5ANY: Electron cryo-microscopy of chikungunya virus

Name: PDB 5ANY: Electron cryo-microscopy of chikungunya virus in complex with neutralizing antibody Fab CHK265
Published: 2015-11-25
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Electron cryo-microscopy of chikungunya virus in complex with neutralizing antibody Fab CHK265. Determined by electron microscopy at 16.9 Å resolution. Released 25 Nov 2015.

Method: Electron microscopy
Resolution: 16.9 Å
Organisms: CHIKUNGUNYA VIRUS, MUS MUSCULUS
Chains: 16
Atoms: 35,620
Mol. weight: 542.42 kDa
Released: 25 Nov 2015

Explore 5ANY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5ANY contains 96 α-helices and 464 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: 8 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	1
β-strand	11	1	2
β-strand	14-19	6	2
β-strand	23	1	3
β-strand	24	1	4
β-strand	27-40	14	2
β-strand	44-48	5	5
β-strand	51-54	4	6
β-strand	59-61	3	7
β-strand	77-82	6	7
β-strand	101-106	6	7
β-strand	107-110	4	6
α-helix	112-115	4
β-strand	119-122	4	5
β-strand	127-137	11	2
β-strand	140-147	8	2
β-strand	153-156	4	1
β-strand	159-163	5	1
β-strand	177-180	4	5
β-strand	183-185	3	5
α-helix	189-191	3
β-strand	203-205	3	5
β-strand	213-215	3	5
β-strand	220-221	2	8
α-helix	223-225	3
β-strand	233-234	2	8
α-helix	236-238	3
α-helix	239-243	5
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	4
α-helix	294-295	2
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	338-339	2	9
β-strand	343-346	4	11
β-strand	349-357	9	9
β-strand	362-369	8	12
β-strand	372-379	8	12
β-strand	381	1	10
β-strand	387-388	2	13

Chains B and D: 5 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	517-519	3	14
β-strand	528-530	3	14
β-strand	534-538	5	15
β-strand	545-556	12	15
β-strand	562-571	10	15
β-strand	574-579	6	15
β-strand	584-586	3	16
β-strand	590	1	16
β-strand	592-604	13	15
β-strand	608-616	9	16
β-strand	622-631	10	16
β-strand	649-656	8	17
β-strand	666-670	5	15
β-strand	675-676	2	18
α-helix	678-680	3
β-strand	681-684	4	19
β-strand	686	1	20
β-strand	687-690	4	19
β-strand	697-701	5	18
β-strand	708-711	4	18
β-strand	715-717	3	19
α-helix	722-724	3
β-strand	725-729	5	18
β-strand	736-737	2	15
α-helix	743-745	3
β-strand	753-756	4	15
β-strand	761-768	8	17
α-helix	769-774	6
β-strand	775-779	5	21
β-strand	782-787	6	21
β-strand	793-799	7	22
β-strand	807-811	5	22
β-strand	815-820	6	21
β-strand	826-830	5	22
α-helix	834-835	2
β-strand	836-838	3	22
β-strand	839-840	2	13

Chains C, E and G: 8 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	23
β-strand	11	1	24
β-strand	14-19	6	24
β-strand	24	1	25
β-strand	27-40	14	24
β-strand	44-48	5	26
β-strand	51-54	4	27
β-strand	59-61	3	28
β-strand	77-82	6	28
β-strand	101-106	6	28
β-strand	107-110	4	27
α-helix	112-115	4
β-strand	119-122	4	26
β-strand	127-137	11	24
β-strand	140-147	8	24
β-strand	153-156	4	23
β-strand	159-163	5	23
β-strand	177-180	4	26
β-strand	183-185	3	26
α-helix	189-191	3
β-strand	203-205	3	26
β-strand	213-215	3	26
β-strand	220-221	2	29
α-helix	223-225	3
β-strand	233-234	2	29
α-helix	236-238	3
α-helix	239-243	5
α-helix	251-254	4
β-strand	260-262	3	24
β-strand	267-269	3	24
β-strand	275-281	7	23
α-helix	284-286	3
β-strand	289	1	25
α-helix	294-295	2
β-strand	296-306	11	30
β-strand	307	1	31
β-strand	314-322	9	30
β-strand	326-329	4	32
β-strand	330-332	3	33
β-strand	338-339	2	30
β-strand	343-346	4	32
β-strand	349-357	9	30
β-strand	362-369	8	33
β-strand	372-379	8	33
β-strand	381	1	31
β-strand	387-388	2	34

Chain F: 5 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	517-519	3	55
β-strand	528-530	3	55
β-strand	534-538	5	56
β-strand	545-556	12	56
β-strand	562-571	10	56
β-strand	574-579	6	56
β-strand	584-586	3	57
β-strand	590	1	57
β-strand	592-604	13	56
β-strand	608-616	9	57
β-strand	622-631	10	57
β-strand	649-656	8	58
β-strand	666-670	5	56
β-strand	675-676	2	59
α-helix	678-680	3
β-strand	681-684	4	60
β-strand	687-690	4	60
β-strand	697-701	5	59
β-strand	708-711	4	59
β-strand	715-719	5	60
α-helix	722-724	3
β-strand	725-729	5	59
β-strand	736-737	2	56
α-helix	743-745	3
β-strand	753-756	4	56
β-strand	761-768	8	58
α-helix	769-774	6
β-strand	775-779	5	61
β-strand	782-787	6	61
β-strand	793-799	7	62
β-strand	807-811	5	62
β-strand	815-820	6	61
β-strand	826-830	5	62
α-helix	834-835	2
β-strand	836-838	3	62
β-strand	839-840	2	54

Chain H: 5 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	517-519	3	75
β-strand	528-530	3	75
β-strand	534-538	5	76
β-strand	545-556	12	76
β-strand	562-571	10	76
β-strand	574-579	6	76
β-strand	584-586	3	77
β-strand	590	1	77
β-strand	592-604	13	76
β-strand	608-616	9	77
β-strand	622-631	10	77
β-strand	649-656	8	78
β-strand	666-670	5	76
β-strand	675-676	2	79
α-helix	678-680	3
β-strand	681-684	4	80
β-strand	686	1	81
β-strand	687-690	4	80
β-strand	697-701	5	79
β-strand	708-711	4	79
β-strand	715-717	3	80
β-strand	719	1	82
α-helix	722-724	3
β-strand	725-729	5	79
β-strand	736-737	2	76
α-helix	743-745	3
β-strand	753-756	4	76
β-strand	761-768	8	78
α-helix	769-774	6
β-strand	775-779	5	83
β-strand	782-787	6	83
β-strand	793-799	7	84
β-strand	807-811	5	84
β-strand	815-820	6	83
β-strand	826-830	5	84
α-helix	834-835	2
β-strand	836-838	3	84
β-strand	839-840	2	74

Chains I, J, K and L: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	85
α-helix	7-9	3
β-strand	10-12	3	86
β-strand	18-25	8	85
α-helix	29-31	3
β-strand	34-40	7	86
β-strand	44-51	8	86
β-strand	57-59	3	86
α-helix	61-63	3
β-strand	64	1	85
β-strand	67-72	6	85
α-helix	73-75	3
β-strand	77-82	6	85
α-helix	84-86	3
β-strand	88-96	9	86
β-strand	99-103	5	86
β-strand	107-111	5	86
β-strand	117	1	87
β-strand	120-124	5	88
β-strand	135-145	11	88
β-strand	146	1	87
β-strand	151-154	4	89
α-helix	155-157	3
β-strand	163-171	9	88
β-strand	174-184	11	88
β-strand	194-199	6	89
α-helix	200-202	3
β-strand	204-209	6	89

Chains M and N: 4 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	505-507	3	105
β-strand	510-513	4	86
β-strand	518-525	8	105
β-strand	530C	1	19
β-strand	534-539	6	86
β-strand	543-549	7	86
β-strand	550	1	20
β-strand	553-554	2	86
α-helix	555	1
β-strand	562-567	6	105
β-strand	570-576	7	105
α-helix	580-582	3
β-strand	584-591	8	86
β-strand	596-598	3	86
β-strand	602-606	5	86
β-strand	611	1	106
β-strand	614-618	5	107
α-helix	619-621	3
β-strand	629-639	11	107
β-strand	640	1	106
β-strand	644-648	5	108
β-strand	649-650	2	109
β-strand	653-654	2	109
β-strand	659-661	3	107
β-strand	665-666	2	107
β-strand	672-681	10	107
α-helix	682-687	6
β-strand	690-697	8	108
β-strand	700-707	8	108

Chain O: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	505-507	3	115
β-strand	510-513	4	96
β-strand	518-525	8	115
β-strand	530B-530C	2	60
β-strand	534-539	6	96
β-strand	543-549	7	96
β-strand	553-554	2	96
α-helix	555	1
β-strand	562-567	6	115
β-strand	570-576	7	115
α-helix	580-582	3
β-strand	584-591	8	96
β-strand	596-598	3	96
β-strand	602-606	5	96
β-strand	611	1	116
β-strand	614-618	5	117
α-helix	619-621	3
β-strand	629-639	11	117
β-strand	640	1	116
β-strand	644-648	5	118
β-strand	649-650	2	119
β-strand	653-654	2	119
β-strand	659-661	3	117
β-strand	665-666	2	117
β-strand	672-681	10	117
α-helix	682-687	6
β-strand	690-697	8	118
β-strand	700-707	8	118

1 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	A, C, E, G	protein	451	CHIKUNGUNYA VIRUS	Q1H8W5
E2	B, D, F, H	protein	354	CHIKUNGUNYA VIRUS	Q1H8W5
FAB CHK265	I, J, K, L	protein	218	MUS MUSCULUS
FAB	M, N, O, P	protein	214	MUS MUSCULUS

Sequence of entity 1 (A, C, E, G), FASTA

>5ANY_1 E1 (chains A, C, E, G)
YEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELLSVTLEPTLSLDYITCEYKTVIPSPYV
KCCGTAECKDKNLPDYSCKVFTGVYPFMWGGAYCFCDAENTQLSEAHVEKSESCKTEFAS
AYRAHTASASAKLRVLYQGNNITVTAYANGDHAVTVKDAKFIVGPMSSAWTPFDNKIVVY
KGDVYNMDYPPFGAGRPGQFGDIQSRTPESKDVYANTQLVLQRPAAGTVHVPYSQAPSGF
KYWLKERGASLQHTAPFGCQIATNPVRAVNCAVGNMPISIDIPEAAFTRVVDAPSLTDMS
CEVPACTHSSDFGGVAIIKYAASKKGKCAVHSMTNAVTIREAEIEVEGNSQLQISFSTAL
ASAEFRVQVCSTQVHCAAECHPPKDHIVNYPASHTTLGVQDISATAMSWVQKGPFEDDDD
KAGWSHPQFEKGGGSGGGSGGGSWSHPQFEK

Sequence of entity 2 (B, D, F, H), FASTA

>5ANY_2 E2 (chains B, D, F, H)
NVYKATRPYLAHCPDCGEGHSCHSPVALERIRNEATDGTLKIQVSLQIGIKTDDSHDWTK
LRYMDNHMPADAERAGLFVRTSAPCTITGTMGHFILARCPKGETLTVGFTDSRKISHSCT
HPFHHDPPVIGREKFHSRPQHGKELPCSTYVQSTAATTEEIEVHMPPDTPDRTLMSQQSG
NVKITVNGQTVRYKCNCGGSNEGLTTTDKVINNCKVDQCHAAVTNHKKWQYNSPLVPRNA
ELGDRKGKIHIPFPLANVTCRVPKARNPTVTYGKNQVIMLLYPDHPTLLSYRNMGEEPNY
QEEWVMHKKEVVLTVPTEGLEVTWGNNEPYKYWPQLSTNGTAHGHPHEIILYYY

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

>5ANY_3 FAB CHK265 (chains I, J, K, L)
QIQLVQSGREVKNPGETVKISCKASGYTFTEYPMLWVKQAPGKGFRWMGLIYTNTGEPTY
AEEFKGRFVFSLEISASTAYLQINNLTNEDTATYFCVRDYFISLDYWGQGTTLTVSSAKT
TAPSVYPLAPVCGGTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPALLQSGLYT
LSSSVTVTSNTWPSQTITCNVAHPASSTKVDKKIESRR

Sequence of entity 4 (M, N, O, P), FASTA

>5ANY_4 FAB (chains M, N, O, P)
QAVVTQESALTTSPGETVTLTCRSNIGAVTSSNCANWVQEKPDHFFTGLIGDTNNRRSGV
PARFSGSLIGDKAALTITGAQTEDEAIYFCALWYNNLWVFGGGTKLTVLGQPKSSPSVTL
FPPSSEELETNKATLVCTITDFYPGVVTVDWKVDGTPVTQGMETTQPSKQSNNKYMASSY
LTLTARAWERHSSYSCQVTHEGHTVEKSLSRADC

Primary citation

Broadly Neutralizing Alphavirus Antibodies Bind an Epitope on E2 and Inhibit Entry and Egress. Fox, J.M., Long, F., Edeling, M.A. et al. Cell (2015) 163:1095. DOI 10.1016/J.CELL.2015.10.050 · 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
2XFC 9.0 Å, Chikungunya E1 E2 envelope glycoproteins fitted in semliki forest virus cryo-EM map

Browse structure collections

About this viewer

MolViewer shows 5ANY directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.