8B8R: VP1

Name: PDB 8B8R: Complex of Echovirus 11 with its attaching receptor decay-accelerating factor (CD55)
Published: 2022-12-07
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Complex of Echovirus 11 with its attaching receptor decay-accelerating factor (CD55). Determined by electron microscopy at 3.1 Å resolution. Released 7 Dec 2022.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: Echovirus E11, Homo sapiens
Chains: 5
Atoms: 8,482
Mol. weight: 125.32 kDa
Ligands: SPH
Released: 7 Dec 2022

Explore 8B8R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8B8R contains 47 α-helices and 98 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: 15 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
β-strand	13	1	2
α-helix	14-16	3
β-strand	17	1	3
α-helix	18-19	2
β-strand	20	1	4
β-strand	31-32	2	5
α-helix	34-36	3
α-helix	44-47	4
β-strand	50	1	4
β-strand	53	1	3
β-strand	58	1	2
α-helix	60-62	3
β-strand	63	1	6
α-helix	64-68	5
β-strand	72-80	9	7
β-strand	90-94	5	8
α-helix	101-107	7
β-strand	110-127	18	7
α-helix	128-129	2
α-helix	137-140	4
β-strand	141-147	7	8
α-helix	152-154	3
α-helix	160-163	4
β-strand	169-173	5	8
α-helix	177-179	3
β-strand	180-183	4	7
β-strand	192-193	2	7
β-strand	198	1	9
β-strand	199	1	10
β-strand	208	1	10
α-helix	210-213	4
β-strand	218-223	6	8
β-strand	232-250	19	7
α-helix	252-254	3
α-helix	257-258	2

Chain B: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	14-18	5	11
β-strand	21-25	5	11
β-strand	28	1	12
β-strand	31-33	3	12
α-helix	52-53	2
β-strand	54	1	12
β-strand	64-65	2	12
α-helix	66-68	3
β-strand	69-71	3	13
β-strand	78-81	4	14
α-helix	90-98	9
β-strand	99-111	13	12
β-strand	119-128	10	14
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
α-helix	155	1
β-strand	156	1	17
β-strand	166	1	15
β-strand	169	1	17
α-helix	170-172	3
α-helix	179-184	6
β-strand	187-191	5	14
β-strand	197-202	6	12
β-strand	211	1	12
β-strand	216	1	9
β-strand	219-230	12	14
β-strand	239-241	3	13
β-strand	242-255	14	12
α-helix	258-259	2

Chain C: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	23	1	7
α-helix	30-33	4
β-strand	39-40	2	7
β-strand	42	1	6
α-helix	43-47	5
β-strand	51-52	2	5
α-helix	65-67	3
α-helix	69	1
β-strand	70-73	4	5
β-strand	81-86	6	18
α-helix	99-104	6
β-strand	107-111	5	19
β-strand	114-120	7	5
β-strand	127-135	9	18
α-helix	140-142	3
α-helix	145-148	4
β-strand	152-157	6	18
β-strand	163-168	6	5
β-strand	177-178	2	19
β-strand	189-199	11	18
β-strand	207-216	10	5
β-strand	221-225	5	19

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	57-58	2	12

Chain E: 13 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	36	1	20
α-helix	39-41	3
β-strand	45-47	3	21
β-strand	55	1	20
β-strand	60-62	3	22
β-strand	63-65	3	21
β-strand	70-71	2	23
β-strand	78-80	3	22
β-strand	81-82	2	24
β-strand	86-87	2	24
α-helix	88-89	2
β-strand	94-95	2	23
α-helix	98-99	2
α-helix	101-103	3
β-strand	107-109	3	25
α-helix	110	1
α-helix	113-115	3
β-strand	124-126	3	26
β-strand	127-129	3	25
α-helix	130	1
β-strand	133-135	3	27
β-strand	142-144	3	26
β-strand	145	1	28
β-strand	151	1	28
α-helix	152-154	3
β-strand	158-160	3	27
α-helix	161	1
β-strand	162	1	29
α-helix	163-165	3
β-strand	172-175	4	30
β-strand	181	1	29
β-strand	185-190	6	30
β-strand	194-197	4	31
β-strand	201-203	3	30
β-strand	204-207	4	32
β-strand	210-213	4	32
β-strand	219-222	4	31
α-helix	225-230	6
β-strand	234-236	3	33
β-strand	248-250	3	34
β-strand	251-253	3	33
α-helix	254	1
β-strand	258-260	3	35
β-strand	264-266	3	34
β-strand	267-270	4	36
β-strand	273-276	4	36
α-helix	279-281	3
β-strand	282-284	3	35

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
VP1	A	protein	292	Echovirus E11	A0A6M5CIM5
VP2	B	protein	262	Echovirus E11	A0A6M5CFG5
VP3	C	protein	238	Echovirus E11	A0A2H4WPJ3
VP4	D	protein	69	Echovirus E11	A0A2Z5X9H0
Decay accelerating factor (CD55)	E	protein	268	Homo sapiens	P08174

Sequence of entity 1 (A), FASTA

>8B8R_1 VP1 (chains A)
GDVVEAIEGAVARVADTISSGPTNSQAVPALTAVETGHTSQVVPGDTMQTRHVKNYHSRS
ESTIENFLSRSACVYMGEYYTTNTDETKRFASWTINARRMVQMRRKLEMFTYVRFDVEVT
FVITSKQDQGTQLGQDMPPLTHQIMYIPPGGPIPKSTTDYAWQTSTNPSIFWTEGNAPPR
MSIPFVSIGNAYSNFYDGWSHFSQNGVYGYNTLNNMGQLYMRHVNGPSPLPMTSIVRVYF
KPKHVKAWVPRPPRLCQYKNASTVNFSSTNITDKRDSITHVPDTVKPDVTTH

Sequence of entity 2 (B), FASTA

>8B8R_2 VP2 (chains B)
SPSAEECGYSDRVRSITLGNSTITTQECANVVVAYGRWPEYLSDKEATAEDQPTQPDVAT
CRFYTLESVTWEKDSPGWWWKFPDALKDMGLFGQNMYYHYLGRAGYTIHVQCNASKFHQG
CLLVVCVPEAEMGCSDVGGTVNEHAISEGEIAKKFSATATNGAHTVQSIVTNAGMGVGVG
NLTIYPHQWVNLRTNNSATIVMPYINSVPMDNMFRHHNFTLMIIPFVSLDYSSDASTYVP
ITVTVAPMCAEYNGLRLATSLQ

Sequence of entity 3 (C), FASTA

>8B8R_3 VP3 (chains C)
GLPVMNTPGSNQFLTSDDFQSPSAMPQFDVTPELDIPGEVKNLMEIAEVDSVVPVNNVVG
KLDTMDIFRIPVQSGNHQSTQVFGFQVQPGLDSVFKHTLLGEILNYYAHWSGSVKLTFVF
CGSAMATGKFLLAYSPPGANAPKTRKDAMLGTHVIWDVGLQSSCVLCIPWISQTHYRLVH
QDEYTSAGNVTCWYQTGIVVPAGTPTLCSIMCFVSACNDFSVRLLKDTPFIEQSALLQ

Sequence of entity 4 (D), FASTA

>8B8R_4 VP4 (chains D)
MGAQVSTQKTGAHETGLNASGNSIIHYTNINYYKDAASNSANRQDFTQDPGKFTEPVKDI
MIKSMPALN

Sequence of entity 5 (E), FASTA

>8B8R_5 DECAY ACCELERATING FACTOR (CD55) (chains E)
MGCVAETGDCGLPPDVPNAQPALEGRTSFPEDTVITYKCEESFVKIPGEKDSVICLKGSQ
WSDIEEFCNRSCEVPTRLNSASLKQPYITQNYFPVGTVVEYECRPGYRREPSLSPKLTCL
QNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGSTSSFCLI
SGSSVQWSDPLPECREIYCPAPPQIDNGIIQGERDHYGYRQSVTYACNKGFTMIGEHSIY
CTVNNDEGEWSGPPPECRGGTKHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
SPH	Sphingosine	C18 H37 N O2	1

Primary citation

Switching of Receptor Binding Poses between Closely Related Enteroviruses. Zhou, D., Qin, L., Duyvesteyn, H.M.E. et al. Viruses (2022) 14. DOI 10.3390/v14122625 · PubMed

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