9BHH: E1 glycoprotein

Cryo-EM structure of Chikungunya virus asymmetric unit with Fab IM-CKV063. Determined by electron microscopy at 3.5 Å resolution. Released 22 Oct 2025.

Method: Electron microscopy
Resolution: 3.5 Å
Organisms: Chikungunya virus, Mus musculus
Chains: 24
Atoms: 46,800
Mol. weight: 667.64 kDa
Released: 22 Oct 2025

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

Secondary structure: helices and β-sheets

9BHH contains 185 α-helices and 550 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: 11 helices, 38 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	27-49	23	2
β-strand	51-54	4	4
α-helix	56-58	3
β-strand	59-61	3	5
α-helix	65-68	4
β-strand	77-82	6	5
β-strand	87-88	2	6
β-strand	90	1	7
β-strand	91-92	2	6
β-strand	101-106	6	5
β-strand	107-110	4	4
α-helix	112-115	4
β-strand	118-137	20	2
β-strand	140-147	8	2
α-helix	153	1
β-strand	154-156	3	1
β-strand	159-163	5	1
β-strand	176-179	4	2
β-strand	184-186	3	2
α-helix	189-191	3
β-strand	203-205	3	2
β-strand	213-215	3	2
β-strand	220-221	2	8
β-strand	233-234	2	8
α-helix	236-238	3
α-helix	239-246	8
α-helix	251-254	4
β-strand	260-262	3	2
β-strand	267-269	3	2
β-strand	275-281	7	1
α-helix	284-286	3
β-strand	289	1	3
β-strand	296-306	11	9
β-strand	307	1	10
β-strand	314-322	9	9
β-strand	326-329	4	11
β-strand	330-332	3	12
β-strand	337-339	3	9
β-strand	343-346	4	11
β-strand	349-358	10	9
β-strand	364-369	6	12
β-strand	372-377	6	12
β-strand	381	1	10
β-strand	387-388	2	13
α-helix	395-397	3
α-helix	409-437	29

Chain B: 12 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	14
β-strand	15-19	5	15
β-strand	24	1	16
α-helix	25-26	2
β-strand	27-48	22	15
β-strand	51-54	4	17
α-helix	56-58	3
β-strand	59-61	3	18
β-strand	77-82	6	18
β-strand	87-88	2	19
β-strand	90	1	20
β-strand	91-92	2	19
β-strand	101-106	6	18
β-strand	107-110	4	17
α-helix	112-115	4
β-strand	119-137	19	15
β-strand	140-147	8	15
β-strand	154-156	3	14
β-strand	159-163	5	14
β-strand	176-179	4	15
β-strand	184-185	2	15
α-helix	189-191	3
α-helix	195-196	2
β-strand	203-204	2	21
β-strand	205	1	15
β-strand	214-215	2	21
β-strand	220-221	2	22
β-strand	233-234	2	22
α-helix	236-238	3
α-helix	239-246	8
α-helix	251-254	4
β-strand	260-262	3	15
β-strand	267-269	3	15
β-strand	275-281	7	14
α-helix	284-286	3
β-strand	289	1	16
β-strand	296-305	10	23
β-strand	307	1	24
β-strand	314-322	9	23
β-strand	326-329	4	25
β-strand	330-332	3	26
β-strand	337-339	3	23
β-strand	343-346	4	25
β-strand	349-358	10	23
β-strand	362-369	8	26
β-strand	372-379	8	26
β-strand	381	1	24
α-helix	382-383	2
β-strand	387-388	2	27
α-helix	395-397	3
α-helix	408-436	29

Chain C: 15 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	28
β-strand	11	1	29
β-strand	15-19	5	29
β-strand	24	1	30
β-strand	27-38	12	29
β-strand	41-49	9	31
β-strand	51-54	4	32
α-helix	56-58	3
β-strand	59	1	33
β-strand	60-61	2	34
α-helix	65-68	4
β-strand	77-82	6	34
β-strand	87-88	2	35
β-strand	90	1	36
β-strand	91-92	2	35
β-strand	101-106	6	34
β-strand	107-110	4	32
α-helix	112-115	4
β-strand	118-125	8	31
β-strand	130-137	8	29
β-strand	140-147	8	29
β-strand	154-156	3	28
β-strand	159-163	5	28
β-strand	176-179	4	31
β-strand	184-186	3	31
α-helix	189-191	3
α-helix	195-196	2
β-strand	203-204	2	37
β-strand	205	1	31
β-strand	214-215	2	37
β-strand	220-221	2	38
α-helix	223-225	3
β-strand	233-234	2	38
α-helix	236-238	3
α-helix	239-246	8
α-helix	251-254	4
β-strand	260-262	3	29
β-strand	267-269	3	29
β-strand	275-281	7	28
α-helix	284-286	3
α-helix	287-288	2
β-strand	289	1	30
β-strand	296-305	10	39
β-strand	307	1	40
β-strand	314-322	9	39
β-strand	326-329	4	41
β-strand	331-332	2	42
β-strand	337-339	3	39
β-strand	343-346	4	41
β-strand	349-358	10	39
β-strand	362-368	7	42
β-strand	373-379	7	42
β-strand	381	1	40
α-helix	382-383	2
β-strand	388	1	43
α-helix	395-397	3
α-helix	403-404	2
α-helix	409-437	29

Chain D: 11 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	44
β-strand	14-19	6	45
β-strand	24	1	46
β-strand	27-49	23	45
β-strand	51-54	4	47
α-helix	56-58	3
β-strand	59-61	3	48
β-strand	77-82	6	48
β-strand	87-88	2	49
β-strand	90	1	50
β-strand	91-92	2	49
β-strand	101-106	6	48
β-strand	107-110	4	47
α-helix	112-115	4
β-strand	118-137	20	45
β-strand	140-147	8	45
β-strand	154-156	3	44
β-strand	159-163	5	44
β-strand	176-179	4	45
β-strand	184-186	3	45
α-helix	189-191	3
α-helix	195-196	2
β-strand	203-204	2	51
β-strand	205	1	45
β-strand	214-215	2	51
β-strand	220-221	2	52
β-strand	233-234	2	52
α-helix	239-245	7
α-helix	251-254	4
α-helix	256-258	3
β-strand	260-262	3	45
β-strand	267-269	3	45
β-strand	275-281	7	44
α-helix	284-286	3
β-strand	289	1	46
β-strand	296-306	11	53
β-strand	314-329	16	53
β-strand	331-332	2	54
β-strand	337-339	3	53
β-strand	343-358	16	53
β-strand	364-368	5	54
β-strand	373-377	5	54
α-helix	381-383	3
β-strand	388	1	55
α-helix	395-397	3
α-helix	408-436	29

Chain E: 12 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	7-11	5
β-strand	12	1	56
β-strand	17-19	3	57
β-strand	28-30	3	57
β-strand	34-38	5	58
β-strand	46-56	11	58
β-strand	62-71	10	58
β-strand	74-79	6	58
α-helix	80-82	3
β-strand	84-86	3	59
β-strand	90	1	59
α-helix	91	1
β-strand	92-104	13	58
β-strand	108-116	9	59
β-strand	122-131	10	59
α-helix	133-136	4
β-strand	139	1	60
β-strand	149-156	8	61
β-strand	166-168	3	62
β-strand	169-170	2	63
α-helix	171-173	3
β-strand	175-176	2	64
β-strand	177	1	7
α-helix	178-180	3
β-strand	182-183	2	65
β-strand	187-189	3	65
β-strand	197-201	5	64
β-strand	210-211	2	64
β-strand	216-218	3	65
α-helix	222-224	3
β-strand	225-229	5	64
β-strand	235	1	56
β-strand	236-237	2	63
β-strand	254-256	3	62
β-strand	261-268	8	61
α-helix	271-274	4
β-strand	275-279	5	66
β-strand	282-287	6	66
β-strand	293-299	7	60
β-strand	307-311	5	60
β-strand	315-320	6	66
β-strand	326-330	5	60
α-helix	334-335	2
β-strand	336-338	3	60
β-strand	339-340	2	13
α-helix	352-359	8
α-helix	364-402	39
α-helix	413-416	4

Chain F: 12 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
β-strand	12	1	67
β-strand	17	1	68
β-strand	30	1	68
β-strand	34-38	5	69
β-strand	46-56	11	69
β-strand	62-71	10	69
β-strand	74-79	6	69
α-helix	80-82	3
β-strand	84-86	3	70
β-strand	90	1	70
α-helix	91	1
β-strand	92-104	13	69
β-strand	108-116	9	70
β-strand	122-131	10	70
α-helix	133-136	4
β-strand	139	1	71
β-strand	149-156	8	72
β-strand	166-170	5	73
α-helix	171-174	4
β-strand	175-176	2	74
β-strand	177	1	20
α-helix	178-180	3
β-strand	181-184	4	75
β-strand	187-190	4	75
β-strand	197-201	5	74
β-strand	208-211	4	74
β-strand	215-217	3	75
α-helix	222-224	3
β-strand	225-229	5	74
β-strand	235	1	67
β-strand	236-237	2	73
β-strand	253-256	4	73
β-strand	261-268	8	72
α-helix	271-274	4
β-strand	275-279	5	76
β-strand	282-287	6	76
β-strand	293-299	7	71
β-strand	307-311	5	71
β-strand	315-320	6	76
β-strand	326-330	5	71
α-helix	334-335	2
β-strand	336-338	3	71
β-strand	339-340	2	27
α-helix	352-360	9
α-helix	366-401	36
α-helix	410-415	6

Chain G: 14 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
β-strand	12	1	77
β-strand	17-19	3	78
β-strand	28-30	3	78
β-strand	34-38	5	79
β-strand	46-56	11	79
β-strand	62-71	10	79
β-strand	74-79	6	79
α-helix	80-82	3
β-strand	84-86	3	80
β-strand	90	1	80
α-helix	91	1
β-strand	92-104	13	79
β-strand	108-116	9	80
β-strand	122-131	10	80
α-helix	133-136	4
β-strand	139	1	81
β-strand	149-156	8	82
β-strand	166-168	3	83
β-strand	169-170	2	84
α-helix	172-174	3
β-strand	175-176	2	85
β-strand	177	1	36
α-helix	178-180	3
β-strand	181-184	4	86
β-strand	187-190	4	86
β-strand	197-201	5	85
β-strand	209-211	3	85
β-strand	215-217	3	86
α-helix	222-224	3
β-strand	225-229	5	85
β-strand	235	1	77
β-strand	236-237	2	84
β-strand	244	1	33
β-strand	254-256	3	83
β-strand	261-268	8	82
α-helix	271-274	4
β-strand	275-279	5	87
β-strand	282-287	6	87
β-strand	293-299	7	81
β-strand	307-311	5	81
β-strand	315-320	6	87
β-strand	326-330	5	81
α-helix	334-335	2
β-strand	336-338	3	81
β-strand	339	1	43
α-helix	352-361	10
α-helix	366-385	20
α-helix	387-390	4
α-helix	392-401	10
α-helix	410-415	6

Chain H: 11 helices, 38 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
β-strand	12	1	88
β-strand	17-19	3	89
β-strand	28-30	3	89
β-strand	34	1	90
β-strand	38	1	91
β-strand	46-56	11	91
β-strand	62-69	8	91
β-strand	76-79	4	91
α-helix	80-82	3
β-strand	84-86	3	92
β-strand	90	1	92
β-strand	92-104	13	91
β-strand	108-116	9	92
β-strand	122-131	10	92
α-helix	133-136	4
β-strand	139	1	93
β-strand	149-156	8	94
β-strand	166-168	3	95
β-strand	170	1	96
α-helix	171-174	4
β-strand	175-176	2	97
β-strand	177	1	50
α-helix	178-180	3
β-strand	181-184	4	98
β-strand	187-190	4	98
β-strand	197-201	5	97
β-strand	208-211	4	97
β-strand	215-217	3	98
β-strand	225-229	5	97
β-strand	235	1	88
β-strand	236	1	96
β-strand	244	1	48
β-strand	254-256	3	95
β-strand	261-268	8	94
α-helix	271-274	4
β-strand	275-279	5	99
β-strand	282-287	6	99
β-strand	293-299	7	93
β-strand	307-311	5	93
β-strand	315-320	6	99
α-helix	321-322	2
β-strand	326-330	5	93
α-helix	334-335	2
β-strand	336-338	3	93
β-strand	339	1	55
α-helix	352-358	7
α-helix	366-402	37
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
E1 glycoprotein	A, B, C, D	protein	438	Chikungunya virus	Q88628
E2 glycoprotein	E, F, G, H	protein	418	Chikungunya virus	Q88628
Capsid protein	I, J, K, L	protein	151	Chikungunya virus	Q88628
Light chain of IM-CKV063	M, O, Q, S	protein	213	Mus musculus
Heavy Chain of IM-CKV063	N, P, R, T	protein	242	Mus musculus
E3 glycoprotein	U, V, W, X	protein	60	Chikungunya virus	D2KBQ2

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

>9BHH_1 E1 glycoprotein (chains A, B, C, D)
YEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELLSVTLEPTLSLDYITCEYKTVIPSPYV
KCCGTAECKDKSLPDYSCKVFTGVYPFMWGGAYCFCDTENTQLSEAHVEKSESCKTEFAS
AYRAHTASASAKLRVLYQGNNVTVSAYANGDHAVTVKDAKFIVGPMSSAWTPFDNKIVVY
KGDVYNMDYPPFGAGRPGQFGDIQSRTPESEDVYANTQLVLQRPSAGTVHVPYSQAPSGF
KYWLKERGASLQHTAPFGCQIATNPVRAMNCAVGNMPISIDIPDAAFTRVVDAPSLTDMS
CEVPACTHSSDFGGVAIIKYAASKKGKCAVHSMTNAVTIREAEIEVEGNSQLQISFSTAL
ASAEFRVQVCSTQVHCAAECHPPKDHIVNYPASHTTLGVQDISVTAMSWVQKITGGVGLV
VAVAALILIVVLCVSFSR

Sequence of entity 2 (E, F, G, H), FASTA

>9BHH_2 E2 glycoprotein (chains E, F, G, H)
NFNVYKAIRPYLAHCPDCGEGHSCHSPVALERIRNEATDGTLKIQVSLQIGIKTDDSHDW
TKLRYMDNHMPADAERARLFVRTSAPCTITGTMGHFILARCPKGETLTVGFTDGRKISHS
CTHPFHHDPPVIGREKFHSRPQHGRELPCSTYAQSTAATAEEIEVHMPPDTPDRTLMSQQ
SGNVKITVNSQTVRYKCNCGDSNEGLTTTDKVINNCKVDQCHAAVTNHKKWQYNSPLVPR
NAELGDRKGKVHIPFPLANVTCRVPKARNPTVTYGKNQVIMLLYPDHPTLLSYRNMGEEP
NYQEEWVTHKKEIRLTVPTEGLEVTWGNNEPYKYWPQLSTNGTAHGHPHEIILYYYELYP
TMTVVVVSVASFVLLSMVGVAVGMCMCARRRCITPYELTPGATVPFLLSLICCIRTAK

Sequence of entity 3 (I, J, K, L), FASTA

>9BHH_3 Capsid protein (chains I, J, K, L)
NDCIFEVKHEGKVTGYACLVGDKVMKPAHVKGTIDNADLAKLAFKRSSKYDLECAQIPVH
MKSDASKFTHEKPEGYYNWHHGAVQYSGGRFTIPTGAGKPGDSGRPIFDNKGRVVAIVLG
GANEGARTALSVVTWNKDIVTKITPEGAEEW

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

>9BHH_4 Light chain of IM-CKV063 (chains M, O, Q, S)
EIVMTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPD
RFSGSGSGTDFTLTISRLEPEDFAVYYCQQYANSRRTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE

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

>9BHH_5 Heavy Chain of IM-CKV063 (chains N, P, R, T)
QVQLVQSGAEVKKPGSAVKVSCKASGGTLRKYAISWLRQAPGQGLEWMGGIIPIFGTANY
AQKFQGRVTITADESTTTPYTTTPYTSTAYIELTSLRSEDTAVYYCARDLGPLTGYSYSY
FDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGAL
TSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKT
HT

Sequence of entity 6 (U, V, W, X), FASTA

>9BHH_6 E3 glycoprotein (chains U, V, W, X)
PVMCLLANTTFPCSQPPCTPCCYEKEPEETLRMLEDNVMRPGYYQLLQASLTCSPHRQRR

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 Q88628), best resolution first:

8FCG 3.09 Å, Cryo-EM structure of Chikungunya virus asymmetric unit
9J6D 3.11 Å, Structure of Chikungunya virus infectious particles, 2f block.
9BBN 3.3 Å, Cryo-EM structure of Chikungunya virus asymmetric unit with Fab C9
6NK7 4.99 Å, Electron Cryo-Microscopy of Chikungunya in Complex with Mouse Mxra8 Receptor
6W09 5.3 Å, Human mAbs broadly protect against infection of arthritiogenic alphaviruses by…

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