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- PDB-8b8r: Complex of Echovirus 11 with its attaching receptor decay-acceler... -

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Basic information

Entry
Database: PDB / ID: 8b8r
TitleComplex of Echovirus 11 with its attaching receptor decay-accelerating factor (CD55)
Components
  • DECAY ACCELERATING FACTOR (CD55)
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS / Echovirus / receptor / DAF / CD55
Function / homologySPHINGOSINE
Function and homology information
Biological speciesHomo sapiens (human)
Echovirus E11
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsStuart, D.I. / Ren, J. / Zhou, D. / Qin, L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)B5R00670-B500.01 United Kingdom
CitationJournal: Viruses / Year: 2022
Title: Switching of Receptor Binding Poses between Closely Related Enteroviruses.
Authors: Daming Zhou / Ling Qin / Helen M E Duyvesteyn / Yuguang Zhao / Tzou-Yien Lin / Elizabeth E Fry / Jingshan Ren / Kuan-Ying A Huang / David I Stuart /
Abstract: Echoviruses, for which there are currently no approved vaccines or drugs, are responsible for a range of human diseases, for example echovirus 11 (E11) is a major cause of serious neonatal morbidity ...Echoviruses, for which there are currently no approved vaccines or drugs, are responsible for a range of human diseases, for example echovirus 11 (E11) is a major cause of serious neonatal morbidity and mortality. Decay-accelerating factor (DAF, also known as CD55) is an attachment receptor for E11. Here, we report the structure of the complex of E11 and the full-length ectodomain of DAF (short consensus repeats, SCRs, 1-4) at 3.1 Å determined by cryo-electron microscopy (cryo-EM). SCRs 3 and 4 of DAF interact with E11 at the southern rim of the canyon via the VP2 EF and VP3 BC loops. We also observe an unexpected interaction between the N-linked glycan (residue 95 of DAF) and the VP2 BC loop of E11. DAF is a receptor for at least 20 enteroviruses and we classify its binding patterns from reported DAF/virus complexes into two distinct positions and orientations, named as E6 and E11 poses. Whilst 60 DAF molecules can attach to the virion in the E6 pose, no more than 30 can attach to E11 due to steric restrictions. Analysis of the distinct modes of interaction and structure and sequence-based phylogenies suggests that the two modes evolved independently, with the E6 mode likely found earlier.
History
DepositionOct 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VP1
B: VP2
C: VP3
D: VP4
E: DECAY ACCELERATING FACTOR (CD55)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,3246
Polymers125,0245
Non-polymers2991
Water0
1
A: VP1
B: VP2
C: VP3
D: VP4
E: DECAY ACCELERATING FACTOR (CD55)
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)7,519,425360
Polymers7,501,456300
Non-polymers17,97060
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

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Protein , 5 types, 5 molecules ABCDE

#1: Protein VP1


Mass: 32838.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E11
#2: Protein VP2


Mass: 28886.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E11
#3: Protein VP3


Mass: 26029.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E11
#4: Protein VP4


Mass: 7498.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E11
#5: Protein DECAY ACCELERATING FACTOR (CD55)


Mass: 29771.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)

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Non-polymers , 1 types, 1 molecules

#6: Chemical ChemComp-SPH / SPHINGOSINE / Sphingosine


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of Echovirus 11 with its attaching receptor DECAY ACCELERATING FACTOR (CD55)
Type: COMPLEX / Entity ID: #1-#5 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Echovirus E11
Buffer solutionpH: 7.4
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: DARK FIELD / Nominal defocus max: 1000 nm / Nominal defocus min: 3000 nm
Image recordingElectron dose: 41 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6394 / Symmetry type: POINT

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