6HBG: Echovirus 18 native particle

Name: PDB 6HBG: Echovirus 18 native particle
Published: 2019-03-20
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Echovirus 18 native particle. Determined by electron microscopy at 3.16 Å resolution. Released 20 Mar 2019.

Method: Electron microscopy
Resolution: 3.16 Å
Organism: Echovirus E18
Chains: 4
Atoms: 6,121
Mol. weight: 95.39 kDa
Ligands: GUN, PLM
Released: 20 Mar 2019

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

Secondary structure: helices and β-sheets

6HBG contains 22 α-helices and 63 β-strands across 4 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, 17 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
β-strand	11	1	1
α-helix	12-13	2
β-strand	25-26	2	2
α-helix	28-30	3
α-helix	38-41	4
β-strand	47	1	1
β-strand	57	1	3
α-helix	58-62	5
β-strand	66-74	9	4
β-strand	85-87	3	5
α-helix	96-102	7
β-strand	105-122	18	4
β-strand	136-141	6	5
α-helix	142-143	2
α-helix	147-149	3
β-strand	164-168	5	5
β-strand	175-177	3	4
β-strand	187-188	2	4
β-strand	193	1	6
β-strand	194	1	7
β-strand	203	1	7
β-strand	214-218	5	5
β-strand	227-245	19	4
α-helix	247-249	3
β-strand	270	1	8

Chain B: 9 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	14-18	5	9
β-strand	21-25	5	9
α-helix	29-31	3
β-strand	32-33	2	10
α-helix	34-36	3
α-helix	41-43	3
α-helix	52-53	2
β-strand	54	1	11
β-strand	64-65	2	10
β-strand	69-71	3	12
β-strand	78-82	5	13
α-helix	84-86	3
α-helix	90-98	9
β-strand	99-103	5	11
β-strand	107-111	5	10
β-strand	119-128	10	13
β-strand	134	1	14
α-helix	143-146	4
β-strand	153-154	2	13
β-strand	156	1	15
β-strand	165	1	14
β-strand	168	1	15
β-strand	171	1	16
β-strand	177	1	16
α-helix	178-183	6
β-strand	186-190	5	13
β-strand	196-200	5	10
β-strand	210	1	11
β-strand	215	1	6
β-strand	218-229	12	13
β-strand	232	1	17
β-strand	234	1	17
β-strand	238-240	3	12
β-strand	241-245	5	10
β-strand	250-254	5	11
α-helix	257-258	2

Chain C: 3 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	23	1	4
α-helix	30-33	4
β-strand	39-40	2	4
β-strand	42	1	3
β-strand	52	1	2
β-strand	58	1	8
β-strand	69-73	5	2
β-strand	85-87	3	18
α-helix	100-105	6
β-strand	108	1	19
β-strand	110-112	3	20
β-strand	115-121	7	2
β-strand	128-136	9	18
α-helix	146-149	4
β-strand	153-159	7	18
β-strand	164-169	6	2
β-strand	178-179	2	20
β-strand	190-200	11	18
β-strand	208-217	10	2
β-strand	222-223	2	20
β-strand	226	1	19

Chain D: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	51-54	4
β-strand	57	1	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Echovirus 18 viral protein 1	A	protein	287	Echovirus E18	Q8V635 (AlphaFold model)
Echovirus 18 viral protein 2	B	protein	260	Echovirus E18	Q8V635 (AlphaFold model)
Echovirus 18 viral protein 3	C	protein	239	Echovirus E18	Q8V635 (AlphaFold model)
Echovirus 18 viral protein 4	D	protein	69	Echovirus E18	Q8V635 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6HBG_1 Echovirus 18 viral protein 1 (chains A)
GDNQDRTVANTQPSGPSNSTEIPALTAVETGHTSQVDPSDTIQTRHVVNFHSRSESTIEN
FMGRAACVFMDQYKINGEETSTDRFAVWTINIREMAQLRRKCEMFTYMRFDIEMTMVITS
CQDQGTILDQDMPVLTHQIMYVPPGGPIPAKVDGYEWQTSTNPSVFWTEGNAPPRISIPF
ISVGNAYSSFYDGWSHFTQDGTYGYTTLNAMGKLYIRHVNRSSPHQITSTIRVYFKPKHI
KAWVPRPPRLCPYINKRDVNFVVTEITDSRTSITDTPHPEHSVLATH

Sequence of entity 2 (B), FASTA

>6HBG_2 Echovirus 18 viral protein 2 (chains B)
SPSAEECGYSDRVRSMTLGNSTITTQESANVVVGYGEWPSYLSDREATAEDQPTQPDVAT
CRFYTLESVQWEKTSPGWWWKFPEALKNMGLFGQNMHYHYLGRAGYTIHVQCNASKFHQG
CLLVVCVPEAEMGCADTDTTFPATELTTEDTPHVFTSDSITGKKVQAAVCNAGMGVGVGN
LTIFPHQWINLRTNNSATIVIPYINSVPMDNMFRHYNFTLMIIPFAPLNFTDGATAYVPI
TVTIAPMYAEYNGLRLASTQ

Sequence of entity 3 (C), FASTA

>6HBG_3 Echovirus 18 viral protein 3 (chains C)
GVPVLNTPGSNQFLTSDDYQSPSAMPQFDETPEMHIPGEVRNLMEIAEVDSVVPVNNVTG
KTKSMDAYQIPVGTGNTDKTKPIFSFQMDPGYSSVLKRTLLGEMLNYYAHWSGSVKLTFL
FCGSAMATGKLLISYSPPGASVPTSRKDAMLGTHIVWDIGLQSSCVLCVPWISQSHYRMV
QQDPYTSAGYITCWYQTNIVVPPGAPTSCDVLCFASACNDFSVRLLRDTPFMAQPGKLQ

Sequence of entity 4 (D), FASTA

>6HBG_4 Echovirus 18 viral protein 4 (chains D)
MGAQVSTQKTGAHETSLSAKGNSIIHYTNINFYKDAASSASNRQDIQQDPGKFTDPVKDL
MIKTLPALN

Ligands and cofactors

ID	Name	Formula	Copies
GUN	Guanine	C5 H5 N5 O	1
PLM	Palmitic acid	C16 H32 O2	1

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
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
9SPU 6.5 Å, Echovirus 18 particle missing one pentamer in situ, symmetrized reconstruction (C5)

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