6LA5: Echovirus 11

Name: PDB 6LA5: Cryo-EM structure of echovirus 11 complexed with its attaching receptor CD55 at pH 7.4
Published: 2020-10-07
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Cryo-EM structure of echovirus 11 complexed with its attaching receptor CD55 at pH 7.4. Determined by electron microscopy at 2.86 Å resolution. Released 7 Oct 2020.

Method: Electron microscopy
Resolution: 2.86 Å
Organisms: Echovirus E11, Homo sapiens
Chains: 5
Atoms: 7,466
Mol. weight: 107.69 kDa
Ligands: SPH
Released: 7 Oct 2020

Explore 6LA5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6LA5 contains 30 α-helices and 79 β-strands across 5 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: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
α-helix	7-8	2
β-strand	13	1	2
α-helix	14-16	3
β-strand	17	1	3
β-strand	31-32	2	4
α-helix	34-36	3
α-helix	44-47	4
β-strand	53	1	3
β-strand	58	1	2
α-helix	64-68	5
β-strand	72-80	9	5
β-strand	90-94	5	6
α-helix	101-107	7
β-strand	110-127	18	5
α-helix	128-129	2
β-strand	141-147	7	6
α-helix	161-163	3
β-strand	169-173	5	6
α-helix	178-179	2
β-strand	180-183	4	5
β-strand	192-193	2	5
β-strand	198	1	7
β-strand	201	1	8
β-strand	205	1	8
α-helix	210-213	4
β-strand	218-223	6	6
β-strand	232-250	19	5
α-helix	252-253	2
β-strand	254	1	9
α-helix	257-258	2

Chain B: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	14-18	5	10
β-strand	21-25	5	10
β-strand	32-33	2	11
α-helix	52-53	2
β-strand	54	1	11
β-strand	64-70	7	11
β-strand	78-82	5	12
α-helix	92-98	7
β-strand	99-111	13	11
β-strand	121-128	8	12
β-strand	134	1	13
β-strand	148	1	14
β-strand	151	1	14
α-helix	152	1
β-strand	153-154	2	12
β-strand	156	1	15
β-strand	166	1	13
β-strand	169	1	15
α-helix	170-172	3
β-strand	177	1	9
α-helix	181-184	4
β-strand	187-191	5	12
β-strand	197-202	6	11
β-strand	211	1	11
β-strand	216	1	7
β-strand	219-227	9	12
β-strand	240-255	16	11
α-helix	258-259	2

Chain C: 7 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	23	1	5
α-helix	30-33	4
β-strand	39-40	2	5
β-strand	52	1	4
α-helix	65-68	4
β-strand	70-73	4	4
β-strand	81-86	6	16
α-helix	99-104	6
β-strand	107-111	5	17
β-strand	114-120	7	4
β-strand	127	1	18
β-strand	129-135	7	16
α-helix	140-142	3
α-helix	145-148	4
β-strand	152-157	6	16
α-helix	158	1
β-strand	163-168	6	4
β-strand	177-178	2	17
β-strand	189-194	6	16
β-strand	199	1	18
β-strand	207-216	10	4
β-strand	221-225	5	17

Chain D: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	26-29	4	1
α-helix	36-38	3
α-helix	50-52	3
β-strand	57	1	11

Chain E: 3 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	19
α-helix	7-9	3
β-strand	16-19	4	20
β-strand	25	1	19
β-strand	29-34	6	20
β-strand	38-41	4	21
β-strand	45-47	3	20
β-strand	48-51	4	22
β-strand	54-57	4	22
β-strand	63-66	4	21
α-helix	67	1
β-strand	69	1	23
α-helix	70-74	5
β-strand	78-80	3	24
β-strand	87	1	23
β-strand	92-94	3	25
β-strand	95-97	3	24
β-strand	102-104	3	26
β-strand	108-110	3	25
β-strand	112-114	3	27
β-strand	117-119	3	27
β-strand	126-128	3	26

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Capsid protein VP1	A	protein	285	Echovirus E11	Q2LJ73
Capsid protein VP2	B	protein	251	Echovirus E11	A0A0R5YS56
Capsid protein VP3	C	protein	238	Echovirus E11	A0A346I7K2
Capsid protein VP4	D	protein	69	Echovirus E11	E0WN77
Complement decay-accelerating factor	E	protein	125	Homo sapiens	P08174

Sequence of entity 1 (A), FASTA

>6LA5_1 Capsid protein VP1 (chains A)
VVEAVENAVARVADTISSGPSNSQAVPALTAVETGHTSQVTPSDTIQTRHVRNYHSRSES
SIENFLCRSACVYMGEYHTTNTDTSKLFASWTINARRMVQMRRKLELFTYVRFDMEVTFV
ITSKQDQGTQLGQDMPPLTHQIMYIPPGGPIPKSVTDYTWQTSTNPSIFWTEGNAPPRMS
IPFISIGNAYSNFYDGWSHFSQNGVYGYNTLNHMGQIYVRHVNGSSPLPMTSTVRMYFKP
KHVKVWVPRPPRLCQYKNASTVNFTPTNITEKRQSINYIPETVKP

Sequence of entity 2 (B), FASTA

>6LA5_2 Capsid protein VP2 (chains B)
DRVRSITLGNSTITTQESANVVVAYGRWPEYLKDNEATAEDQPTQPDVATCRFYTLESVT
WERDSPGWWWKFPDALKDMGLFGQNMYYHYLGRAGYTIHVQCNASKFHQGCLMVVCVPEA
EMGCSQVDGTVNEHSLSEGETAKKFASTSTNGTNTVQSIVTNAGMGVGVGNLTIFPHQWI
NLRTNNCATIVMPYINNVPMDNMFRHHNFTLMIIPFVPLDYSSDSSTYVPITVTVAPMCA
EYNGLRLATSL

Sequence of entity 3 (C), FASTA

>6LA5_3 Capsid protein VP3 (chains C)
GLPVMNTPGSNQFLTSDDFQSPSAMPQFDVTPELNIPGEVQNLMEIAEVDSVVPVNNVEG
KLDTMEIYRIPVQSGNHQSSQVFGFQVQPGLDNVFKHTLLGEILNYYAHWSGSIKLTFVF
CGSAMATGKFLLAYAPPGANAPKSRKDAMLGTHIIWDVGLQSSCVLCIPWISQTHYRLVQ
QDEYTSAGNVTCWYQTGIVVPAGTPTSCSIMCFVSACNDFSVRLLKDTPFIEQSALLQ

Sequence of entity 4 (D), FASTA

>6LA5_4 Capsid protein VP4 (chains D)
MGAQVSTQKTGAHETGLNASGRSIIHYTNINYYKDAASNSANRQDFSQDPGKFTEPVKDI
MVKSLPALN

Sequence of entity 5 (E), FASTA

>6LA5_5 Complement decay-accelerating factor (chains E)
KSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGSTSSFCLISGSSVQWSDPLPEC
REIYCPAPPQIDNGIIQGERDHYGYRQSVTYACNKGFTMIGEHSIYCTVNNDEGEWSGPP
PECRG

Ligands and cofactors

ID	Name	Formula	Copies
SPH	Sphingosine	C18 H37 N O2	1

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
6LBO 3.18 Å, Cryo-EM structure of echovirus 11 empty particle at pH 7.4

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