6HBK: Echovirus 18 Open particle without one pentamer

Name: PDB 6HBK: Echovirus 18 Open particle without one pentamer
Published: 2019-03-20
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Echovirus 18 Open particle without one pentamer. Determined by electron microscopy at 3.8 Å resolution. Released 20 Mar 2019.

Method: Electron microscopy
Resolution: 3.8 Å
Organism: Echovirus E18
Chains: 33
Atoms: 57,156
Mol. weight: 961.21 kDa
Released: 20 Mar 2019

Explore 6HBK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6HBK contains 209 α-helices and 747 β-strands across 33 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.

Chains a, d, L, O, R, U and X: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3002-3006	5	86
α-helix	3007	1
β-strand	3014	1	43
α-helix	3021-3022	2
β-strand	3023	1	102
α-helix	3030-3032	3
β-strand	3039-3040	2	102
α-helix	3044-3047	4
β-strand	3052	1	118
β-strand	3058	1	108
β-strand	3070-3072	3	118
β-strand	3084	1	119
β-strand	3087-3088	2	119
α-helix	3100-3104	5
β-strand	3108	1	120
β-strand	3111-3121	11	118
β-strand	3128	1	121
β-strand	3130-3136	7	119
α-helix	3141-3143	3
α-helix	3146-3150	5
β-strand	3153-3158	6	119
β-strand	3164-3166	3	118
β-strand	3169-3174	6	118
β-strand	3189-3195	7	119
β-strand	3200	1	121
β-strand	3209-3223	15	118
β-strand	3226	1	120

Chains A, b, D, e, G, J, M, P, S, V and Y: 7 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	1059-1062	4
β-strand	1066-1073	8	1
β-strand	1086	1	2
α-helix	1096-1102	7
β-strand	1105-1119	15	1
β-strand	1136	1	3
β-strand	1137-1142	6	2
α-helix	1155-1158	4
β-strand	1164-1165	2	2
α-helix	1167	1
β-strand	1168	1	3
α-helix	1173-1174	2
β-strand	1175-1178	4	1
β-strand	1187-1188	2	1
β-strand	1193	1	4
β-strand	1194	1	5
β-strand	1203	1	5
β-strand	1213-1218	6	2
β-strand	1229-1235	7	1
β-strand	1237-1245	9	1
α-helix	1247-1248	2
β-strand	1249	1	6
α-helix	1252-1253	2
β-strand	1270	1	7

Chains B, E, f, H, K, Q, T and W: 5 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	2014	1	92
β-strand	2017-2018	2	93
β-strand	2021-2022	2	93
β-strand	2025	1	92
β-strand	2032-2033	2	94
α-helix	2034-2036	3
β-strand	2053-2054	2	95
β-strand	2064-2065	2	94
β-strand	2069-2071	3	96
β-strand	2078-2082	5	97
α-helix	2084-2086	3
α-helix	2090-2098	9
β-strand	2102-2103	2	95
β-strand	2107-2111	5	94
β-strand	2119	1	98
β-strand	2121-2125	5	97
β-strand	2128	1	97
β-strand	2134	1	99
β-strand	2148	1	100
β-strand	2151	1	100
α-helix	2152	1
β-strand	2153-2154	2	97
β-strand	2156	1	101
β-strand	2165	1	99
β-strand	2168	1	101
β-strand	2176	1	6
β-strand	2186-2190	5	97
β-strand	2197-2200	4	94
β-strand	2210	1	95
β-strand	2215	1	4
β-strand	2218-2224	7	97
α-helix	2227-2228	2
β-strand	2229	1	98
β-strand	2238-2240	3	96
β-strand	2241-2245	5	94
β-strand	2250-2252	3	95

Chains c, N and Z: 5 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	2014	1	73
β-strand	2017-2018	2	74
β-strand	2021-2023	3	74
β-strand	2025	1	73
β-strand	2032-2033	2	75
α-helix	2034-2036	3
β-strand	2053-2054	2	76
β-strand	2064-2065	2	75
β-strand	2069-2071	3	77
β-strand	2078-2082	5	78
α-helix	2084-2086	3
α-helix	2090-2098	9
β-strand	2102-2103	2	76
β-strand	2107-2111	5	75
β-strand	2119	1	79
β-strand	2121-2125	5	78
β-strand	2128	1	78
β-strand	2134	1	80
β-strand	2148	1	81
β-strand	2151	1	81
α-helix	2152	1
β-strand	2153-2154	2	78
β-strand	2156	1	82
β-strand	2165	1	80
β-strand	2168	1	82
β-strand	2176	1	67
β-strand	2186-2190	5	78
β-strand	2197-2200	4	75
β-strand	2210	1	76
β-strand	2215	1	65
β-strand	2218-2224	7	78
α-helix	2227-2228	2
β-strand	2229	1	79
β-strand	2238-2240	3	77
β-strand	2241-2245	5	75
β-strand	2250-2252	3	76

Chain C: 7 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	3006-3007	2
α-helix	3021-3022	2
β-strand	3023	1	1
α-helix	3030-3032	3
β-strand	3039-3040	2	1
α-helix	3044-3047	4
β-strand	3051-3052	2	83
β-strand	3058	1	7
β-strand	3070-3072	3	83
β-strand	3084	1	74
β-strand	3087-3088	2	74
α-helix	3100-3104	5
β-strand	3108	1	84
β-strand	3111-3121	11	83
β-strand	3128	1	85
β-strand	3130-3136	7	74
α-helix	3141-3143	3
α-helix	3146-3150	5
β-strand	3153-3158	6	74
β-strand	3164-3166	3	83
β-strand	3169-3174	6	83
β-strand	3189-3195	7	74
β-strand	3200	1	85
β-strand	3209-3223	15	83
β-strand	3226	1	84

Chains F and g: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3002-3006	5	86
α-helix	3007	1
β-strand	3014	1	63
α-helix	3021-3022	2
β-strand	3023	1	42
α-helix	3030-3032	3
β-strand	3039-3040	2	42
α-helix	3044-3047	4
β-strand	3051-3052	2	69
β-strand	3058	1	48
β-strand	3070-3072	3	69
β-strand	3084	1	70
β-strand	3087-3088	2	70
α-helix	3100-3104	5
β-strand	3108	1	71
β-strand	3111-3121	11	69
β-strand	3128	1	72
β-strand	3130-3136	7	70
α-helix	3141-3143	3
α-helix	3146-3150	5
β-strand	3153-3158	6	70
β-strand	3164-3166	3	69
β-strand	3169-3174	6	69
β-strand	3189-3195	7	70
β-strand	3200	1	72
β-strand	3209-3223	15	69
β-strand	3226	1	71

Chain I: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3002-3006	5	18
α-helix	3007	1
β-strand	3014	1	205
α-helix	3021-3022	2
β-strand	3023	1	225
α-helix	3030-3032	3
β-strand	3039-3040	2	225
α-helix	3044-3047	4
β-strand	3052	1	26
β-strand	3058	1	230
β-strand	3070-3072	3	26
β-strand	3084	1	27
β-strand	3087-3088	2	27
α-helix	3100-3104	5
β-strand	3108	1	28
β-strand	3111-3121	11	26
β-strand	3124	1	14
β-strand	3128	1	29
β-strand	3130-3136	7	27
α-helix	3141-3143	3
α-helix	3146-3150	5
β-strand	3153-3158	6	27
β-strand	3164-3166	3	26
β-strand	3169-3174	6	26
β-strand	3189-3195	7	27
β-strand	3200	1	29
β-strand	3209-3223	15	26
β-strand	3226	1	28

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Echovirus 18 capsid protein 1	A, D, G, J, M, P, S, V, Y, b, e	protein	287	Echovirus E18	Q8V635 (AlphaFold model)
Echovirus 18 capsid protein 2	C, F, I, L, O, R, U, X, a, d, g	protein	239	Echovirus E18	Q8V635 (AlphaFold model)
Echovirus 18 capsid protein 3	B, E, H, K, N, Q, T, W, Z, c, f	protein	259	Echovirus E18	Q8V635 (AlphaFold model)

Sequence of entity 1 (A, D, G, J, M, P, S, V, Y, b, e), FASTA

>6HBK_1 Echovirus 18 capsid protein 1 (chains A, D, G, J, M, P, S, V, Y, b, e)
GDNQDRTVANTQPSGPSNSTEIPALTAVETGHTSQVDPSDTIQTRHVVNFHSRSESTIEN
FMGRAACVFMDQYKINGEETSTDRFAVWTINIREMAQLRRKCEMFTYMRFDIEMTMVITS
CQDQGTILDQDMPVLTHQIMYVPPGGPIPAKVDGYEWQTSTNPSVFWTEGNAPPRISIPF
ISVGNAYSSFYDGWSHFTQDGTYGYTTLNAMGKLYIRHVNRSSPHQITSTIRVYFKPKHI
KAWVPRPPRLCPYINKRDVNFVVTEITDSRTSITDTPHPEHSVLATH

Sequence of entity 2 (C, F, I, L, O, R, U, X, a, d, g), FASTA

>6HBK_2 Echovirus 18 capsid protein 2 (chains C, F, I, L, O, R, U, X, a, d, g)
GVPVLNTPGSNQFLTSDDYQSPSAMPQFDETPEMHIPGEVRNLMEIAEVDSVVPVNNVTG
KTKSMDAYQIPVGTGNTDKTKPIFSFQMDPGYSSVLKRTLLGEMLNYYAHWSGSVKLTFL
FCGSAMATGKLLISYSPPGASVPTSRKDAMLGTHIVWDIGLQSSCVLCVPWISQSHYRMV
QQDPYTSAGYITCWYQTNIVVPPGAPTSCDVLCFASACNDFSVRLLRDTPFMAQPGKLQ

Sequence of entity 3 (B, E, H, K, N, Q, T, W, Z, c, f), FASTA

>6HBK_3 Echovirus 18 capsid protein 3 (chains B, E, H, K, N, Q, T, W, Z, c, f)
SPSAEECGYSDRVRSMTLGNSTITTQESANVVVGYGEWPSYLSDREATAEDQPTQPDVAT
CRFYTLESVQWEKTSPGWWWKFPEALKNMGLFGQNMHYHYLGRAGYTIHVQCNASKFHQG
CLLVVCVPEAEMGCADTDTTFPATELTTEDTPHVFTSDSITGKKVQAAVCNAGMGVGVGN
LTIFPHQWINLRTNNSATIVIPYINSVPMDNMFRHYNFTLMIIPFAPLNFTDGATAYVPI
TVTIAPMYAEYNGLRLAST

Primary citation

Enterovirus particles expel capsid pentamers to enable genome release. Buchta, D., Fuzik, T., Hrebik, D. et al. Nat Commun (2019) 10:1138-1138. DOI 10.1038/s41467-019-09132-x · PubMed

Other PDB entries of the same protein (UniProt Q8V635 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9TF0 2.26 Å, Structure of echovirus 18 in complex with neonatal Fc receptor
9TF1 2.44 Å, Structure of echovirus 18, activated particle
9TF2 2.86 Å, Structure of echovirus 18, empty particle
7B5F 2.9 Å, Structure of echovirus 18 in complex with neonatal Fc receptor
6HBG 3.16 Å, Echovirus 18 native particle
6HBJ 3.16 Å, Echovirus 18 empty particle
6HBH 3.36 Å, Echovirus 18 A-particle
6HBL 3.7 Å, Echovirus 18 Open particle without three pentamers
6HHT 4.05 Å, Echovirus 18 Open particle without two pentamers
9S63 4.3 Å, Echovirus 18 in situ, virion, I4
9SPU 6.5 Å, Echovirus 18 particle missing one pentamer in situ, symmetrized reconstruction (C5)

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