9BBN: Chikungunya virus asymmetric unit with Fab C9

Cryo-EM structure of Chikungunya virus asymmetric unit with Fab C9. Determined by electron microscopy at 3.3 Å resolution. Released 8 Oct 2025.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: Chikungunya virus, Mus musculus
Chains: 24
Atoms: 46,492
Mol. weight: 663.07 kDa
Released: 8 Oct 2025

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

Secondary structure: helices and β-sheets

9BBN contains 181 α-helices and 545 β-strands across 24 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: 14 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	29
β-strand	11	1	30
β-strand	14-19	6	30
β-strand	24	1	31
β-strand	27-49	23	30
β-strand	51-54	4	32
β-strand	59-61	3	33
β-strand	77-82	6	33
β-strand	87-88	2	34
β-strand	91-92	2	34
β-strand	101-106	6	33
β-strand	107-110	4	32
α-helix	112-115	4
β-strand	118-137	20	30
β-strand	140-146	7	30
α-helix	153	1
β-strand	154-156	3	29
β-strand	159-163	5	29
β-strand	176-179	4	30
β-strand	184-186	3	30
α-helix	189-191	3
β-strand	203-204	2	35
β-strand	205	1	30
β-strand	214-215	2	35
β-strand	220-221	2	36
α-helix	223-225	3
β-strand	233-234	2	36
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	30
β-strand	266-269	4	30
β-strand	275-281	7	29
α-helix	284-286	3
α-helix	287-288	2
β-strand	289	1	31
β-strand	296-306	11	37
β-strand	307	1	38
β-strand	314-329	16	37
β-strand	330-332	3	39
β-strand	337-339	3	37
β-strand	343-358	16	37
β-strand	364-369	6	39
β-strand	372-377	6	39
β-strand	381	1	38
α-helix	382-383	2
β-strand	387-388	2	40
α-helix	395-397	3
α-helix	405-408	4
α-helix	409-435	27

Chain B: 12 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	66
β-strand	14-19	6	67
β-strand	24	1	68
β-strand	27-49	23	67
β-strand	51-54	4	69
α-helix	56-58	3
β-strand	59-61	3	70
β-strand	77-82	6	70
β-strand	87	1	71
β-strand	92	1	71
β-strand	101-106	6	70
β-strand	107-110	4	69
α-helix	112-115	4
β-strand	118-137	20	67
β-strand	140-147	8	67
β-strand	154-156	3	66
β-strand	159-163	5	66
β-strand	176-180	5	67
β-strand	183-185	3	67
α-helix	189-191	3
β-strand	203-204	2	72
β-strand	205	1	67
β-strand	214-215	2	72
β-strand	220-221	2	73
α-helix	223-225	3
β-strand	233-234	2	73
α-helix	236-238	3
α-helix	239-246	8
α-helix	251-254	4
β-strand	260-263	4	67
β-strand	266-269	4	67
β-strand	275-281	7	66
α-helix	284-286	3
β-strand	289	1	68
β-strand	296-307	12	74
β-strand	314-329	16	74
β-strand	330-332	3	75
β-strand	337-339	3	74
β-strand	343-358	16	74
β-strand	364-369	6	75
β-strand	372-377	6	75
β-strand	380-381	2	74
α-helix	382-383	2
β-strand	387-388	2	76
α-helix	395-397	3
α-helix	403-404	2
α-helix	409-437	29

Chain C: 11 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	3
β-strand	15-19	5	4
β-strand	24	1	5
β-strand	27-49	23	4
β-strand	51-54	4	6
β-strand	59-61	3	7
β-strand	77-82	6	7
β-strand	87-88	2	8
β-strand	91-92	2	8
β-strand	101-106	6	7
β-strand	107-110	4	6
α-helix	112-115	4
β-strand	118-137	20	4
β-strand	140-144	5	4
β-strand	147	1	4
β-strand	152	1	9
β-strand	153-156	4	3
β-strand	159-163	5	3
β-strand	176-180	5	4
β-strand	183-186	4	4
α-helix	189-191	3
α-helix	195-196	2
β-strand	203-204	2	10
β-strand	205	1	4
β-strand	214-215	2	10
β-strand	220-221	2	11
α-helix	223-225	3
β-strand	233-234	2	11
α-helix	239-246	8
α-helix	251-254	4
β-strand	260-261	2	4
β-strand	268-269	2	4
β-strand	275-281	7	3
α-helix	284-286	3
β-strand	289	1	5
β-strand	296-306	11	12
β-strand	307	1	13
β-strand	314-322	9	12
β-strand	326-329	4	14
β-strand	331-332	2	15
β-strand	337-339	3	12
β-strand	343-346	4	14
β-strand	349-358	10	12
β-strand	364-369	6	15
β-strand	372-377	6	15
α-helix	380	1
β-strand	381	1	13
α-helix	382-383	2
β-strand	387-388	2	16
α-helix	405-407	3
α-helix	408-436	29

Chain D: 13 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	125
β-strand	11	1	126
β-strand	15-19	5	126
β-strand	24	1	127
α-helix	25-26	2
β-strand	27-49	23	126
β-strand	51-54	4	128
β-strand	59-61	3	129
β-strand	77-82	6	129
β-strand	87-88	2	130
β-strand	91-92	2	130
β-strand	101-106	6	129
β-strand	107-110	4	128
α-helix	112-115	4
β-strand	118-137	20	126
β-strand	140-147	8	126
β-strand	154-156	3	125
β-strand	159-163	5	125
β-strand	176-180	5	126
β-strand	183-186	4	126
α-helix	189-191	3
β-strand	192	1	9
β-strand	203-204	2	131
β-strand	205	1	126
β-strand	214-215	2	131
β-strand	220-221	2	132
α-helix	223-225	3
β-strand	233-234	2	132
α-helix	236-238	3
α-helix	239-245	7
α-helix	251-254	4
β-strand	260-263	4	126
β-strand	266-269	4	126
β-strand	275-281	7	125
α-helix	284-286	3
β-strand	289	1	127
β-strand	296-306	11	133
β-strand	307	1	134
β-strand	314-322	9	133
β-strand	326-329	4	135
β-strand	330-332	3	136
β-strand	337-339	3	133
β-strand	343-346	4	135
β-strand	349-358	10	133
β-strand	362-369	8	136
β-strand	373-379	7	136
β-strand	381	1	134
α-helix	382-383	2
β-strand	387-388	2	137
α-helix	391-392	2
α-helix	395-397	3
α-helix	403-404	2
α-helix	409-437	29

Chain E: 12 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
β-strand	12	1	41
β-strand	17-19	3	42
β-strand	28-30	3	42
β-strand	34-38	5	43
β-strand	46-56	11	43
β-strand	62-71	10	43
β-strand	74-79	6	43
α-helix	80-82	3
β-strand	84-86	3	44
β-strand	90	1	44
β-strand	92-104	13	43
β-strand	108-116	9	44
β-strand	122-131	10	44
α-helix	133-136	4
β-strand	139	1	45
β-strand	148-156	9	46
β-strand	166-168	3	47
β-strand	169-170	2	48
α-helix	171-174	4
β-strand	175-176	2	49
α-helix	178-180	3
β-strand	181-185	5	50
β-strand	187-190	4	50
β-strand	197-201	5	49
β-strand	209-211	3	49
β-strand	215-217	3	50
α-helix	222-224	3
β-strand	225-229	5	49
β-strand	235	1	41
β-strand	236-237	2	48
β-strand	254-256	3	47
α-helix	260	1
β-strand	261-269	9	46
α-helix	271-274	4
β-strand	275-279	5	51
β-strand	282-287	6	51
β-strand	293-299	7	45
β-strand	307-311	5	45
β-strand	315-320	6	51
β-strand	326-330	5	45
α-helix	334-335	2
β-strand	336-338	3	45
β-strand	339-340	2	40
α-helix	352-362	11
α-helix	364-401	38
α-helix	410-415	6

Chain F: 12 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	6-11	6
β-strand	12	1	91
β-strand	17-19	3	92
β-strand	28-30	3	92
β-strand	34-38	5	93
β-strand	45-54	10	93
β-strand	66-71	6	93
β-strand	74-79	6	93
α-helix	80-82	3
β-strand	84-86	3	94
β-strand	90	1	94
β-strand	92-104	13	93
β-strand	108-116	9	94
β-strand	122-131	10	94
α-helix	133-135	3
β-strand	139	1	95
β-strand	149-156	8	96
β-strand	166-170	5	97
α-helix	171-174	4
β-strand	175-176	2	98
α-helix	178-180	3
β-strand	181-183	3	99
β-strand	188-190	3	99
β-strand	197-201	5	98
β-strand	209-211	3	98
β-strand	215-217	3	99
α-helix	222-224	3
β-strand	225-229	5	98
β-strand	235	1	91
β-strand	236-237	2	97
β-strand	253-256	4	97
α-helix	257	1
β-strand	261-268	8	96
α-helix	271-274	4
β-strand	275-279	5	100
β-strand	282-287	6	100
β-strand	293-299	7	95
β-strand	307-311	5	95
β-strand	315-320	6	100
β-strand	326-330	5	95
α-helix	334-335	2
β-strand	336-338	3	95
β-strand	339-340	2	76
α-helix	352-362	11
α-helix	364-401	38
α-helix	410-415	6

Chain G: 12 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
β-strand	12	1	17
β-strand	17-19	3	18
β-strand	28-30	3	18
β-strand	34-38	5	19
β-strand	45-56	12	19
β-strand	62-71	10	19
β-strand	74-79	6	19
α-helix	80-82	3
β-strand	84-86	3	20
β-strand	90	1	20
α-helix	91	1
β-strand	92-104	13	19
β-strand	108-116	9	20
β-strand	122-131	10	20
α-helix	133-135	3
β-strand	139	1	21
β-strand	149-156	8	22
β-strand	166-168	3	23
β-strand	169-170	2	24
α-helix	171-174	4
β-strand	175-176	2	25
α-helix	178-180	3
β-strand	181-183	3	26
β-strand	188-190	3	26
β-strand	197-201	5	25
β-strand	209-211	3	25
β-strand	215-217	3	26
α-helix	222-224	3
β-strand	225-229	5	25
β-strand	235	1	17
β-strand	236-237	2	24
β-strand	246	1	27
β-strand	249	1	27
β-strand	254-256	3	23
β-strand	261-268	8	22
α-helix	271-274	4
β-strand	275-279	5	28
β-strand	282-287	6	28
β-strand	293-299	7	21
β-strand	307-311	5	21
β-strand	315-320	6	28
β-strand	326-330	5	21
α-helix	334-335	2
β-strand	336-338	3	21
β-strand	339-340	2	16
α-helix	352-362	11
α-helix	364-402	39
α-helix	410-415	6

Chain H: 12 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	6-10	5
β-strand	12	1	152
β-strand	17-19	3	153
β-strand	28-30	3	153
β-strand	34-38	5	154
β-strand	46-54	9	154
β-strand	66-67	2	154
β-strand	71	1	155
β-strand	74	1	155
β-strand	78-79	2	154
α-helix	80-82	3
β-strand	84-86	3	156
β-strand	90	1	156
α-helix	91	1
β-strand	92-104	13	154
β-strand	108-116	9	156
β-strand	122-131	10	156
α-helix	133-136	4
β-strand	139	1	157
β-strand	149-156	8	158
β-strand	166-169	4	159
β-strand	170	1	160
β-strand	175-176	2	161
α-helix	178-180	3
β-strand	181-184	4	162
β-strand	187-190	4	162
β-strand	197-201	5	161
β-strand	209-211	3	161
β-strand	215-217	3	162
α-helix	222-224	3
β-strand	225-229	5	161
β-strand	235	1	152
β-strand	236	1	160
β-strand	253-256	4	159
α-helix	257	1
β-strand	261-268	8	158
α-helix	271-274	4
β-strand	275-279	5	163
β-strand	282-287	6	163
β-strand	293-299	7	157
β-strand	307-311	5	157
β-strand	315-320	6	163
β-strand	326-330	5	157
α-helix	334-335	2
β-strand	336-338	3	157
β-strand	339-340	2	137
α-helix	352-362	11
α-helix	364-402	39
α-helix	410-415	6

16 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
E3 glycoprotein	U, V, W, X	protein	60	Chikungunya virus	D2KBQ2
E1 glycoprotein	A, B, C, D	protein	439	Chikungunya virus	Q88628
E2 glycoprotein	E, F, G, H	protein	419	Chikungunya virus	Q88628
Heavy chain of C9	M, O, Q, S	protein	234	Mus musculus
Light chain of C9	N, P, R, T	protein	212	Mus musculus
Capsid protein	I, J, K, L	protein	151	Chikungunya virus	Q88628

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

>9BBN_1 E3 glycoprotein (chains U, V, W, X)
PVMCLLANTTFPCSQPPCTPCCYEKEPEETLRMLEDNVMRPGYYQLLQASLTCSPHRQRR

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

>9BBN_2 E1 glycoprotein (chains A, B, C, D)
YEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELLSVTLEPTLSLDYITCEYKTVIPSPYV
KCCGTAECKDKSLPDYSCKVFTGVYPFMWGGAYCFCDTENTQLSEAHVEKSESCKTEFAS
AYRAHTASASAKLRVLYQGNNVTVSAYANGDHAVTVKDAKFIVGPMSSAWTPFDNKIVVY
KGDVYNMDYPPFGAGRPGQFGDIQSRTPESEDVYANTQLVLQRPSAGTVHVPYSQAPSGF
KYWLKERGASLQHTAPFGCQIATNPVRAMNCAVGNMPISIDIPDAAFTRVVDAPSLTDMS
CEVPACTHSSDFGGVAIIKYAASKKGKCAVHSMTNAVTIREAEIEVEGNSQLQISFSTAL
ASAEFRVQVCSTQVHCAAECHPPKDHIVNYPASHTTLGVQDISVTAMSWVQKITGGVGLV
VAVAALILIVVLCVSFSRH

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

>9BBN_3 E2 glycoprotein (chains E, F, G, H)
NFNVYKAIRPYLAHCPDCGEGHSCHSPVALERIRNEATDGTLKIQVSLQIGIKTDDSHDW
TKLRYMDNHMPADAERARLFVRTSAPCTITGTMGHFILARCPKGETLTVGFTDGRKISHS
CTHPFHHDPPVIGREKFHSRPQHGRELPCSTYAQSTAATAEEIEVHMPPDTPDRTLMSQQ
SGNVKITVNSQTVRYKCNCGDSNEGLTTTDKVINNCKVDQCHAAVTNHKKWQYNSPLVPR
NAELGDRKGKVHIPFPLANVTCRVPKARNPTVTYGKNQVIMLLYPDHPTLLSYRNMGEEP
NYQEEWVTHKKEIRLTVPTEGLEVTWGNNEPYKYWPQLSTNGTAHGHPHEIILYYYELYP
TMTVVVVSVASFVLLSMVGVAVGMCMCARRRCITPYELTPGATVPFLLSLICCIRTAKA

Sequence of entity 4 (M, O, Q, S), FASTA

>9BBN_4 Heavy chain of C9 (chains M, O, Q, S)
EVQLVQSGAEVKKPGSSVKVSCKAFGGTFSSYAITWVRQAPGQGLEWMGGIIPILGTTDY
AQKFQGRVTITADKSTSTAYMELSSLRSEDTAVYYCARDPPTHGGDFNYYYYGVAVWGQG
TTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH

Sequence of entity 5 (N, P, R, T), FASTA

>9BBN_5 Light chain of C9 (chains N, P, R, T)
EIVLTQSPGTLSLSPGERATLSCRASQSNNYLAWYQQKPGQAPRLLIYGASIRATGIPDR
FSGSGSGTDFTLTISRLAPEDFAVYYCQQYGSSPLTFGPGTKVDIKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRGE

Sequence of entity 6 (I, J, K, L), FASTA

>9BBN_6 Capsid protein (chains I, J, K, L)
NDCIFEVKHEGKVTGYACLVGDKVMKPAHVKGTIDNADLAKLAFKRSSKYDLECAQIPVH
MKSDASKFTHEKPEGYYNWHHGAVQYSGGRFTIPTGAGKPGDSGRPIFDNKGRVVAIVLG
GANEGARTALSVVTWNKDIVTKITPEGAEEW

Primary citation

Cryogenic Electron Microscopy Reveals Dual-Inhibition Mechanisms and Explains the Differential Neutralization Potency of Two anti-CHIKV Antibodies. Su, G.C., Galaz-Montoya, J.G., Pintilie, G. et al. To be published.

Other PDB entries of the same protein (UniProt D2KBQ2), best resolution first:

9BHH 3.5 Å, Cryo-EM structure of Chikungunya virus asymmetric unit with Fab IM-CKV063
6NK7 4.99 Å, Electron Cryo-Microscopy of Chikungunya in Complex with Mouse Mxra8 Receptor

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