8FCG: Chikungunya virus asymmetric unit

Name: PDB 8FCG: Cryo-EM structure of Chikungunya virus asymmetric unit
Published: 2024-03-20
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Cryo-EM structure of Chikungunya virus asymmetric unit. Determined by electron microscopy at 3.09 Å resolution. Released 20 Mar 2024.

Method: Electron microscopy
Resolution: 3.09 Å
Organism: Chikungunya virus
Chains: 12
Atoms: 31,382
Mol. weight: 447.95 kDa
Ligands: PCW
Released: 20 Mar 2024

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

Secondary structure: helices and β-sheets

8FCG contains 102 α-helices and 380 β-strands across 12 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: 8 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	27-48	22	2
β-strand	51-54	4	4
α-helix	56-58	3
β-strand	59-61	3	5
β-strand	77-82	6	5
β-strand	87-88	2	6
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	119-136	18	2
β-strand	141-147	7	2
β-strand	153-156	4	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	214-215	2	2
β-strand	220-221	2	7
β-strand	233-234	2	7
α-helix	236-238	3
α-helix	239-245	7
α-helix	251-254	4
β-strand	260-262	3	2
β-strand	267-269	3	2
β-strand	275-281	7	1
β-strand	289	1	3
β-strand	296-302	7	8
β-strand	306	1	8
β-strand	307	1	9
β-strand	314-322	9	8
β-strand	326-328	3	10
β-strand	330-332	3	11
β-strand	337-339	3	8
β-strand	344-346	3	10
β-strand	349-358	10	8
β-strand	364-369	6	11
β-strand	372-377	6	11
β-strand	381	1	9
β-strand	387-388	2	12
α-helix	395-398	4
α-helix	408-437	30

Chain B: 12 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	13
β-strand	15-19	5	14
β-strand	24	1	15
β-strand	27-38	12	14
β-strand	42-48	7	16
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	91-92	2	19
β-strand	101-106	6	18
β-strand	107-110	4	17
α-helix	113-115	3
β-strand	119-124	6	16
β-strand	130-137	8	14
β-strand	140-147	8	14
β-strand	154-156	3	13
β-strand	159-163	5	13
β-strand	176-179	4	16
β-strand	184-185	2	16
α-helix	189-191	3
α-helix	195-196	2
β-strand	203-205	3	16
β-strand	213-215	3	16
β-strand	220-221	2	20
α-helix	223-225	3
β-strand	233-234	2	20
α-helix	236-238	3
α-helix	239-245	7
α-helix	251-254	4
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	21
β-strand	307	1	22
β-strand	314-322	9	21
β-strand	326-329	4	23
β-strand	330-332	3	24
β-strand	337-339	3	21
β-strand	343-346	4	23
β-strand	349-358	10	21
β-strand	362-369	8	24
β-strand	372-379	8	24
β-strand	381	1	22
α-helix	382-383	2
β-strand	387-388	2	25
α-helix	403-404	2
α-helix	408-437	30

Chain C: 9 helices, 47 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	26
β-strand	11	1	27
β-strand	17-19	3	28
β-strand	24	1	29
β-strand	27-29	3	28
β-strand	31-38	8	27
β-strand	40	1	30
β-strand	46-48	3	31
β-strand	51-54	4	32
α-helix	56-58	3
β-strand	59-61	3	33
β-strand	77-84	8	33
β-strand	87	1	34
β-strand	90	1	35
β-strand	92	1	34
β-strand	100-106	7	33
β-strand	107-110	4	32
α-helix	112-115	4
β-strand	119-122	4	31
β-strand	127	1	30
β-strand	130-137	8	27
β-strand	140-147	8	27
β-strand	154-156	3	26
β-strand	159-163	5	26
β-strand	177-179	3	31
β-strand	184-185	2	31
α-helix	189-191	3
β-strand	192	1	36
α-helix	195-196	2
β-strand	203-205	3	31
β-strand	214-215	2	31
β-strand	220-221	2	37
β-strand	233-234	2	37
α-helix	236-238	3
α-helix	239-245	7
α-helix	251-254	4
β-strand	260-262	3	27
β-strand	267-269	3	27
β-strand	275-281	7	26
β-strand	289	1	29
β-strand	301-305	5	38
β-strand	307	1	39
β-strand	314-319	6	38
β-strand	326-328	3	40
β-strand	330-332	3	41
β-strand	337-339	3	38
β-strand	344-346	3	40
β-strand	351-358	8	38
β-strand	362-366	5	42
β-strand	367-369	3	41
β-strand	372	1	41
β-strand	375-379	5	42
β-strand	381	1	39
β-strand	387-388	2	43
α-helix	398-399	2
α-helix	408-437	30

Chain D: 10 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	44
β-strand	15-21	7	45
β-strand	24-38	15	45
β-strand	40-42	3	46
β-strand	46-48	3	47
β-strand	51-54	4	48
α-helix	56-58	3
β-strand	59-61	3	49
β-strand	77-82	6	49
β-strand	87	1	50
β-strand	92	1	50
β-strand	101-106	6	49
β-strand	107-110	4	48
β-strand	119-123	5	47
β-strand	124-127	4	46
β-strand	130-137	8	45
β-strand	140-147	8	45
β-strand	152	1	36
β-strand	153-156	4	44
β-strand	159-163	5	44
β-strand	176-180	5	47
β-strand	183-186	4	47
α-helix	189-191	3
α-helix	195-196	2
β-strand	203-205	3	47
β-strand	213-215	3	47
β-strand	220-221	2	51
α-helix	223-225	3
β-strand	233-234	2	51
α-helix	236-238	3
α-helix	239-244	6
α-helix	251-254	4
β-strand	260-262	3	45
β-strand	267-269	3	45
β-strand	275-281	7	44
β-strand	289	1	45
β-strand	296-305	10	52
β-strand	307	1	53
β-strand	314-322	9	52
β-strand	326-328	3	54
β-strand	331	1	55
β-strand	337-339	3	52
β-strand	344-346	3	54
β-strand	349-358	10	52
β-strand	364-368	5	55
β-strand	373-377	5	55
β-strand	381	1	53
β-strand	387-388	2	56
α-helix	399-401	3
α-helix	405-407	3
α-helix	408-437	30

Chain E: 13 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	8-11	4
β-strand	12	1	57
β-strand	17-19	3	58
β-strand	28-30	3	58
β-strand	34-38	5	59
β-strand	46-56	11	59
β-strand	62-71	10	59
β-strand	74-79	6	59
α-helix	80-82	3
β-strand	84-86	3	60
β-strand	90	1	60
β-strand	92-104	13	59
α-helix	105-106	2
β-strand	108-116	9	60
β-strand	122-131	10	60
α-helix	133-136	4
β-strand	139	1	61
β-strand	149-156	8	62
β-strand	166-168	3	63
β-strand	169-170	2	64
α-helix	171-174	4
β-strand	175-176	2	65
β-strand	183-184	2	66
β-strand	187-188	2	66
β-strand	197-201	5	65
β-strand	210-211	2	65
β-strand	217	1	66
α-helix	222-224	3
β-strand	225-229	5	65
β-strand	235	1	57
β-strand	236-237	2	64
β-strand	254-256	3	63
β-strand	261-268	8	62
α-helix	271-274	4
β-strand	275-279	5	67
β-strand	282-287	6	67
β-strand	293-299	7	61
β-strand	307-311	5	61
β-strand	315-319	5	67
α-helix	320-322	3
β-strand	326-330	5	61
α-helix	334-335	2
β-strand	336-338	3	61
β-strand	339-340	2	12
α-helix	352-362	11
α-helix	364-395	32
α-helix	399-402	4
α-helix	410-416	7

Chain F: 11 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
β-strand	12	1	68
β-strand	17	1	69
β-strand	30	1	69
β-strand	34-38	5	70
β-strand	45-57	13	70
β-strand	61-70	10	70
β-strand	75-79	5	70
α-helix	80-82	3
β-strand	84-86	3	71
β-strand	90	1	71
β-strand	92-104	13	70
β-strand	108-116	9	71
β-strand	122-131	10	71
α-helix	133-136	4
β-strand	139	1	72
β-strand	149-156	8	73
β-strand	166-170	5	74
β-strand	176	1	75
β-strand	183-184	2	76
β-strand	187-188	2	76
β-strand	197-201	5	75
β-strand	209-211	3	75
α-helix	216	1
β-strand	217	1	76
α-helix	218	1
α-helix	222-224	3
β-strand	225-229	5	75
β-strand	235	1	68
β-strand	236-237	2	74
β-strand	253-256	4	74
β-strand	261-268	8	73
α-helix	271-274	4
β-strand	275-279	5	77
β-strand	282-287	6	77
β-strand	293-299	7	72
β-strand	307-311	5	72
β-strand	315-320	6	77
β-strand	326-330	5	72
α-helix	334-335	2
β-strand	336-338	3	72
β-strand	339-340	2	25
α-helix	352-362	11
α-helix	364-402	39
α-helix	410-416	7

Chain G: 9 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
β-strand	12	1	78
β-strand	17-19	3	79
β-strand	28-30	3	79
β-strand	34-38	5	80
β-strand	45-56	12	80
β-strand	62-71	10	80
β-strand	74-79	6	80
β-strand	84-86	3	81
β-strand	90	1	81
β-strand	92-104	13	80
β-strand	108-116	9	81
β-strand	122-131	10	81
α-helix	133-135	3
β-strand	139	1	82
β-strand	149-156	8	83
β-strand	166-168	3	84
β-strand	169-170	2	85
α-helix	171-174	4
β-strand	175-176	2	86
β-strand	177	1	35
α-helix	178-180	3
β-strand	183-184	2	87
β-strand	187-188	2	87
β-strand	197-201	5	86
β-strand	208-211	4	86
β-strand	225-229	5	86
β-strand	235	1	78
β-strand	236-237	2	85
β-strand	254-256	3	84
β-strand	261-268	8	83
α-helix	271-274	4
β-strand	275-279	5	88
β-strand	282-287	6	88
β-strand	293-299	7	82
β-strand	307-311	5	82
β-strand	315-320	6	88
β-strand	326-330	5	82
α-helix	334-335	2
β-strand	336-338	3	82
β-strand	339-340	2	43
α-helix	352-362	11
α-helix	364-402	39
α-helix	410-415	6

Chain H: 13 helices, 38 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
β-strand	12	1	89
β-strand	17-19	3	90
β-strand	28-30	3	90
β-strand	34-38	5	91
β-strand	46-56	11	91
β-strand	62-71	10	91
β-strand	74-79	6	91
β-strand	84-86	3	92
β-strand	90	1	92
β-strand	92-104	13	91
β-strand	108-114	7	92
β-strand	115-116	2	93
β-strand	122-123	2	93
β-strand	126-131	6	92
α-helix	133-136	4
β-strand	139	1	94
β-strand	148-153	6	95
β-strand	156	1	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	183-184	2	99
β-strand	187-188	2	99
β-strand	197-201	5	98
β-strand	210-211	2	98
β-strand	217	1	99
α-helix	222-224	3
β-strand	225-229	5	98
β-strand	235	1	89
β-strand	236-237	2	97
β-strand	253-256	4	97
β-strand	261	1	96
β-strand	264-269	6	95
α-helix	271-273	3
β-strand	275-279	5	100
β-strand	282-287	6	100
β-strand	293-299	7	94
β-strand	307-311	5	94
β-strand	315-320	6	100
β-strand	326-330	5	94
α-helix	334-335	2
β-strand	336-338	3	94
β-strand	339-340	2	56
α-helix	352-362	11
α-helix	364-395	32
α-helix	398-402	5
α-helix	406-409	4
α-helix	410-416	7
α-helix	418-419	2

4 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	Q88628
E2 glycoprotein	E, F, G, H	protein	419	Chikungunya virus	Q88628
Capsid protein	I, J, K, L	protein	151	Chikungunya virus	Q88628

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

>8FCG_1 E1 glycoprotein (chains A, B, C, D)
YEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELLSVTLEPTLSLDYITCEYKTVIPSPYV
KCCGTAECKDKSLPDYSCKVFTGVYPFMWGGAYCFCDTENTQLSEAHVEKSESCKTEFAS
AYRAHTASASAKLRVLYQGNNVTVSAYANGDHAVTVKDAKFIVGPMSSAWTPFDNKIVVY
KGDVYNMDYPPFGAGRPGQFGDIQSRTPESEDVYANTQLVLQRPSAGTVHVPYSQAPSGF
KYWLKERGASLQHTAPFGCQIATNPVRAMNCAVGNMPISIDIPDAAFTRVVDAPSLTDMS
CEVPACTHSSDFGGVAIIKYAASKKGKCAVHSMTNAVTIREAEIEVEGNSQLQISFSTAL
ASAEFRVQVCSTQVHCAAECHPPKDHIVNYPASHTTLGVQDISVTAMSWVQKITGGVGLV
VAVAALILIVVLCVSFSRH

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

>8FCG_2 E2 glycoprotein (chains E, F, G, H)
NFNVYKAIRPYLAHCPDCGEGHSCHSPVALERIRNEATDGTLKIQVSLQIGIKTDDSHDW
TKLRYMDNHMPADAERARLFVRTSAPCTITGTMGHFILARCPKGETLTVGFTDGRKISHS
CTHPFHHDPPVIGREKFHSRPQHGRELPCSTYAQSTAATAEEIEVHMPPDTPDRTLMSQQ
SGNVKITVNSQTVRYKCNCGDSNEGLTTTDKVINNCKVDQCHAAVTNHKKWQYNSPLVPR
NAELGDRKGKVHIPFPLANVTCRVPKARNPTVTYGKNQVIMLLYPDHPTLLSYRNMGEEP
NYQEEWVTHKKEIRLTVPTEGLEVTWGNNEPYKYWPQLSTNGTAHGHPHEIILYYYELYP
TMTVVVVSVASFVLLSMVGVAVGMCMCARRRCITPYELTPGATVPFLLSLICCIRTAKA

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

>8FCG_3 Capsid protein (chains I, J, K, L)
NDCIFEVKHEGKVTGYACLVGDKVMKPAHVKGTIDNADLAKLAFKRSSKYDLECAQIPVH
MKSDASKFTHEKPEGYYNWHHGAVQYSGGRFTIPTGAGKPGDSGRPIFDNKGRVVAIVLG
GANEGARTALSVVTWNKDIVTKITPEGAEEW

Ligands and cofactors

ID	Name	Formula	Copies
PCW	1,2-dioleoyl-sn-glycero-3-phosphocholine	C44 H85 N O8 P	5

Primary citation

Cryogenic electron microscopy and tomography reveal imperfect icosahedral symmetry in alphaviruses. Chmielewski, D., Su, G.C., Kaelber, J.T. et al. PNAS Nexus (2024) 3:pgae102-pgae102. DOI 10.1093/pnasnexus/pgae102 · PubMed

Other PDB entries of the same protein (UniProt Q88628), best resolution first:

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
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
6W09 5.3 Å, Human mAbs broadly protect against infection of arthritiogenic alphaviruses by…

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