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- EMDB-15930: Structure of Echovirus 11 complexed with DAF (CD55) calculated fr... -

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Basic information

Entry
Database: EMDB / ID: EMD-15930
TitleStructure of Echovirus 11 complexed with DAF (CD55) calculated from symmetry expansion
Map data
Sample
  • Complex: Complex of Echovirus 11 with DAF
    • Protein or peptide: Complement decay-accelerating factor
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
  • Ligand: SPHINGOSINE
Function / homology
Function and homology information


regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / negative regulation of complement activation, classical pathway / regulation of complement-dependent cytotoxicity / RNA-protein covalent cross-linking / regulation of complement activation / T cell mediated immunity / : / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation ...regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / negative regulation of complement activation, classical pathway / regulation of complement-dependent cytotoxicity / RNA-protein covalent cross-linking / regulation of complement activation / T cell mediated immunity / : / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / : / Class B/2 (Secretin family receptors) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ficolin-1-rich granule membrane / side of membrane / COPI-mediated anterograde transport / transport vesicle / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / endoplasmic reticulum-Golgi intermediate compartment membrane / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / secretory granule membrane / T=pseudo3 icosahedral viral capsid / complement activation, classical pathway / Regulation of Complement cascade / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / positive regulation of T cell cytokine production / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / virus receptor activity / symbiont-mediated suppression of host gene expression / positive regulation of cytosolic calcium ion concentration / DNA replication / RNA helicase activity / induction by virus of host autophagy / membrane raft / RNA-directed RNA polymerase / Golgi membrane / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / innate immune response / DNA-templated transcription / lipid binding / host cell nucleus / Neutrophil degranulation / virion attachment to host cell / structural molecule activity / cell surface / proteolysis / RNA binding / extracellular exosome / extracellular region / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Picornavirus coat protein VP4 superfamily / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain ...Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Picornavirus coat protein VP4 superfamily / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Complement decay-accelerating factor
Similarity search - Component
Biological speciesEchovirus E11 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.93 Å
AuthorsStuart DI / Ren J / Qin L / Zhou D
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) 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 5, 2022-
Header (metadata) releaseDec 7, 2022-
Map releaseDec 7, 2022-
UpdateJan 4, 2023-
Current statusJan 4, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15930.png

Downloads & links

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Map

FileDownload / File: emd_15930.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 400 pix.
= 420. Å		1.05 Å/pix.
x 400 pix.
= 420. Å		1.05 Å/pix.
x 400 pix.
= 420. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-4.773263 - 5.571968
Average (Standard dev.)0.001072152 (±0.070211746)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 419.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_15930_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_15930_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of Echovirus 11 with DAF

EntireName: Complex of Echovirus 11 with DAF
Components
  • Complex: Complex of Echovirus 11 with DAF
    • Protein or peptide: Complement decay-accelerating factor
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
  • Ligand: SPHINGOSINE

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Supramolecule #1: Complex of Echovirus 11 with DAF

SupramoleculeName: Complex of Echovirus 11 with DAF / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Echovirus E11

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Macromolecule #1: Complement decay-accelerating factor

MacromoleculeName: Complement decay-accelerating factor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.771059 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: (MSE)GCVAETGDC GLPPDVPNAQ PALEGRTSFP EDTVITYKCE ESFVKIPGEK DSVICLKGSQ WSDIEEFCNR SCEVPT RLN SASLKQPYIT QNYFPVGTVV EYECRPGYRR EPSLSPKLTC LQNLKWSTAV EFCKKKSCPN PGEIRNGQID VPGGILF GA TISFSCNTGY ...String:
(MSE)GCVAETGDC GLPPDVPNAQ PALEGRTSFP EDTVITYKCE ESFVKIPGEK DSVICLKGSQ WSDIEEFCNR SCEVPT RLN SASLKQPYIT QNYFPVGTVV EYECRPGYRR EPSLSPKLTC LQNLKWSTAV EFCKKKSCPN PGEIRNGQID VPGGILF GA TISFSCNTGY KLFGSTSSFC LISGSSVQWS DPLPECREIY CPAPPQIDNG IIQGERDHYG YRQSVTYACN KGFT (MSE)IGEH SIYCTVNNDE GEWSGPPPEC RGGTKHHHHH H

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Macromolecule #2: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Echovirus E11
Molecular weightTheoretical: 28.886428 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SPSAEECGYS DRVRSITLGN STITTQECAN VVVAYGRWPE YLSDKEATAE DQPTQPDVAT CRFYTLESVT WEKDSPGWWW KFPDALKDM GLFGQNMYYH YLGRAGYTIH VQCNASKFHQ GCLLVVCVPE AEMGCSDVGG TVNEHAISEG EIAKKFSATA T NGAHTVQS ...String:
SPSAEECGYS DRVRSITLGN STITTQECAN VVVAYGRWPE YLSDKEATAE DQPTQPDVAT CRFYTLESVT WEKDSPGWWW KFPDALKDM GLFGQNMYYH YLGRAGYTIH VQCNASKFHQ GCLLVVCVPE AEMGCSDVGG TVNEHAISEG EIAKKFSATA T NGAHTVQS IVTNAGMGVG VGNLTIYPHQ WVNLRTNNSA TIVMPYINSV PMDNMFRHHN FTLMIIPFVS LDYSSDASTY VP ITVTVAP MCAEYNGLRL ATSLQ

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Macromolecule #3: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Echovirus E11
Molecular weightTheoretical: 26.029674 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GLPVMNTPGS NQFLTSDDFQ SPSAMPQFDV TPELDIPGEV KNLMEIAEVD SVVPVNNVVG KLDTMDIFRI PVQSGNHQST QVFGFQVQP GLDSVFKHTL LGEILNYYAH WSGSVKLTFV FCGSAMATGK FLLAYSPPGA NAPKTRKDAM LGTHVIWDVG L QSSCVLCI ...String:
GLPVMNTPGS NQFLTSDDFQ SPSAMPQFDV TPELDIPGEV KNLMEIAEVD SVVPVNNVVG KLDTMDIFRI PVQSGNHQST QVFGFQVQP GLDSVFKHTL LGEILNYYAH WSGSVKLTFV FCGSAMATGK FLLAYSPPGA NAPKTRKDAM LGTHVIWDVG L QSSCVLCI PWISQTHYRL VHQDEYTSAG NVTCWYQTGI VVPAGTPTLC SIMCFVSACN DFSVRLLKDT PFIEQSALLQ

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Macromolecule #4: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Echovirus E11
Molecular weightTheoretical: 32.284262 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GDVVEAIEGA VARVADTISS GPTNSQAVPA LTAVETGHTS QVVPGDTMQT RHVKNYHSRS ESTIENFLSR SACVYMGEYY TTNTDETKR FASWTINARR MVQMRRKLEM FTYVRFDVEV TFVITSKQDQ GTQLGQDMPP LTHQIMYIPP GGPIPKSTTD Y AWQTSTNP ...String:
GDVVEAIEGA VARVADTISS GPTNSQAVPA LTAVETGHTS QVVPGDTMQT RHVKNYHSRS ESTIENFLSR SACVYMGEYY TTNTDETKR FASWTINARR MVQMRRKLEM FTYVRFDVEV TFVITSKQDQ GTQLGQDMPP LTHQIMYIPP GGPIPKSTTD Y AWQTSTNP SIFWTEGNAP PRMSIPFVSI GNAYSNFYDG WSHFSQNGVY GYNTLNNMGQ LYMRHVNGPS PLPMTSIVRV YF KPKHVKA WVPRPPRLCQ YKNASTVNFS STNITDKRDS ITHVPDTVKP

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Macromolecule #5: SPHINGOSINE

MacromoleculeName: SPHINGOSINE / type: ligand / ID: 5 / Number of copies: 1 / Formula: SPH
Molecular weightTheoretical: 299.492 Da
Chemical component information

ChemComp-SPH:
SPHINGOSINE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 41.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DARK FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1h8t

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.93 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 201358
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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