6ILK: Echovirus 6

Name: PDB 6ILK: Cryo-EM structure of Echovirus 6 complexed with its attachment receptor CD55 at PH 7.4
Published: 2019-05-15
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Cryo-EM structure of Echovirus 6 complexed with its attachment receptor CD55 at PH 7.4. Determined by electron microscopy at 3.0 Å resolution. Released 15 May 2019.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Echovirus E6, Homo sapiens
Chains: 5
Atoms: 8,025
Mol. weight: 115.1 kDa
Ligands: SPH
Released: 15 May 2019

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

Secondary structure: helices and β-sheets

6ILK contains 35 α-helices and 93 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: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	13	1	1
α-helix	14-16	3
β-strand	17	1	2
α-helix	18-19	2
β-strand	32	1	3
α-helix	34-36	3
β-strand	53	1	2
β-strand	58	1	1
β-strand	63	1	4
α-helix	64-68	5
β-strand	75-80	6	5
β-strand	90-94	5	6
α-helix	101-107	7
β-strand	110-127	18	5
β-strand	141-147	7	6
α-helix	160-162	3
β-strand	169-173	5	6
α-helix	177-179	3
β-strand	180-183	4	5
β-strand	192-193	2	5
β-strand	198	1	7
β-strand	199	1	8
β-strand	208	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
β-strand	275	1	10

Chain B: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	14-18	5	11
β-strand	21-25	5	11
β-strand	32	1	12
α-helix	37-39	3
α-helix	41-43	3
α-helix	52-53	2
β-strand	54	1	13
β-strand	64-65	2	13
β-strand	69-70	2	13
β-strand	78-81	4	14
α-helix	82-85	4
α-helix	90-98	9
β-strand	99-112	14	13
β-strand	119-128	10	14
α-helix	132-133	2
β-strand	134	1	15
α-helix	143-146	4
β-strand	148	1	16
β-strand	151	1	16
α-helix	152	1
β-strand	153-154	2	14
β-strand	166	1	15
β-strand	177	1	9
α-helix	179-184	6
β-strand	187-191	5	14
β-strand	198-202	5	13
β-strand	211	1	13
β-strand	216	1	7
β-strand	219-230	12	14
β-strand	233	1	17
β-strand	235	1	17
β-strand	240-255	16	13

Chain C: 7 helices, 20 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	42	1	4
α-helix	44-47	4
β-strand	51-52	2	3
β-strand	58	1	10
α-helix	61-63	3
α-helix	65-68	4
β-strand	70-72	3	3
β-strand	83-86	4	18
α-helix	99-104	6
β-strand	109-111	3	19
β-strand	114-121	8	3
β-strand	127	1	20
β-strand	129-135	7	18
β-strand	137	1	21
β-strand	139	1	21
α-helix	145-148	4
β-strand	152-157	6	18
β-strand	163-168	6	3
β-strand	177-178	2	19
β-strand	189-194	6	18
β-strand	199	1	20
β-strand	208-216	9	3
β-strand	221-222	2	19

Chain D: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	22
α-helix	7-8	2
β-strand	25-28	4	22
α-helix	35-37	3
α-helix	39-40	2
β-strand	56	1	12

Chain E: 6 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	69-70	2
β-strand	75-77	3	23
β-strand	92-94	3	24
β-strand	95-97	3	23
β-strand	101-103	3	25
β-strand	110-112	3	24
β-strand	113	1	26
β-strand	119	1	26
α-helix	120-121	2
β-strand	126-128	3	25
α-helix	129	1
β-strand	130	1	27
α-helix	131-133	3
β-strand	140-143	4	28
β-strand	149	1	27
β-strand	153-158	6	28
β-strand	162-165	4	29
β-strand	169-171	3	28
β-strand	172-175	4	30
β-strand	178-181	4	30
β-strand	187-190	4	29
α-helix	191	1
β-strand	193	1	31
α-helix	195-199	5
β-strand	204	1	32
β-strand	211	1	31
β-strand	216-218	3	33
β-strand	219	1	32
β-strand	227-228	2	34
β-strand	232-234	3	33
β-strand	235-238	4	35
β-strand	241-244	4	35
β-strand	250-251	2	34

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Capsid protein VP1	A	protein	278	Echovirus E6
Capsid protein VP2	B	protein	252	Echovirus E6
Capsid protein VP3	C	protein	238	Echovirus E6
Capsid protein VP4	D	protein	68	Echovirus E6
Complement decay-accelerating factor	E	protein	192	Homo sapiens	P08174 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6ILK_1 Capsid protein VP1 (chains A)
VVRVADTMPSGPSNSESIPALTAAETGHTSQVVPSDTIQTRHVRNFHVRSESSVENFLSR
SACVYIVEYKTRDDTPDKMYDSWVINTRQVAQLRRKLEFFTYVRFDVEVTFVITSVQDDS
TRQNTDTPALTHQIMYVPPGGPIPQAVDDYNWQTSTNPSVFWTEGNAPPRMSIPFMSVGN
AYSNFYDGWSHFSQTGVYGFNTLNNMGKLYFRHVNDKTISPITSKVRIYFKPKHVKAWVP
RPPRLCEYTHKDNVDFEPKGVTTSRTQLTISNSTHVEN

Sequence of entity 2 (B), FASTA

>6ILK_2 Capsid protein VP2 (chains B)
SDRVRSITLGNSTITTQESANVVVGYGVWPDYLSDEEATAEDQPTQPDVATCRFYTLDSV
SWMKESQGWWWKFPDALRDMGLFGQNMQYHYLGRSGYTIHVQCNASKFHQGCLLVVCVPE
AEMGAANINEKINREHLSNGEVANTFSGTKSSNTNDVQQAVFNAGMGVAVGNLTIFPHQW
INLRTNNCATIVMPYINSVPMDNMFRHYNFTLMIIPFAKLDYAAGSSTYIPITVTVAPMC
AEYNGLRLAGHQ

Sequence of entity 3 (C), FASTA

>6ILK_3 Capsid protein VP3 (chains C)
GLPVMNTPGSNQFLTSDDYQSPTAMPQFDVTPEMNIPGEVKNLMEIAEVDSVVPVNNVNE
NVNSLEAYRIPVHSVTETGAQVFGFTLQPGADTVMERTLLGEILNYYANWSGSIKLTFMY
CGSAMATGKFLLAYSPPGAGVPKNRREAMLGTHIIWDIGLQSSCVLCVPWISQTHYRFVS
KDIYTDAGFITCWYQTSIVVPAEVQNQSVILCFVSACNDFSVRLLRDSPFVRQTAFYQ

Sequence of entity 4 (D), FASTA

>6ILK_4 Capsid protein VP4 (chains D)
GAQVSTQKTGAHETSLSASGNSIIHYTNINYYKDAASNSANRQDFTQDPGKFTEPVKDIM
VKSLPALN

Sequence of entity 5 (E), FASTA

>6ILK_5 Complement decay-accelerating factor (chains E)
CNRSCEVPTRLNSASLKQPYITQNYFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWST
AVEFCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGSTSSFCLISGSSVQW
SDPLPECREIYCPAPPQIDNGIIQGERDHYGYRQSVTYACNKGFTMIGEHSIYCTVNNDE
GEWSGPPPECRG

Ligands and cofactors

ID	Name	Formula	Copies
SPH	Sphingosine	C18 H37 N O2	1

Primary citation

Human Neonatal Fc Receptor Is the Cellular Uncoating Receptor for Enterovirus B. Zhao, X., Zhang, G., Liu, S. et al. Cell (2019) 177:1553-1565.e16. DOI 10.1016/j.cell.2019.04.035 · PubMed

Other PDB entries of the same protein (UniProt P08174 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1H03 1.7 Å, Human CD55 domains 3 & 4
1H04 2.0 Å, Human CD55 domains 3 & 4
1OK3 2.2 Å, Decay accelerating factor (cd55): the structure of an intact human complement regulator.
1OJV 2.3 Å, Decay accelerating factor (CD55): the structure of an intact human complement regulator.
1OJW 2.3 Å, Decay accelerating factor (CD55): the structure of an intact human complement regulator.
1OK2 2.5 Å, Decay accelerating factor (CD55): the structure of an intact human complement regulator.
1OJY 2.6 Å, Decay accelerating factor (cd55): the structure of an intact human complement regulator.
1OK1 2.6 Å, Decay accelerating factor (cd55) : the structure of an intact human complement regulator.
8K9T 2.66 Å, Cryo-EM structure of the products-bound PGAP1(Bst1)-S327A from Chaetonium thermophilum
8K9R 2.68 Å, Cryo EM structure of the products-bound PGAP1(Bst1)-H443N from Chaetomium thermophilum
1H2P 2.8 Å, Human CD55 domains 3 & 4
6LA5 2.86 Å, Cryo-EM structure of echovirus 11 complexed with its attaching receptor CD55 at pH 7.4

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