDCIFEVKHEGKVMGYACLVGDKVMKPAHVKGTIDNADLAKLAFKRSSKYDLECAQIPVH
MKSDASKFTHEKPEGYYNWHHGAVQYSGGRFTIPTGAGKPGDSGRPIFDNKGRVVAIVLG
GANEGARTALSVVTWNKDIVTKITPEGAEEW

Sequence of entity 4 (L, U, W, Y), FASTA

>8DWX_4 506.C01 light chain (chains L, U, W, Y)
DIQMTQSPSSVSASVGDRVTITCRASQGISSWLGWYQQKPGKAPKLLIYAASSLQSGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQANSFPRTFGQGTKVEIK

Sequence of entity 5 (H, V, X, Z), FASTA

>8DWX_5 506.C01 heavy chain (chains H, V, X, Z)
QVQLQESGPGLVKPSQTLSLTCTVSGGSISSDDYYWTWIRLPPGKGLEWIGYIFYTGGTY
YNPSLKSRVTISLDRSKNQFSLKLSSVTAADTAVYFCARAPETYCSTTNCYKGYFDSWGQ
GTLVTVSS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	12

Primary citation

A chikungunya virus-like particle vaccine induces broadly neutralizing and protective antibodies against alphaviruses in humans. Raju, S., Adams, L.J., Earnest, J.T. et al. Sci Transl Med (2023) 15:eade8273-eade8273. DOI 10.1126/scitranslmed.ade8273 · 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)
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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