3J2W: Electron cryo-microscopy of Chikungunya virus

Name: PDB 3J2W: Electron cryo-microscopy of Chikungunya virus
Published: 2013-04-24
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Electron cryo-microscopy of Chikungunya virus. Determined by electron microscopy at 5.0 Å resolution. Released 24 Apr 2013.

Method: Electron microscopy
Resolution: 5.0 Å
Organism: Chikungunya virus
Chains: 20
Atoms: 30,928
Mol. weight: 441.69 kDa
Released: 24 Apr 2013

Explore 3J2W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3J2W contains 87 α-helices and 369 β-strands across 20 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: 7 helices, 43 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	24	1	3
β-strand	27-36	10	2
β-strand	37-38	2	4
β-strand	39-40	2	5
β-strand	44-48	5	6
β-strand	51-54	4	7
β-strand	59-61	3	8
β-strand	77-82	6	8
β-strand	87-88	2	9
β-strand	91-92	2	9
β-strand	101-106	6	8
β-strand	107-110	4	7
α-helix	112-115	4
β-strand	119-122	4	6
β-strand	127-128	2	5
β-strand	131-137	7	2
β-strand	140-146	7	2
β-strand	153-156	4	1
β-strand	159-163	5	1
β-strand	177-180	4	6
β-strand	183-185	3	6
α-helix	189-191	3
β-strand	203-205	3	6
β-strand	213-215	3	6
β-strand	220-221	2	10
α-helix	223-225	3
β-strand	233-234	2	10
α-helix	236-238	3
α-helix	239-243	5
α-helix	251-254	4
β-strand	260-262	3	4
β-strand	267-269	3	4
β-strand	275-281	7	1
α-helix	284-286	3
β-strand	289	1	3
β-strand	297-306	10	11
β-strand	307	1	12
β-strand	314-321	8	11
β-strand	326-329	4	13
β-strand	330-332	3	14
β-strand	338-339	2	11
β-strand	343-346	4	13
β-strand	349-357	9	11
β-strand	362-369	8	14
β-strand	372-379	8	14
β-strand	381	1	12
β-strand	387	1	15

Chain B: 8 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	1002-1008	7	27
β-strand	1014-1019	6	28
β-strand	1024	1	29
β-strand	1027-1042	16	28
β-strand	1046-1048	3	30
β-strand	1051-1054	4	31
β-strand	1059-1061	3	32
β-strand	1077-1082	6	32
β-strand	1087-1088	2	33
β-strand	1091-1092	2	33
β-strand	1101-1106	6	32
β-strand	1107-1110	4	31
α-helix	1112-1115	4
β-strand	1119-1122	4	30
β-strand	1124-1137	14	28
β-strand	1140-1146	7	28
β-strand	1153-1156	4	27
β-strand	1159-1163	5	27
β-strand	1177-1180	4	30
β-strand	1183-1185	3	30
α-helix	1189-1191	3
β-strand	1203-1205	3	30
β-strand	1213-1215	3	30
β-strand	1220-1221	2	34
α-helix	1223-1225	3
β-strand	1233-1234	2	34
α-helix	1236-1238	3
α-helix	1239-1243	5
α-helix	1251-1254	4
β-strand	1260-1262	3	28
β-strand	1267-1269	3	28
β-strand	1275-1281	7	27
α-helix	1284-1286	3
β-strand	1289	1	29
α-helix	1290-1292	3
β-strand	1297	1	35
β-strand	1301-1306	6	35
β-strand	1307	1	36
β-strand	1314-1321	8	35
β-strand	1326-1329	4	37
β-strand	1330-1332	3	35
β-strand	1338-1339	2	35
β-strand	1343-1346	4	37
β-strand	1349-1357	9	35
β-strand	1362-1369	8	35
β-strand	1372-1379	8	35
β-strand	1381	1	36

Chain C: 7 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	2002-2008	7	47
β-strand	2014-2019	6	48
β-strand	2024	1	49
β-strand	2027-2033	7	48
β-strand	2037-2048	12	50
β-strand	2051-2054	4	51
β-strand	2059-2061	3	52
β-strand	2077-2082	6	52
β-strand	2087-2088	2	53
β-strand	2091-2092	2	53
β-strand	2101-2106	6	52
β-strand	2107-2110	4	51
α-helix	2112-2115	4
β-strand	2119-2130	12	50
β-strand	2133-2137	5	48
β-strand	2140-2144	5	48
β-strand	2153-2156	4	47
β-strand	2159-2163	5	47
β-strand	2177-2180	4	50
β-strand	2183-2185	3	50
α-helix	2189-2191	3
β-strand	2203-2205	3	50
β-strand	2213-2215	3	50
β-strand	2220-2221	2	54
α-helix	2223-2225	3
β-strand	2233-2234	2	54
α-helix	2236-2238	3
α-helix	2239-2243	5
α-helix	2251-2254	4
β-strand	2260-2262	3	50
β-strand	2267-2269	3	50
β-strand	2275-2281	7	47
α-helix	2284-2286	3
β-strand	2289	1	49
β-strand	2296-2306	11	55
β-strand	2307	1	56
β-strand	2314-2322	9	55
β-strand	2326-2329	4	57
β-strand	2330-2332	3	58
β-strand	2338-2339	2	55
β-strand	2343-2346	4	57
β-strand	2349-2357	9	55
β-strand	2362-2369	8	58
β-strand	2372-2379	8	58
β-strand	2381	1	56

Chain D: 7 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	3002-3008	7	68
β-strand	3011	1	69
β-strand	3014-3019	6	69
β-strand	3024	1	70
β-strand	3027-3040	14	69
β-strand	3044-3048	5	71
β-strand	3051-3054	4	72
β-strand	3059-3061	3	73
β-strand	3077-3082	6	73
β-strand	3087-3088	2	74
β-strand	3090	1	75
β-strand	3091-3092	2	74
β-strand	3101-3106	6	73
β-strand	3107-3110	4	72
α-helix	3112-3115	4
β-strand	3119-3122	4	71
β-strand	3127-3137	11	69
β-strand	3140-3147	8	69
β-strand	3153-3156	4	68
β-strand	3159-3163	5	68
β-strand	3177-3180	4	71
β-strand	3183-3185	3	71
α-helix	3189-3191	3
β-strand	3203-3205	3	71
β-strand	3213-3215	3	71
β-strand	3220-3221	2	76
α-helix	3223-3225	3
β-strand	3233-3234	2	76
α-helix	3236-3238	3
α-helix	3239-3243	5
α-helix	3251-3254	4
β-strand	3260-3262	3	69
β-strand	3267-3269	3	69
β-strand	3275-3281	7	68
α-helix	3284-3286	3
β-strand	3289	1	70
β-strand	3296-3297	2	77
β-strand	3301-3306	6	77
β-strand	3307	1	78
β-strand	3314-3322	9	77
β-strand	3326-3329	4	79
β-strand	3330-3332	3	80
β-strand	3338-3339	2	77
β-strand	3343-3346	4	79
β-strand	3349-3357	9	77
β-strand	3362-3369	8	80
β-strand	3372-3379	8	80
β-strand	3381	1	78

Chain E: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	405-411	7
α-helix	416-438	23

Chain F: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	1405-1411	7
α-helix	1416-1438	23

Chain G: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2405-2411	7
α-helix	2416-2438	23

Chain H: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3405-3411	7
α-helix	3416-3438	23

12 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
Glycoprotein E1	A, B, C, D	protein	393	Chikungunya virus	Q1H8W5
Glycoprotein E2	M, N, O	protein	336	Chikungunya virus	Q1H8W5
Glycoprotein E2	P	protein	336	Chikungunya virus	Q1H8W5
Glycoprotein E1	E, F, G, H	protein	46	Chikungunya virus	Q5XXP3
Glycoprotein E2	Q, R, S, T	protein	81	Chikungunya virus	Q5XXP3
Capsid protein	I, J, K, L	protein	149	Chikungunya virus	Q5XXP3

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

>3J2W_1 Glycoprotein E1 (chains A, B, C, D)
YEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELLSVTLEPTLSLDYITCEYKTVIPSPYV
KCCGTAECKDKNLPDYSCKVFTGVYPFMWGGAYCFCDAENTQLSEAHVEKSESCKTEFAS
AYRAHTASASAKLRVLYQGNNITVTAYANGDHAVTVKDAKFIVGPMSSAWTPFDNKIVVY
KGDVYNMDYPPFGAGRPGQFGDIQSRTPESKDVYANTQLVLQRPAAGTVHVPYSQAPSGF
KYWLKERGASLQHTAPFGCQIATNPVRAVNCAVGNMPISIDIPEAAFTRVVDAPSLTDMS
CEVPACTHSSDFGGVAIIKYAASKKGKCAVHSMTNAVTIREAEIEVEGNSQLQISFSTAL
ASAEFRVQVCSTQVHCAAECHPPKDHIVNYPAS

Sequence of entity 2 (M, N, O), FASTA

>3J2W_2 Glycoprotein E2 (chains M, N, O)
NVYKATRPYLAHCPDCGEGHSCHSPVALERIRNEATDGTLKIQVSLQIGIKTDDSHDWTK
LRYMDNHMPADAERAGLFVRTSAPCTITGTMGHFILARCPKGETLTVGFTDSRKISHSCT
HPFHHDPPVIGREKFHSRPQHGKELPCSTYVQSTAATTEEIEVHMPPDTPDRTLMSQQSG
NVKITVNGQTVRYKCNCGGSNEGLTTTDKVINNCKVDQCHAAVTNHKKWQYNSPLVPRNA
ELGDRKGKIHIPFPLANVTCRVPKARNPTVTYGKNQVIMLLYPDHPTLLSYRNMGEEPNY
QEEWVMHKKEVVLTVPTEGLEVTWGNNEPYKYWPQL

Sequence of entity 3 (P), FASTA

>3J2W_3 Glycoprotein E2 (chains P)
NVYKATRPYLAHCPDCGEGHSCHSPVALERIRNEATDGTLKIQVSLQIGIKTDDSHDWTK
LRYMDNHMPADAERAGLFVRTSAPCTITGTMGHFILARCPKGETLTVGFTDSRKISHSCT
HPFHHDPPVIGREKFHSRPQHGKELPCSTYVQSTAATTEEIEVHMPPDTPDRTLMSQQSG
NVKITVNGQTVRYKCNCGGSNEGLTTTDKVINNCKVDQCHAAVTNHKKWQYNSPLVPRNA
ELGDRKGKIHIPFPLANVTCRVPKARNPTVTYGKNQVIMLLYPDHPTLLSYRNMGEEPNY
QEEWVMHKKEVVLTVPTEGLEVTWGNNEPYKYWPQM

Sequence of entity 4 (E, F, G, H), FASTA

>3J2W_4 Glycoprotein E1 (chains E, F, G, H)
HTTLGVQDISTTAMSWVQKITGGVGLIVAVAALILIVVLCVSFSRH

Sequence of entity 5 (Q, R, S, T), FASTA

>3J2W_5 Glycoprotein E2 (chains Q, R, S, T)
STNGTAHGHPHEIILYYYELYPTMTVVIVSVASFVLLSMVGTAVGMCVCARRRCITPYEL
TPGATVPFLLSLLCCVRTTKA

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

>3J2W_6 Capsid protein (chains I, J, K, L)
CIFEVKHEGKVMGYACLVGDKVMKPAHVKGTIDNADLAKLAFKRSSKYDLECAQIPVHMK
SDASKFTHEKPEGYYNWHHGAVQYSGGRFTIPTGAGKPGDSGRPIFDNKGRVVAIVLGGA
NEGARTALSVVTWNKDIVTKITPEGAEEW

Primary citation

Structural analyses at pseudo atomic resolution of Chikungunya virus and antibodies show mechanisms of neutralization. Sun, S., Xiang, Y., Akahata, W. et al. Elife (2013) 2:e00435-e00435. DOI 10.7554/eLife.00435 · 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
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
5ANY 16.9 Å, Electron cryo-microscopy of chikungunya virus in complex with neutralizing antibody Fab…

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