9J6D: Chikungunya virus infectious particles, 2f block

Name: PDB 9J6D: Structure of Chikungunya virus infectious particles, 2f block.
Published: 2025-12-03
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Structure of Chikungunya virus infectious particles, 2f block. Determined by electron microscopy at 3.11 Å resolution. Released 3 Dec 2025.

Method: Electron microscopy
Resolution: 3.11 Å
Organism: Chikungunya virus
Chains: 16
Atoms: 32,993
Mol. weight: 472.04 kDa
Released: 3 Dec 2025

Explore 9J6D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9J6D contains 130 α-helices and 363 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: 11 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	2
β-strand	14-19	6	3
β-strand	24	1	4
β-strand	27-48	22	3
β-strand	51-54	4	5
α-helix	56-58	3
β-strand	59-62	4	5
β-strand	76-82	7	5
β-strand	87-88	2	6
β-strand	91-92	2	6
β-strand	100-110	11	5
α-helix	112-115	4
β-strand	119-137	19	3
β-strand	140-147	8	3
β-strand	153-156	4	2
β-strand	159-163	5	2
β-strand	176-179	4	3
β-strand	184-185	2	3
α-helix	189-191	3
β-strand	203-205	3	3
β-strand	213-215	3	3
β-strand	220-221	2	7
α-helix	223-225	3
β-strand	233-234	2	7
α-helix	236-238	3
α-helix	239-245	7
α-helix	251-254	4
α-helix	256-258	3
β-strand	260-262	3	3
β-strand	267-269	3	3
β-strand	275-281	7	2
α-helix	284-286	3
β-strand	289	1	4
β-strand	296-305	10	8
β-strand	307	1	9
β-strand	314-322	9	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	362-369	8	11
β-strand	372-379	8	11
β-strand	381	1	9
β-strand	387-388	2	12
α-helix	395-397	3
α-helix	404-437	34

Chain B: 12 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	13
β-strand	14-19	6	14
β-strand	24	1	15
β-strand	27-48	22	14
β-strand	51-54	4	16
α-helix	56-58	3
β-strand	59-62	4	17
β-strand	77-82	6	17
β-strand	87-88	2	18
β-strand	91-92	2	18
β-strand	100-106	7	17
β-strand	107-110	4	16
α-helix	112-115	4
β-strand	119-137	19	14
β-strand	140-147	8	14
β-strand	154-156	3	13
β-strand	159-163	5	13
β-strand	176-179	4	14
β-strand	184-186	3	14
α-helix	189-191	3
β-strand	203-205	3	14
β-strand	213-215	3	14
β-strand	220-221	2	19
α-helix	223-225	3
β-strand	233-234	2	19
α-helix	236-238	3
α-helix	239-245	7
α-helix	251-254	4
α-helix	256-258	3
β-strand	260-262	3	14
β-strand	267-269	3	14
β-strand	275-281	7	13
α-helix	284-286	3
β-strand	289	1	15
β-strand	296-306	11	20
β-strand	307	1	21
β-strand	314-322	9	20
β-strand	326-329	4	22
β-strand	330-332	3	23
β-strand	337-339	3	20
β-strand	343-346	4	22
β-strand	349-358	10	20
β-strand	362-369	8	23
β-strand	372-379	8	23
α-helix	380	1
β-strand	381	1	21
α-helix	382-383	2
β-strand	387-388	2	24
α-helix	404-437	34

Chain C: 12 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	25
β-strand	11	1	26
β-strand	14-19	6	26
β-strand	24	1	27
β-strand	27-48	22	26
β-strand	51-54	4	28
α-helix	56-58	3
β-strand	59-61	3	29
β-strand	77-82	6	29
β-strand	87-88	2	30
β-strand	91-92	2	30
β-strand	101-106	6	29
β-strand	107-110	4	28
α-helix	112-115	4
β-strand	119-137	19	26
β-strand	140-147	8	26
β-strand	154-156	3	25
β-strand	159-163	5	25
β-strand	176-179	4	26
β-strand	184-185	2	26
α-helix	189-191	3
β-strand	192	1	31
β-strand	203-205	3	26
β-strand	213-215	3	26
β-strand	220-221	2	32
α-helix	223-225	3
β-strand	233-234	2	32
α-helix	236-238	3
α-helix	239-246	8
α-helix	251-254	4
β-strand	260-262	3	26
β-strand	267-269	3	26
β-strand	275-281	7	25
α-helix	284-286	3
β-strand	289	1	27
β-strand	296-305	10	33
β-strand	307	1	34
β-strand	315-322	8	33
β-strand	326-329	4	35
β-strand	330-332	3	36
β-strand	337-339	3	37
β-strand	343-346	4	35
β-strand	349-355	7	33
β-strand	356-358	3	37
β-strand	362-369	8	36
β-strand	372-379	8	36
α-helix	380	1
β-strand	381	1	34
α-helix	382-383	2
β-strand	387-388	2	38
α-helix	396-398	3
α-helix	404-435	32

Chain D: 14 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	39
β-strand	15-19	5	40
β-strand	24	1	41
β-strand	27-49	23	40
β-strand	51-54	4	42
α-helix	56-58	3
β-strand	59-61	3	43
β-strand	77-82	6	43
β-strand	87-88	2	44
β-strand	91-92	2	44
β-strand	101-106	6	43
β-strand	107-110	4	42
α-helix	112-115	4
β-strand	118-137	20	40
β-strand	140-147	8	40
β-strand	152	1	31
β-strand	153-156	4	39
β-strand	159-163	5	39
β-strand	176-180	5	40
β-strand	183-186	4	40
α-helix	189-191	3
β-strand	203-205	3	40
β-strand	213-215	3	40
β-strand	220-221	2	45
α-helix	223-225	3
β-strand	233-234	2	45
α-helix	236-238	3
α-helix	239-245	7
α-helix	251-254	4
α-helix	256-258	3
β-strand	260-262	3	40
β-strand	267-269	3	40
β-strand	275-281	7	39
α-helix	284-286	3
β-strand	289	1	41
α-helix	290-292	3
α-helix	294-295	2
β-strand	296-305	10	46
β-strand	307	1	47
β-strand	314-322	9	46
β-strand	326-329	4	48
β-strand	331-332	2	49
β-strand	337-339	3	46
β-strand	343-346	4	48
β-strand	349-358	10	46
β-strand	362	1	50
β-strand	365-368	4	49
β-strand	373-376	4	49
β-strand	379	1	50
α-helix	380	1
β-strand	381	1	47
α-helix	382-383	2
β-strand	387-388	2	51
α-helix	404-435	32

Chain E: 14 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	8-11	4
β-strand	12	1	52
β-strand	17-19	3	53
β-strand	28-30	3	53
β-strand	34-38	5	54
β-strand	45-54	10	54
β-strand	66-71	6	54
β-strand	74-79	6	54
α-helix	80-82	3
β-strand	84-86	3	55
β-strand	90	1	55
α-helix	91	1
β-strand	92-104	13	54
α-helix	105-106	2
β-strand	108-116	9	55
β-strand	122-131	10	55
α-helix	133-136	4
β-strand	139	1	56
β-strand	149-156	8	57
β-strand	166-170	5	58
α-helix	171-174	4
β-strand	175-176	2	59
β-strand	181-183	3	60
β-strand	188-190	3	60
α-helix	191	1
β-strand	197-201	5	59
β-strand	208-211	4	59
β-strand	215-217	3	60
α-helix	222-224	3
β-strand	225-229	5	59
β-strand	235	1	52
β-strand	236-237	2	58
β-strand	244	1	5
β-strand	253-256	4	58
α-helix	257	1
β-strand	261-268	8	57
α-helix	271-274	4
β-strand	275-279	5	61
β-strand	282-287	6	61
β-strand	293-299	7	56
β-strand	307-311	5	56
β-strand	315-320	6	61
β-strand	326-330	5	56
α-helix	334-335	2
β-strand	336-338	3	56
β-strand	339-340	2	12
α-helix	352-362	11
α-helix	366-401	36
α-helix	410-415	6

Chain F: 13 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	8-11	4
β-strand	12	1	62
β-strand	17-19	3	63
β-strand	28-30	3	63
β-strand	34-38	5	64
β-strand	45-56	12	64
β-strand	62-70	9	64
β-strand	75-79	5	64
α-helix	80-82	3
β-strand	84-86	3	65
β-strand	90	1	65
α-helix	91	1
β-strand	92-104	13	64
α-helix	105-106	2
β-strand	108-116	9	65
β-strand	122-131	10	65
α-helix	133-136	4
β-strand	139	1	66
β-strand	149-156	8	67
β-strand	166-170	5	68
α-helix	171-174	4
β-strand	175-176	2	69
β-strand	181-184	4	70
β-strand	187-190	4	70
β-strand	197-201	5	69
β-strand	208-211	4	69
β-strand	217-218	2	70
α-helix	222-224	3
β-strand	225-229	5	69
β-strand	235	1	62
β-strand	236-237	2	68
β-strand	253-256	4	68
α-helix	257	1
β-strand	261-268	8	67
α-helix	271-274	4
β-strand	275-279	5	71
β-strand	282-287	6	71
β-strand	293-299	7	66
β-strand	307-311	5	66
β-strand	315-320	6	71
β-strand	326-330	5	66
α-helix	334-335	2
β-strand	336-338	3	66
β-strand	339-340	2	24
α-helix	352-362	11
α-helix	364-402	39
α-helix	410-415	6

Chain G: 14 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	8-11	4
β-strand	12	1	72
β-strand	17-19	3	73
β-strand	28-30	3	73
β-strand	34-38	5	74
β-strand	45-56	12	74
β-strand	62-71	10	74
β-strand	74-79	6	74
α-helix	80-82	3
β-strand	84-86	3	75
β-strand	90-91	2	75
β-strand	92-104	13	74
α-helix	105-106	2
β-strand	108-116	9	75
β-strand	122-131	10	75
α-helix	133-136	4
β-strand	139	1	76
β-strand	148-156	9	77
β-strand	166-170	5	78
α-helix	171-174	4
β-strand	175-176	2	79
α-helix	178-180	3
β-strand	181-183	3	80
β-strand	188-190	3	80
α-helix	191	1
β-strand	196-201	6	79
β-strand	209-211	3	79
β-strand	215-216	2	80
α-helix	222-224	3
β-strand	225-230	6	79
β-strand	235	1	72
β-strand	236-237	2	78
β-strand	253-256	4	78
α-helix	257	1
β-strand	261-269	9	77
α-helix	271-274	4
β-strand	275-279	5	81
β-strand	282-287	6	81
β-strand	293-299	7	76
β-strand	307-311	5	76
β-strand	315-320	6	81
β-strand	326-330	5	76
α-helix	334-335	2
β-strand	336-338	3	76
β-strand	339-340	2	38
α-helix	352-362	11
α-helix	366-401	36
α-helix	410-415	6

Chain H: 14 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	8-11	4
β-strand	12	1	82
β-strand	17-19	3	83
β-strand	28-30	3	83
β-strand	34-38	5	84
β-strand	45-56	12	84
β-strand	62-71	10	84
β-strand	74-79	6	84
α-helix	80-82	3
β-strand	84-86	3	85
β-strand	90	1	85
α-helix	91	1
β-strand	92-104	13	84
α-helix	105-106	2
β-strand	108-116	9	85
β-strand	122-131	10	85
α-helix	133-136	4
β-strand	139	1	86
β-strand	149-156	8	87
β-strand	166-170	5	88
α-helix	171-174	4
β-strand	175-176	2	89
α-helix	178-180	3
β-strand	181-184	4	90
β-strand	187-190	4	90
β-strand	197-201	5	89
β-strand	209-211	3	89
β-strand	215-217	3	90
α-helix	222-224	3
β-strand	225-229	5	89
β-strand	235	1	82
β-strand	236-237	2	88
β-strand	244	1	43
β-strand	253-256	4	88
β-strand	261-268	8	87
α-helix	271-274	4
β-strand	275-279	5	91
β-strand	282-287	6	91
β-strand	293-299	7	86
β-strand	307-311	5	86
β-strand	315-320	6	91
β-strand	326-330	5	86
α-helix	334-335	2
β-strand	336-338	3	86
β-strand	339-340	2	51
α-helix	352-362	11
α-helix	364-401	38
α-helix	410-412	3
α-helix	413-417	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
chikungunya E3	U, V, W, X	protein	55	Chikungunya virus	A0A7S7YHM2
chikungunya virus E1	A, B, C, D	protein	439	Chikungunya virus	A4L7I5
chikungunya E2	E, F, G, H	protein	414	Chikungunya virus	Q88628
CHIKV capsid protein	I, J, K, L	protein	151	Chikungunya virus	A0A6B9KBE1

Sequence of entity 1 (U, V, W, X), FASTA

>9J6D_1 chikungunya E3 (chains U, V, W, X)
PVMCLLANTTFPCSQPPCTPCCYEKEPEETLRMLEDNVMRPGYYQLLQASLTCSP

Sequence of entity 2 (A, B, C, D), FASTA

>9J6D_2 chikungunya virus E1 (chains A, B, C, D)
YEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELLSVTLEPTLSLDYITCEYKTVIPSPYV
KCCGTAECKDKSLPDYSCKVFTGVYPFMWGGAYCFCDTENTQLSEAHVEKSESCKTEFAS
AYRAHTASASAKLRVLYQGNNVTVSAYANGDHAVTVKDAKFIVGPMSSAWTPFDNKIVVY
KGDVYNMDYPPFGAGRPGQFGDIQSRTPESEDVYANTQLVLQRPSAGTVHVPYSQAPSGF
KYWLKERGASLQHTAPFGCQIATNPVRAMNCAVGNMPISIDIPDAAFTRVVDAPSLTDMS
CEVPACTHSSDFGGVAIIKYAASKKGKCAVHSMTNAVTIREAEIEVEGNSQLQISFSTAL
ASAEFRVQVCSTQVHCAAECHPPKDHIVNYPASHTTLGVQDISVTAMSWVQKITGGVGLV
VAVAALILIVVLCVSFSRH

Sequence of entity 3 (E, F, G, H), FASTA

>9J6D_3 chikungunya E2 (chains E, F, G, H)
NFNVYKAIRPYLAHCPDCGEGHSCHSPVALERIRNEATDGTLKIQVSLQIGIKTDDSHDW
TKLRYMDNHMPADAERARLFVRTSAPCTITGTMGHFILARCPKGETLTVGFTDGRKISHS
CTHPFHHDPPVIGREKFHSRPQHGRELPCSTYAQSTAATAEEIEVHMPPDTPDRTLMSQQ
SGNVKITVNSQTVRYKCNCGDSNEGLTTTDKVINNCKVDQCHAAVTNHKKWQYNSPLVPR
NAELGDRKGKVHIPFPLANVTCRVPKARNPTVTYGKNQVIMLLYPDHPTLLSYRNMGEEP
NYQEEWVTHKKEIRLTVPTEGLEVTWGNNEPYKYWPQLSTNGTAHGHPHEIILYYYELYP
TMTVVVVSVASFVLLSMVGVAVGMCMCARRRCITPYELTPGATVPFLLSLICCI

Sequence of entity 4 (I, J, K, L), FASTA

>9J6D_4 CHIKV capsid protein (chains I, J, K, L)
NDCIFEVKHEGKVTGYACLVGDKVMKPAHVKGTIDNADLAKLAFKRSSKYDLECAQIPVH
MKSDASKFTHEKPEGYYNWHHGAVQYSGGRFTIPTGAGKPGDSGRPIFDNKGRVVAIVLG
GANEGARTALSVVTWNKDIVTKITPEGAEEW

Primary citation

Neutralizing antibodies against Chikungunya virus and structural elucidation of their mechanism of action. Han, X., Ji, C., Tian, S. et al. Nat Commun (2025) 16:9682-9682. DOI 10.1038/s41467-025-64687-2 · PubMed

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