9SPU: Echovirus 18 viral protein 1

Name: PDB 9SPU: Echovirus 18 particle missing one pentamer in situ, symmetrized reconstruction (C5)
Published: 2026-06-17
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Echovirus 18 particle missing one pentamer in situ, symmetrized reconstruction (C5). Determined by electron microscopy at 6.5 Å resolution. Released 17 Jun 2026.

Method: Electron microscopy
Resolution: 6.5 Å
Organism: Echovirus E18
Chains: 33
Atoms: 57,156
Mol. weight: 962.62 kDa
Released: 17 Jun 2026

Explore 9SPU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9SPU contains 231 α-helices and 597 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, F, I and R: 9 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3002-3006	5	74
α-helix	3007	1
α-helix	3021-3022	2
β-strand	3023	1	91
α-helix	3029-3032	4
β-strand	3039	1	91
α-helix	3044-3047	4
β-strand	3051	1	103
β-strand	3058	1	92
α-helix	3059-3061	3
α-helix	3066-3068	3
β-strand	3084-3087	4	104
α-helix	3100-3106	7
β-strand	3108-3121	14	103
β-strand	3128	1	105
β-strand	3130-3131	2	106
β-strand	3132-3136	5	104
α-helix	3141-3143	3
α-helix	3146-3151	6
β-strand	3157-3158	2	106
β-strand	3164-3172	9	103
β-strand	3190-3194	5	104
β-strand	3200	1	105
β-strand	3211-3226	16	103

Chains A, b, D, e, G, M, P, S and Y: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	1054-1056	3
α-helix	1058-1062	5
β-strand	1066-1073	8	1
β-strand	1086	1	2
α-helix	1096-1102	7
β-strand	1105-1115	11	3
β-strand	1116-1121	6	1
β-strand	1136-1142	7	2
α-helix	1155-1158	4
β-strand	1164-1168	5	2
α-helix	1172-1174	3
β-strand	1175-1178	4	3
β-strand	1187-1188	2	3
β-strand	1213-1216	4	2
β-strand	1228-1235	8	1
β-strand	1236-1245	10	3
α-helix	1247-1249	3
α-helix	1252-1253	2
β-strand	1270	1	4

Chains B, c, E, f, H, K, N, Q, T, W and Z: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	2014	1	79
β-strand	2017-2018	2	80
β-strand	2021-2022	2	80
β-strand	2025	1	79
β-strand	2032-2033	2	81
α-helix	2034-2036	3
β-strand	2064-2065	2	81
β-strand	2069-2071	3	82
β-strand	2078-2079	2	83
β-strand	2082	1	84
α-helix	2084-2086	3
α-helix	2090-2098	9
β-strand	2102-2103	2	85
β-strand	2107-2111	5	81
β-strand	2121-2125	5	83
β-strand	2128	1	84
α-helix	2131-2133	3
β-strand	2134	1	86
β-strand	2148	1	87
β-strand	2151	1	87
β-strand	2153-2154	2	83
β-strand	2156	1	88
β-strand	2165	1	86
β-strand	2168	1	88
β-strand	2188-2190	3	83
β-strand	2196-2200	5	81
β-strand	2210	1	85
β-strand	2218	1	84
β-strand	2221-2224	4	83
α-helix	2227-2228	2
β-strand	2238-2240	3	82
β-strand	2241-2245	5	81
β-strand	2250-2251	2	85

Chain C: 9 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	3006-3007	2
α-helix	3021-3022	2
β-strand	3023	1	3
α-helix	3029-3032	4
β-strand	3039	1	3
α-helix	3044-3047	4
β-strand	3051	1	70
β-strand	3058	1	4
α-helix	3059-3061	3
α-helix	3066-3068	3
β-strand	3084-3087	4	71
α-helix	3100-3106	7
β-strand	3108-3121	14	70
β-strand	3128	1	72
β-strand	3130-3131	2	73
β-strand	3132-3136	5	71
α-helix	3141-3143	3
α-helix	3146-3151	6
β-strand	3157-3158	2	73
β-strand	3164-3172	9	70
β-strand	3190-3194	5	71
β-strand	3200	1	72
β-strand	3211-3226	16	70

Chain g: 9 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3004-3006	3	15
α-helix	3007	1
α-helix	3021-3023	3
α-helix	3029-3032	4
α-helix	3044-3047	4
β-strand	3051	1	16
β-strand	3058	1	17
α-helix	3059-3061	3
α-helix	3066-3068	3
β-strand	3084-3087	4	18
α-helix	3100-3106	7
β-strand	3108-3121	14	16
β-strand	3128	1	19
β-strand	3130-3131	2	20
β-strand	3132-3136	5	18
α-helix	3141-3143	3
α-helix	3146-3151	6
β-strand	3157-3158	2	20
β-strand	3164-3172	9	16
β-strand	3190-3194	5	18
β-strand	3200	1	19
β-strand	3211-3226	16	16

Chains J and V: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	1054-1056	3
α-helix	1058-1062	5
β-strand	1066-1073	8	178
β-strand	1086	1	179
α-helix	1096-1102	7
β-strand	1105-1115	11	180
β-strand	1116-1121	6	178
β-strand	1136-1142	7	179
α-helix	1155-1158	4
β-strand	1164-1168	5	179
α-helix	1172-1174	3
β-strand	1175-1178	4	180
β-strand	1187-1188	2	180
β-strand	1213-1216	4	179
β-strand	1228-1235	8	178
β-strand	1236-1245	10	180
α-helix	1247-1249	3
α-helix	1252-1253	2

Chain L: 9 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3002-3006	5	15
α-helix	3007	1
α-helix	3021-3022	2
β-strand	3023	1	180
α-helix	3029-3032	4
β-strand	3039	1	180
α-helix	3044-3047	4
β-strand	3051	1	191
α-helix	3059-3061	3
α-helix	3066-3068	3
β-strand	3084-3087	4	192
α-helix	3100-3106	7
β-strand	3108-3121	14	191
β-strand	3128	1	193
β-strand	3130-3131	2	194
β-strand	3132-3136	5	192
α-helix	3141-3143	3
α-helix	3146-3151	6
β-strand	3157-3158	2	194
β-strand	3164-3172	9	191
β-strand	3190-3194	5	192
β-strand	3200	1	193
β-strand	3211-3226	16	191

Chain O: 9 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3002-3004	3	15
β-strand	3006	1	15
α-helix	3007	1
α-helix	3021-3022	2
β-strand	3023	1	162
α-helix	3029-3032	4
β-strand	3039	1	162
α-helix	3044-3047	4
β-strand	3051	1	174
β-strand	3058	1	163
α-helix	3059-3061	3
α-helix	3066-3068	3
β-strand	3084-3087	4	175
α-helix	3100-3106	7
β-strand	3108-3121	14	174
β-strand	3128	1	176
β-strand	3130-3131	2	177
β-strand	3132-3136	5	175
α-helix	3141-3143	3
α-helix	3146-3151	6
β-strand	3157-3158	2	177
β-strand	3164-3172	9	174
β-strand	3190-3194	5	175
β-strand	3200	1	176
β-strand	3211-3226	16	174

2 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
Echovirus 18 viral protein 1	A, D, G, J, M, P, S, V, Y, b, e	protein	287	Echovirus E18	Q8V635 (AlphaFold model)
Echovirus 18 viral protein 3	C, F, I, L, O, R, U, X, a, d, g	protein	239	Echovirus E18	Q8V635 (AlphaFold model)
Echovirus 18 viral protein 2	B, E, H, K, N, Q, T, W, Z, c, f	protein	260	Echovirus E18	Q8V635 (AlphaFold model)

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

>9SPU_1 Echovirus 18 viral 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

>9SPU_2 Echovirus 18 viral protein 3 (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

>9SPU_3 Echovirus 18 viral protein 2 (chains B, E, H, K, N, Q, T, W, Z, c, f)
SPSAEECGYSDRVRSMTLGNSTITTQESANVVVGYGEWPSYLSDREATAEDQPTQPDVAT
CRFYTLESVQWEKTSPGWWWKFPEALKNMGLFGQNMHYHYLGRAGYTIHVQCNASKFHQG
CLLVVCVPEAEMGCADTDTTFPATELTTEDTPHVFTSDSITGKKVQAAVCNAGMGVGVGN
LTIFPHQWINLRTNNSATIVIPYINSVPMDNMFRHYNFTLMIIPFAPLNFTDGATAYVPI
TVTIAPMYAEYNGLRLASTQ

Primary citation

Particles of echovirus 18 open to release their genomes in vivo. Mukhamedova, L., Buchta, D., Trebichalska, Z. et al. Proc Natl Acad Sci U S A (2026) 123:e2601182123-e2601182123. DOI 10.1073/pnas.2601182123 · 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
6HBK 3.8 Å, Echovirus 18 Open particle without one pentamer
6HHT 4.05 Å, Echovirus 18 Open particle without two pentamers
9S63 4.3 Å, Echovirus 18 in situ, virion, I4

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