[English] 日本語
Yorodumi
- EMDB-15920: Complex of Echovirus 11 with its attaching receptor decay-acceler... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-15920
TitleComplex of Echovirus 11 with its attaching receptor decay-accelerating factor (CD55)
Map data
Sample
  • Complex: Complex of Echovirus 11 with its attaching receptor DECAY ACCELERATING FACTOR (CD55)
    • Protein or peptide: VP1
    • Protein or peptide: VP2
    • Protein or peptide: VP3
    • Protein or peptide: VP4
    • Protein or peptide: DECAY ACCELERATING FACTOR (CD55)
  • Ligand: SPHINGOSINE
Biological speciesEchovirus E11 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsStuart DI / Ren J / Zhou D / Qin L
Funding support United Kingdom, 1 items
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, 2022-
Header (metadata) releaseDec 7, 2022-
Map releaseDec 7, 2022-
UpdateJan 4, 2023-
Current statusJan 4, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_15920.png

Downloads & links

-
Map

FileDownload / File: emd_15920.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.20724827 - 0.35750955
Average (Standard dev.)0.0028601286 (±0.025445044)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Half map: #1

Fileemd_15920_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_15920_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex of Echovirus 11 with its attaching receptor DECAY ACCELER...

EntireName: Complex of Echovirus 11 with its attaching receptor DECAY ACCELERATING FACTOR (CD55)
Components
  • Complex: Complex of Echovirus 11 with its attaching receptor DECAY ACCELERATING FACTOR (CD55)
    • Protein or peptide: VP1
    • Protein or peptide: VP2
    • Protein or peptide: VP3
    • Protein or peptide: VP4
    • Protein or peptide: DECAY ACCELERATING FACTOR (CD55)
  • Ligand: SPHINGOSINE

-
Supramolecule #1: Complex of Echovirus 11 with its attaching receptor DECAY ACCELER...

SupramoleculeName: Complex of Echovirus 11 with its attaching receptor DECAY ACCELERATING FACTOR (CD55)
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Echovirus E11

-
Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E11
Molecular weightTheoretical: 32.838828 KDa
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 DVTTH

-
Macromolecule #2: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E11
Molecular weightTheoretical: 28.886428 KDa
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

-
Macromolecule #3: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E11
Molecular weightTheoretical: 26.029674 KDa
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

-
Macromolecule #4: VP4

MacromoleculeName: VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E11
Molecular weightTheoretical: 7.498273 KDa
SequenceString:
MGAQVSTQKT GAHETGLNAS GNSIIHYTNI NYYKDAASNS ANRQDFTQDP GKFTEPVKDI MIKSMPALN

-
Macromolecule #5: DECAY ACCELERATING FACTOR (CD55)

MacromoleculeName: DECAY ACCELERATING FACTOR (CD55) / type: protein_or_peptide / ID: 5 / 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

-
Macromolecule #6: SPHINGOSINE

MacromoleculeName: SPHINGOSINE / type: ligand / ID: 6 / Number of copies: 1 / Formula: SPH
Molecular weightTheoretical: 299.492 Da
Chemical component information

ChemComp-SPH:
SPHINGOSINE / Sphingosine

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy

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

-
Image processing

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

1h8t

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 6394

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more