6HBJ: Echovirus 18 empty particle

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

Echovirus 18 empty 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: 3
Atoms: 5,016
Mol. weight: 87.51 kDa
Released: 20 Mar 2019

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

Secondary structure: helices and β-sheets

6HBJ contains 20 α-helices and 55 β-strands across 3 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, 15 β-strands

Element	Residues	Length	Sheet
α-helix	54-56	3
β-strand	57	1	1
α-helix	58-62	5
β-strand	66-74	9	2
α-helix	82-84	3
β-strand	86	1	3
α-helix	96-102	7
β-strand	105-118	14	2
β-strand	136-142	7	3
α-helix	146-149	4
α-helix	155-158	4
β-strand	164-168	5	3
α-helix	173-174	2
β-strand	175-178	4	2
β-strand	187-188	2	2
β-strand	193	1	4
β-strand	194	1	5
β-strand	203	1	5
β-strand	213-218	6	3
β-strand	228-245	18	2
α-helix	247-248	2
β-strand	249	1	6
α-helix	252-253	2
β-strand	270	1	7

Chain B: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	15-18	4	8
β-strand	21-24	4	8
β-strand	32-33	2	9
α-helix	34-36	3
β-strand	64-65	2	9
α-helix	66-68	3
β-strand	69-71	3	10
β-strand	78-82	5	11
α-helix	84-86	3
α-helix	90-98	9
β-strand	102-103	2	12
β-strand	107-111	5	9
β-strand	119-125	7	11
β-strand	128	1	11
β-strand	134	1	13
β-strand	153-154	2	11
β-strand	156	1	14
β-strand	165	1	13
β-strand	168	1	14
β-strand	176	1	6
β-strand	186-190	5	11
β-strand	196-200	5	9
β-strand	210	1	12
β-strand	215	1	4
β-strand	218-229	12	11
β-strand	238-240	3	10
β-strand	241-245	5	9
β-strand	250-251	2	12
α-helix	256-257	2

Chain C: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	23	1	2
α-helix	30-33	4
β-strand	39-40	2	2
β-strand	42	1	1
α-helix	44-47	4
β-strand	51-52	2	15
β-strand	58	1	7
α-helix	65-67	3
β-strand	70-72	3	15
β-strand	84-87	4	16
α-helix	100-105	6
β-strand	108	1	17
β-strand	111-121	11	15
β-strand	128-136	9	16
α-helix	141-143	3
α-helix	146-150	5
β-strand	153-158	6	16
β-strand	164-173	10	15
β-strand	190-200	11	16
β-strand	209-217	9	15
β-strand	222-223	2	15
β-strand	226	1	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Viral protein 1	A	protein	287	Echovirus E18	Q8V635 (AlphaFold model)
Viral protein 2	B	protein	260	Echovirus E18	Q8V635 (AlphaFold model)
Viral protein 3	C	protein	239	Echovirus E18	Q8V635 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6HBJ_1 Viral protein 1 (chains A)
GDNQDRTVANTQPSGPSNSTEIPALTAVETGHTSQVDPSDTIQTRHVVNFHSRSESTIEN
FMGRAACVFMDQYKINGEETSTDRFAVWTINIREMAQLRRKCEMFTYMRFDIEMTMVITS
CQDQGTILDQDMPVLTHQIMYVPPGGPIPAKVDGYEWQTSTNPSVFWTEGNAPPRISIPF
ISVGNAYSSFYDGWSHFTQDGTYGYTTLNAMGKLYIRHVNRSSPHQITSTIRVYFKPKHI
KAWVPRPPRLCPYINKRDVNFVVTEITDSRTSITDTPHPEHSVLATH

Sequence of entity 2 (B), FASTA

>6HBJ_2 Viral protein 2 (chains B)
SPSAEECGYSDRVRSMTLGNSTITTQESANVVVGYGEWPSYLSDREATAEDQPTQPDVAT
CRFYTLESVQWEKTSPGWWWKFPEALKNMGLFGQNMHYHYLGRAGYTIHVQCNASKFHQG
CLLVVCVPEAEMGCADTDTTFPATELTTEDTPHVFTSDSITGKKVQAAVCNAGMGVGVGN
LTIFPHQWINLRTNNSATIVIPYINSVPMDNMFRHYNFTLMIIPFAPLNFTDGATAYVPI
TVTIAPMYAEYNGLRLASTQ

Sequence of entity 3 (C), FASTA

>6HBJ_3 Viral protein 3 (chains C)
GVPVLNTPGSNQFLTSDDYQSPSAMPQFDETPEMHIPGEVRNLMEIAEVDSVVPVNNVTG
KTKSMDAYQIPVGTGNTDKTKPIFSFQMDPGYSSVLKRTLLGEMLNYYAHWSGSVKLTFL
FCGSAMATGKLLISYSPPGASVPTSRKDAMLGTHIVWDIGLQSSCVLCVPWISQSHYRMV
QQDPYTSAGYITCWYQTNIVVPPGAPTSCDVLCFASACNDFSVRLLRDTPFMAQPGKLQ

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
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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