7B5F: Echovirus 18

Name: PDB 7B5F: Structure of echovirus 18 in complex with neonatal Fc receptor
Published: 2022-01-12
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Structure of echovirus 18 in complex with neonatal Fc receptor. Determined by electron microscopy at 2.9 Å resolution. Released 12 Jan 2022.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Echovirus E18, Homo sapiens
Chains: 6
Atoms: 7,489
Mol. weight: 136.86 kDa
Ligands: GUN, PLM
Released: 12 Jan 2022

Explore 7B5F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7B5F contains 35 α-helices and 74 β-strands across 6 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: 11 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
β-strand	11	1	8
α-helix	12-13	2
β-strand	25-26	2	2
α-helix	28-30	3
α-helix	38-40	3
β-strand	47	1	8
α-helix	58-62	5
β-strand	66-74	9	1
β-strand	85-87	3	9
α-helix	96-102	7
β-strand	105-121	17	1
β-strand	136-142	7	9
α-helix	147-149	3
α-helix	155-157	3
β-strand	164-168	5	9
α-helix	172-174	3
β-strand	175-178	4	1
β-strand	187-188	2	1
β-strand	193	1	10
β-strand	194	1	11
β-strand	203	1	11
β-strand	213-218	6	9
β-strand	228-235	8	1
β-strand	237-245	9	1
α-helix	247-248	2
β-strand	249	1	12
α-helix	252-253	2
β-strand	270	1	3

Chain B: 11 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	14-17	4	13
β-strand	22-25	4	13
β-strand	28-33	6	7
α-helix	34-36	3
α-helix	41-43	3
α-helix	52-53	2
β-strand	54	1	7
α-helix	57-60	4
β-strand	64-65	2	7
α-helix	66-68	3
β-strand	69-71	3	14
β-strand	78-82	5	15
α-helix	84-86	3
α-helix	90-98	9
β-strand	99-111	13	7
β-strand	119-128	10	15
β-strand	134	1	16
α-helix	143-145	3
α-helix	151-152	2
β-strand	153-154	2	15
β-strand	156	1	17
β-strand	165	1	16
β-strand	168	1	17
β-strand	176	1	12
α-helix	178-183	6
β-strand	186-190	5	15
β-strand	196-201	6	7
β-strand	210	1	7
β-strand	215	1	10
β-strand	218-229	12	15
β-strand	232	1	18
β-strand	234	1	18
β-strand	238-240	3	14
β-strand	241-254	14	7
α-helix	257-258	2

Chain C: 6 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	23	1	1
α-helix	30-33	4
β-strand	39-40	2	1
α-helix	43-47	5
β-strand	51-53	3	2
β-strand	58	1	3
α-helix	65-67	3
β-strand	69-73	5	2
β-strand	84-87	4	4
α-helix	100-106	7
β-strand	108	1	5
β-strand	110-112	3	6
β-strand	115-121	7	2
β-strand	128-136	9	4
α-helix	146-149	4
β-strand	153-159	7	4
β-strand	164-169	6	2
β-strand	178-179	2	6
α-helix	184-186	3
β-strand	190-200	11	4
β-strand	208-217	10	2
β-strand	222-223	2	6
β-strand	226	1	5

Chain D: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	51-54	4
β-strand	57	1	7

Chain G: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	7-14	8	19
β-strand	24-30	7	19
β-strand	33-39	7	19
α-helix	69-76	8
α-helix	79-81	3
β-strand	89-97	9	19
β-strand	105-112	8	19
β-strand	116-121	6	19
β-strand	126-129	4	19
α-helix	132-142	11
α-helix	147-153	7
α-helix	154-158	5
α-helix	159-168	10

Chain H: 0 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	20
β-strand	6	1	21
β-strand	28	1	21
β-strand	30	1	22
β-strand	31	1	20
β-strand	55-56	2	22
β-strand	62-63	2	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
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)
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)
IgG receptor FcRn large subunit p51	G	protein	267	Homo sapiens	P55899 (AlphaFold model)
Beta-2-microglobulin	H	protein	99	Homo sapiens	P61769 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>7B5F_1 Echovirus 18 viral protein 3 (chains C)
GVPVLNTPGSNQFLTSDDYQSPSAMPQFDETPEMHIPGEVRNLMEIAEVDSVVPVNNVTG
KTKSMDAYQIPVGTGNTDKTKPIFSFQMDPGYSSVLKRTLLGEMLNYYAHWSGSVKLTFL
FCGSAMATGKLLISYSPPGASVPTSRKDAMLGTHIVWDIGLQSSCVLCVPWISQSHYRMV
QQDPYTSAGYITCWYQTNIVVPPGAPTSCDVLCFASACNDFSVRLLRDTPFMAQPGKLQ

Sequence of entity 2 (D), FASTA

>7B5F_2 Echovirus 18 viral protein 4 (chains D)
MGAQVSTQKTGAHETSLSAKGNSIIHYTNINFYKDAASSASNRQDIQQDPGKFTDPVKDL
MIKTLPALN

Sequence of entity 3 (A), FASTA

>7B5F_3 Echovirus 18 viral protein 1 (chains A)
GDNQDRTVANTQPSGPSNSTEIPALTAVETGHTSQVDPSDTIQTRHVVNFHSRSESTIEN
FMGRAACVFMDQYKINGEETSTDRFAVWTINIREMAQLRRKCEMFTYMRFDIEMTMVITS
CQDQGTILDQDMPVLTHQIMYVPPGGPIPAKVDGYEWQTSTNPSVFWTEGNAPPRISIPF
ISVGNAYSSFYDGWSHFTQDGTYGYTTLNAMGKLYIRHVNRSSPHQITSTIRVYFKPKHI
KAWVPRPPRLCPYINKRDVNFVVTEITDSRTSITDTPHPEHSVLATH

Sequence of entity 4 (B), FASTA

>7B5F_4 Echovirus 18 viral protein 2 (chains B)
SPSAEECGYSDRVRSMTLGNSTITTQESANVVVGYGEWPSYLSDREATAEDQPTQPDVAT
CRFYTLESVQWEKTSPGWWWKFPEALKNMGLFGQNMHYHYLGRAGYTIHVQCNASKFHQG
CLLVVCVPEAEMGCADTDTTFPATELTTEDTPHVFTSDSITGKKVQAAVCNAGMGVGVGN
LTIFPHQWINLRTNNSATIVIPYINSVPMDNMFRHYNFTLMIIPFAPLNFTDGATAYVPI
TVTIAPMYAEYNGLRLASTQ

Sequence of entity 5 (G), FASTA

>7B5F_5 IgG receptor FcRn large subunit p51 (chains G)
AESHLSLLYHLTAVSSPAPGTPAFWVSGWLGPQQYLSYNSLRGEAEPCGAWVWENQVSWY
WEKETTDLRIKEKLFLEAFKALGGKGPYTLQGLLGCELGPDNTSVPTAKFALNGEEFMNF
DLKQGTWGGDWPEALAISQRWQQQDKAANKELTFLLFSCPHRLREHLERGRGNLEWKEPP
SMRLKARPSSPGFSVLTCSAFSFYPPELQLRFLRNGLAAGTGQGDFGPNSDGSFHASSSL
TVKSGDEHHYCCIVQHAGLAQPLRVEL

Sequence of entity 6 (H), FASTA

>7B5F_6 Beta-2-microglobulin (chains H)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Ligands and cofactors

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

Primary citation

Structure of echovirus 18 in complex with neonatal Fc receptor. Buchta, D., Levdansky, Y., Fuzik, T. et al. To be published.

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

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