6LBO: Echovirus 11 empty particle at pH 7.4

Name: PDB 6LBO: Cryo-EM structure of echovirus 11 empty particle at pH 7.4
Published: 2020-10-07
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Cryo-EM structure of echovirus 11 empty particle at pH 7.4. Determined by electron microscopy at 3.18 Å resolution. Released 7 Oct 2020.

Method: Electron microscopy
Resolution: 3.18 Å
Organism: Echovirus E11
Chains: 3
Atoms: 5,405
Mol. weight: 78.71 kDa
Released: 7 Oct 2020

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

Secondary structure: helices and β-sheets

6LBO contains 20 α-helices and 51 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: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	63	1	1
α-helix	64-68	5
β-strand	72-80	9	2
β-strand	91-94	4	3
α-helix	101-107	7
β-strand	110-127	18	2
α-helix	138-140	3
β-strand	141-147	7	3
α-helix	160-163	4
β-strand	169-173	5	3
α-helix	177-179	3
β-strand	180-183	4	2
β-strand	192-193	2	2
β-strand	198	1	4
β-strand	199	1	5
β-strand	208	1	5
α-helix	212-214	3
β-strand	218-223	6	3
α-helix	229-231	3
β-strand	232-250	19	2
α-helix	252-254	3
α-helix	257-258	2
α-helix	282-284	3

Chain B: 3 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	14-18	5	6
β-strand	21-25	5	6
β-strand	31-33	3	7
β-strand	53-54	2	7
β-strand	64-65	2	7
β-strand	69-71	3	7
β-strand	78-82	5	8
α-helix	90-98	9
β-strand	102-112	11	7
β-strand	119-128	10	8
β-strand	134	1	9
β-strand	148	1	10
β-strand	151	1	10
α-helix	152	1
β-strand	153-154	2	8
β-strand	156	1	11
β-strand	166	1	9
β-strand	169	1	11
α-helix	179-184	6
β-strand	187-191	5	8
β-strand	197-202	6	7
β-strand	211	1	7
β-strand	216	1	4
β-strand	219-230	12	8
β-strand	239-253	15	7

Chain C: 7 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	23	1	2
α-helix	29-34	6
β-strand	39-40	2	2
β-strand	42	1	1
α-helix	44-47	4
β-strand	51-52	2	12
α-helix	65-68	4
β-strand	70-72	3	12
β-strand	81-86	6	13
α-helix	99-104	6
β-strand	107-111	5	14
β-strand	112-120	9	12
β-strand	127	1	15
β-strand	129-135	7	13
α-helix	140-142	3
α-helix	145-149	5
β-strand	152-157	6	13
β-strand	163-171	9	12
β-strand	189-194	6	13
β-strand	199	1	15
β-strand	208-216	9	12
β-strand	221-225	5	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Capsid protein VP1	A	protein	226	Echovirus E11	Q2LJ73
Capsid protein VP2	B	protein	245	Echovirus E11	A0A0R5YS56
Capsid protein VP3	C	protein	231	Echovirus E11	A8ILJ7

Sequence of entity 1 (A), FASTA

>6LBO_1 Capsid protein VP1 (chains A)
SESSIENFLCRSACVYMGEYHTTNTDTSKLFASWTINARRMVQMRRKLELFTYVRFDMEV
TFVITSKQDQGTQLGQDMPPLTHQIMYIPPGGPIPKSVTDYTWQTSTNPSIFWTEGNAPP
RMSIPFISIGNAYSNFYDGWSHFSQNGVYGYNTLNHMGQIYVRHVNGSSPLPMTSTVRMY
FKPKHVKVWVPRPPRLCQYKNASTVNFTPTNITEKRQSINYIPETV

Sequence of entity 2 (B), FASTA

>6LBO_2 Capsid protein VP2 (chains B)
RVRSITLGNSTITTQESANVVVAYGRWPEYLKDNEATAEDQPTQPDVATCRFYTLESVTW
ERDSPGWWWKFPDALKDMGLFGQNMYYHYLGRAGYTIHVQCNASKFHQGCLMVVCVPEAE
MGCSQVDGTVNEHSLSEGETAKKFASTSTNGTNTVQSIVTNAGMGVGVGNLTIFPHQWIN
LRTNNCATIVMPYINNVPMDNMFRHHNFTLMIIPFVPLDYSSDSSTYVPITVTVAPMCAE
YNGLR

Sequence of entity 3 (C), FASTA

>6LBO_3 Capsid protein VP3 (chains C)
GLPVMNTPGSNQFLTSDDFQSPSAMPQFDVTPELNIPGEVQNLMEIAEVDSVVPVNNVEG
KLDTMEIYRIPVQSGNHQSSQVFGFQVQPGLDNVFKHTLLGEILNYYAHWSGSIKLTFVF
CGSAMATGKFLLAYAPPGANAPKSRKDAMLGTHIIWDVGLQSSCVLCIPWISQTHYRLVQ
QDEYTSAGNVTCWYQTGIVVPAGTPTSCSIMCFVSACNDFSVRLLKDTPFI

Primary citation

Molecular and structural basis of Echovirus 11 infection by using the dual-receptor system of CD55 and FcRn. Niu, S., Liu, C., Liu, C. et al. Chin Sci Bull (2020). DOI 10.1360/TB-2019-0786

Other PDB entries of the same protein (UniProt Q2LJ73), best resolution first:

6LA3 2.32 Å, Cryo-EM structure of full echovirus 11 particle at pH 7.4
6LA4 2.34 Å, Cryo-EM structure of full echovirus 11 particle at pH 5.5
6LA6 2.39 Å, Cryo-EM structure of echovirus 11 complexed with its uncoating receptor FcRn at pH 7.4
6LAP 2.49 Å, Cryo-EM structure of echovirus 11 A-particle at pH 7.4
6LB1 2.58 Å, Cryo-EM structure of echovirus 11 A-particle at pH 5.5
6LBQ 2.6 Å, Cryo-EM structure of echovirus 11 empty particle at pH 5.5
6LAO 2.64 Å, Cryo-EM structure of echovirus 11 complexed with its attaching receptor CD55 at pH 5.5
6LA7 2.82 Å, Cryo-EM structure of echovirus 11 complexed with its uncoating receptor FcRn at pH 5.5
6LA5 2.86 Å, Cryo-EM structure of echovirus 11 complexed with its attaching receptor CD55 at pH 7.4

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