2XFC: E1 envelope glycoprotein

Name: PDB 2XFC: Chikungunya E1 E2 envelope glycoproteins fitted in semliki forest virus cryo-EM map
Published: 2010-11-24
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Chikungunya E1 E2 envelope glycoproteins fitted in semliki forest virus cryo-EM map. Determined by electron microscopy at 9.0 Å resolution. Released 24 Nov 2010.

Method: Electron microscopy
Resolution: 9.0 Å
Organism: CHIKUNGUNYA VIRUS
Chains: 8
Atoms: 22,420
Mol. weight: 379.34 kDa
Released: 24 Nov 2010

Explore 2XFC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2XFC contains 67 α-helices and 304 β-strands across 8 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, 40 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	27-32	6	2
β-strand	36-48	13	4
β-strand	51-54	4	5
β-strand	59-61	3	6
β-strand	77-81	5	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	119-131	13	4
β-strand	134-137	4	2
β-strand	140-142	3	2
β-strand	153-156	4	1
β-strand	159-163	5	1
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	8
β-strand	205	1	4
β-strand	214-215	2	8
β-strand	220-221	2	9
α-helix	223-225	3
β-strand	233-234	2	9
α-helix	239-246	8
α-helix	251-254	4
β-strand	260-262	3	4
β-strand	267-269	3	4
β-strand	275-281	7	1
β-strand	289	1	3
α-helix	294-296	3
β-strand	300-305	6	10
β-strand	307	1	11
β-strand	314-319	6	10
β-strand	326-329	4	12
β-strand	330-332	3	13
β-strand	337-339	3	10
β-strand	343-346	4	12
β-strand	351-358	8	10
β-strand	362-369	8	13
β-strand	372-379	8	13
α-helix	380	1
β-strand	381	1	11
α-helix	382-383	2
β-strand	387-388	2	14

Chain B: 7 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	76	1	15
β-strand	81-83	3	16
β-strand	85	1	17
β-strand	92-94	3	16
β-strand	98-102	5	18
β-strand	110-120	11	18
β-strand	126-135	10	18
β-strand	138-143	6	18
β-strand	148-150	3	17
β-strand	154	1	17
β-strand	156-168	13	18
β-strand	172-180	9	17
β-strand	186-195	10	17
α-helix	197-199	3
β-strand	203	1	19
α-helix	208-209	2
β-strand	213-220	8	20
β-strand	230-234	5	21
β-strand	239-240	2	22
α-helix	242-244	3
β-strand	245-247	3	23
β-strand	252-254	3	23
β-strand	261-265	5	22
β-strand	274-275	2	22
β-strand	279-281	3	23
α-helix	286-288	3
β-strand	289-293	5	22
β-strand	299	1	15
β-strand	300-301	2	21
α-helix	307-309	3
β-strand	317-320	4	21
β-strand	325-332	8	20
α-helix	335-338	4
β-strand	339-343	5	24
β-strand	346-351	6	24
β-strand	357-362	6	19
β-strand	371-375	5	19
β-strand	379-384	6	24
β-strand	390-394	5	19
α-helix	398-399	2
β-strand	400-402	3	19
β-strand	403-404	2	14

Chain D: 10 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	25
β-strand	15-19	5	26
β-strand	24	1	27
β-strand	27-32	6	26
β-strand	37-48	12	28
β-strand	51	1	29
β-strand	54	1	30
β-strand	59-61	3	31
β-strand	77-81	5	31
β-strand	87-88	2	32
β-strand	91-92	2	32
β-strand	101-106	6	31
β-strand	107	1	30
β-strand	110	1	29
α-helix	112-115	4
β-strand	119-130	12	28
β-strand	134-137	4	26
β-strand	140-143	4	26
β-strand	153-156	4	25
β-strand	159-163	5	25
β-strand	176-180	5	28
β-strand	183-186	4	28
α-helix	189-191	3
α-helix	195-196	2
β-strand	203-204	2	33
β-strand	205	1	28
β-strand	214-215	2	33
β-strand	220-221	2	34
α-helix	223-225	3
β-strand	233-234	2	34
α-helix	239-246	8
α-helix	251-254	4
β-strand	260-262	3	28
β-strand	267-269	3	28
β-strand	275-281	7	25
α-helix	284-286	3
β-strand	289	1	27
α-helix	294-295	2
β-strand	296-305	10	35
β-strand	307	1	36
β-strand	314-322	9	35
β-strand	326-329	4	37
β-strand	330-332	3	38
β-strand	337-339	3	35
β-strand	343-346	4	37
β-strand	351-358	8	35
β-strand	362-369	8	38
β-strand	372-379	8	38
α-helix	380	1
β-strand	381	1	36
α-helix	382	1
β-strand	387-388	2	39

Chain E: 6 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	76	1	40
β-strand	81-83	3	41
β-strand	85	1	42
β-strand	92-94	3	41
β-strand	98-102	5	43
β-strand	110-120	11	43
β-strand	126-135	10	43
β-strand	138-143	6	43
β-strand	148-150	3	42
β-strand	154	1	42
β-strand	156-168	13	43
β-strand	172-180	9	42
β-strand	186-195	10	42
α-helix	197-199	3
β-strand	203	1	44
α-helix	208-209	2
β-strand	213-220	8	45
β-strand	230-234	5	46
β-strand	239-240	2	47
α-helix	242-244	3
β-strand	245-247	3	48
β-strand	252-254	3	48
β-strand	260-265	6	47
β-strand	274-275	2	47
β-strand	279-281	3	48
α-helix	286-288	3
β-strand	289-294	6	47
β-strand	299	1	40
β-strand	300-301	2	46
α-helix	307-309	3
β-strand	317-320	4	46
β-strand	325-332	8	45
β-strand	339-343	5	49
β-strand	346-351	6	49
β-strand	357-362	6	44
β-strand	371-375	5	44
β-strand	379-384	6	49
β-strand	390-394	5	44
α-helix	398-399	2
β-strand	400-402	3	44
β-strand	403-404	2	39

Chain F: 12 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	50
β-strand	15-19	5	51
β-strand	24	1	52
β-strand	27-48	22	51
β-strand	51	1	53
β-strand	54	1	54
β-strand	59-61	3	55
β-strand	77-81	5	55
β-strand	87-88	2	56
β-strand	91-92	2	56
β-strand	101-106	6	55
β-strand	107	1	54
α-helix	109	1
β-strand	110	1	53
α-helix	111	1
α-helix	112-115	4
β-strand	119-137	19	51
β-strand	140-142	3	51
β-strand	145-147	3	51
β-strand	153-156	4	50
β-strand	159-163	5	50
β-strand	176-180	5	51
β-strand	183-186	4	51
α-helix	189-191	3
α-helix	195-196	2
β-strand	203-204	2	57
β-strand	205	1	51
β-strand	214-215	2	57
β-strand	220-221	2	58
α-helix	223-225	3
β-strand	233-234	2	58
α-helix	239-246	8
α-helix	251-254	4
β-strand	260-262	3	51
β-strand	267-269	3	51
β-strand	275-281	7	50
α-helix	284-286	3
β-strand	289	1	52
α-helix	294-295	2
β-strand	296-305	10	59
β-strand	307	1	60
β-strand	314-322	9	59
β-strand	326-329	4	61
β-strand	330-332	3	62
β-strand	337-339	3	59
β-strand	343-346	4	61
β-strand	351-358	8	59
β-strand	362-369	8	62
β-strand	372-379	8	62
α-helix	380	1
β-strand	381	1	60
α-helix	382-383	2
β-strand	387-388	2	63

Chain G: 7 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	76	1	64
β-strand	81-83	3	65
β-strand	85	1	66
β-strand	92-94	3	65
β-strand	98-102	5	67
β-strand	110-120	11	67
β-strand	126-135	10	67
β-strand	138-143	6	67
β-strand	148-150	3	66
β-strand	154	1	66
β-strand	156-168	13	67
β-strand	172-180	9	66
β-strand	186-195	10	66
α-helix	197-199	3
β-strand	203	1	68
α-helix	208-209	2
β-strand	214-220	7	69
β-strand	230-234	5	70
β-strand	239-240	2	71
α-helix	242-244	3
β-strand	245-247	3	72
β-strand	252-254	3	72
β-strand	260-265	6	71
β-strand	274-275	2	71
β-strand	279-281	3	72
α-helix	286-288	3
β-strand	289-294	6	71
β-strand	299	1	64
β-strand	300-301	2	70
α-helix	307-309	3
β-strand	317-320	4	70
β-strand	325-331	7	69
α-helix	336-338	3
β-strand	339-343	5	73
β-strand	346-351	6	73
β-strand	357-362	6	68
β-strand	371-375	5	68
β-strand	379-384	6	73
β-strand	390-394	5	68
α-helix	398-399	2
β-strand	400-402	3	68
β-strand	403-404	2	63

Chain H: 10 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	74
β-strand	15-19	5	75
β-strand	24	1	76
β-strand	27-31	5	75
β-strand	36-48	13	77
β-strand	51-54	4	78
β-strand	59-61	3	79
β-strand	77-81	5	79
β-strand	87-88	2	80
β-strand	91-92	2	80
β-strand	101-106	6	79
β-strand	107-110	4	78
α-helix	112-115	4
β-strand	119-132	14	77
β-strand	135-137	3	75
β-strand	140-142	3	75
β-strand	145-147	3	77
β-strand	153-156	4	74
β-strand	159-163	5	74
β-strand	176-180	5	77
β-strand	183-186	4	77
α-helix	189-191	3
α-helix	195-196	2
β-strand	203-204	2	81
β-strand	205	1	77
β-strand	214-215	2	81
β-strand	220-221	2	82
α-helix	223-225	3
β-strand	233-234	2	82
α-helix	239-246	8
α-helix	251-254	4
β-strand	260-262	3	77
β-strand	267-269	3	77
β-strand	275-281	7	74
α-helix	284-286	3
β-strand	289	1	76
α-helix	294-295	2
β-strand	296-305	10	83
β-strand	307	1	84
β-strand	314-322	9	83
β-strand	326-329	4	85
β-strand	330-332	3	86
β-strand	337-339	3	83
β-strand	343-346	4	85
β-strand	351-358	8	83
β-strand	362-369	8	86
β-strand	372-379	8	86
α-helix	380	1
β-strand	381	1	84
α-helix	382-383	2
β-strand	387-388	2	87

Chain I: 6 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	76	1	88
β-strand	81-83	3	89
β-strand	85	1	90
β-strand	92-94	3	89
β-strand	98-102	5	91
β-strand	110-120	11	91
β-strand	126-135	10	91
β-strand	138-143	6	91
β-strand	148-150	3	90
β-strand	154	1	90
β-strand	156-168	13	91
β-strand	172-180	9	90
β-strand	186-195	10	90
α-helix	197-199	3
β-strand	203	1	92
α-helix	208-209	2
β-strand	213-220	8	93
β-strand	230-234	5	94
β-strand	240	1	95
α-helix	242-244	3
β-strand	245-247	3	96
β-strand	252-254	3	96
β-strand	261-265	5	95
β-strand	274-275	2	95
β-strand	279-281	3	96
α-helix	286-288	3
β-strand	289-293	5	95
β-strand	299	1	88
β-strand	300-301	2	94
α-helix	307-309	3
β-strand	317-320	4	94
β-strand	325-332	8	93
β-strand	339-343	5	97
β-strand	346-351	6	97
β-strand	357-362	6	92
β-strand	371-375	5	92
β-strand	379-384	6	97
β-strand	390-394	5	92
α-helix	398-399	2
β-strand	400-402	3	92
β-strand	403-404	2	87

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E1 envelope glycoprotein	A, D, F, H	protein	439	CHIKUNGUNYA VIRUS	Q1H8W5
E2 envelope glycoprotein	B, E, G, I	protein	423	CHIKUNGUNYA VIRUS	Q1H8W5

Sequence of entity 1 (A, D, F, H), FASTA

>2XFC_1 E1 ENVELOPE GLYCOPROTEIN (chains A, D, F, H)
YEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELLSVTLEPTLSLDYITCEYKTVIPSPYV
KCCGTAECKDKNLPDYSCKVFTGVYPFMWGGAYCFCDAENTQLSEAHVEKSESCKTEFAS
AYRAHTASASAKLRVLYQGNNITVTAYANGDHAVTVKDAKFIVGPMSSAWTPFDNKIVVY
KGDVYNMDYPPFGAGRPGQFGDIQSRTPESKDVYANTQLVLQRPAAGTVHVPYSQAPSGF
KYWLKERGASLQHTAPFGCQIATNPVRAVNCAVGNMPISIDIPEAAFTRVVDAPSLTDMS
CEVPACTHSSDFGGVAIIKYAASKKGKCAVHSMTNAVTIREAEIEVEGNSQLQISFSTAL
ASAEFRVQVCSTQVHCAAECHPPKDHIVNYPASHTTLGVQDISATAMSWVQKITGGVGLV
VAVAALILIVVLCVSFSRH

Sequence of entity 2 (B, E, G, I), FASTA

>2XFC_2 E2 ENVELOPE GLYCOPROTEIN (chains B, E, G, I)
STKDNFNVYKATRPYLAHCPDCGEGHSCHSPVALERIRNEATDGTLKIQVSLQIGIKTDD
SHDWTKLRYMDNHMPADAERAGLFVRTSAPCTITGTMGHFILARCPKGETLTVGFTDSRK
ISHSCTHPFHHDPPVIGREKFHSRPQHGKELPCSTYVQSTAATTEEIEVHMPPDTPDRTL
MSQQSGNVKITVNGQTVRYKCNCGGSNEGLTTTDKVINNCKVDQCHAAVTNHKKWQYNSP
LVPRNAELGDRKGKIHIPFPLANVTCRVPKARNPTVTYGKNQVIMLLYPDHPTLLSYRNM
GEEPNYQEEWVMHKKEVVLTVPTEGLEVTWGNNEPYKYWPQLSTNGTAHGHPHEIILYYY
ELYPTMTVVVVSVATFILLSMVGMAAGMCMCARRRCITPYELTPGATVPFLLSLICCIRT
AKA

Primary citation

Glycoprotein Organization of Chikungunya Virus Particles Revealed by X-Ray Crystallography. Voss, J.E., Vaney, M.C., Duquerroy, S. et al. Nature (2010) 468:709. DOI 10.1038/NATURE09555 · PubMed

Other PDB entries of the same protein (UniProt Q1H8W5), best resolution first:

3N40 2.17 Å, Crystal structure of the immature envelope glycoprotein complex of Chikungunya virus.
3N44 2.35 Å, Crystal structure of the mature envelope glycoprotein complex (trypsin cleavage; Osmium…
3N43 2.58 Å, Crystal structures of the mature envelope glycoprotein complex (trypsin cleavage) of…
3N42 3.0 Å, Crystal structures of the mature envelope glycoprotein complex (furin cleavage) of…
3N41 3.01 Å, Crystal structure of the mature envelope glycoprotein complex (spontaneous cleavage) of…
9IW2 3.2 Å, Chikungunya virus E protein complexed with C37 Fab
3J2W 5.0 Å, Electron cryo-microscopy of Chikungunya virus
2XFB 9.0 Å, Chikungunya E1 E2 envelope glycoproteins fitted in sindbis virus cryo- EM map
5ANY 16.9 Å, Electron cryo-microscopy of chikungunya virus in complex with neutralizing antibody Fab…

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