[English] 日本語
Yorodumi
- EMDB-1412: Interaction of decay-accelerating factor with coxsackievirus B3. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1412
TitleInteraction of decay-accelerating factor with coxsackievirus B3.
Map dataSurface rendered cvb3 complexed with DAF. Calculated map was used to scaled complexmap to 2.92 for fitting of DAF into the cryoEM density.
Sample
  • Sample: coxsackievirus B3, RD strain, complexed with decay-accelerating factor
  • Virus: coxsackievirus B3 passaged through rhabdomysarcoma cells rhabdomyosarcoma cells
  • Protein or peptide: decay-accelerating factor
Function / homology
Function and homology information


negative regulation of complement activation / regulation of lipopolysaccharide-mediated signaling pathway / regulation of complement-dependent cytotoxicity / regulation of complement activation / 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) / ficolin-1-rich granule membrane / side of membrane ...negative regulation of complement activation / regulation of lipopolysaccharide-mediated signaling pathway / regulation of complement-dependent cytotoxicity / regulation of complement activation / 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) / ficolin-1-rich granule membrane / side of membrane / COPI-mediated anterograde transport / complement activation, classical pathway / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / secretory granule membrane / Regulation of Complement cascade / positive regulation of T cell cytokine production / virus receptor activity / positive regulation of cytosolic calcium ion concentration / membrane raft / Golgi membrane / innate immune response / lipid binding / Neutrophil degranulation / cell surface / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/SCR/CCP superfamily / Sushi/CCP/SCR domain profile.
Similarity search - Domain/homology
Complement decay-accelerating factor
Similarity search - Component
Biological speciesHomo sapiens (human) / coxsackievirus B3 passaged through rhabdomysarcoma cells rhabdomyosarcoma cells
Methodsingle particle reconstruction / cryo EM / Resolution: 14.0 Å
AuthorsHafenstein S
CitationJournal: J Virol / Year: 2007
Title: Interaction of decay-accelerating factor with coxsackievirus B3.
Authors: Susan Hafenstein / Valorie D Bowman / Paul R Chipman / Carol M Bator Kelly / Feng Lin / M Edward Medof / Michael G Rossmann /
Abstract: Many entero-, parecho-, and rhinoviruses use immunoglobulin (Ig)-like receptors that bind into the viral canyon and are required to initiate viral uncoating during infection. However, some of these ...Many entero-, parecho-, and rhinoviruses use immunoglobulin (Ig)-like receptors that bind into the viral canyon and are required to initiate viral uncoating during infection. However, some of these viruses use an alternative or additional receptor that binds outside the canyon. Both the coxsackievirus-adenovirus receptor (CAR), an Ig-like molecule that binds into the viral canyon, and decay-accelerating factor (DAF) have been identified as cellular receptors for coxsackievirus B3 (CVB3). A cryoelectron microscopy reconstruction of a variant of CVB3 complexed with DAF shows full occupancy of the DAF receptor in each of 60 binding sites. The DAF molecule bridges the canyon, blocking the CAR binding site and causing the two receptors to compete with one another. The binding site of DAF on CVB3 differs from the binding site of DAF on the surface of echoviruses, suggesting independent evolutionary processes.
History
DepositionAug 17, 2007-
Header (metadata) releaseAug 20, 2007-
Map releaseAug 20, 2007-
UpdateAug 31, 2011-
Current statusAug 31, 2011Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2qzd
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2qzf
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2qzh
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1412.gif

Downloads & links

-
Map

FileDownload / File: emd_1412.map.gz / Format: CCP4 / Size: 22.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSurface rendered cvb3 complexed with DAF. Calculated map was used to scaled complexmap to 2.92 for fitting of DAF into the cryoEM density.
Voxel sizeX=Y=Z: 2.92 Å
Density
Contour Level1: 0.762
Minimum - Maximum-1.412 - 1.9499
Average (Standard dev.)-0.243779 (±0.366685)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-90-90-90
Dimensions181181181
Spacing181181181
CellA=B=C: 528.52 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.922.922.92
M x/y/z181181181
origin x/y/z0.0000.0000.000
length x/y/z528.520528.520528.520
α/β/γ90.00090.00090.000
start NX/NY/NZ-90-90-90
NX/NY/NZ181181181
MAP C/R/S213
start NC/NR/NS-90-90-90
NC/NR/NS181181181
D min/max/mean-1.4121.950-0.244

-
Supplemental data

-
Sample components

-
Entire : coxsackievirus B3, RD strain, complexed with decay-accelerating factor

EntireName: coxsackievirus B3, RD strain, complexed with decay-accelerating factor
Components
  • Sample: coxsackievirus B3, RD strain, complexed with decay-accelerating factor
  • Virus: coxsackievirus B3 passaged through rhabdomysarcoma cells rhabdomyosarcoma cells
  • Protein or peptide: decay-accelerating factor

-
Supramolecule #1000: coxsackievirus B3, RD strain, complexed with decay-accelerating factor

SupramoleculeName: coxsackievirus B3, RD strain, complexed with decay-accelerating factor
type: sample / ID: 1000
Oligomeric state: one DAF binds each binding site, one per each protomer
Number unique components: 2
Molecular weightExperimental: 7.0 MDa / Theoretical: 7.0 MDa

-
Supramolecule #1: coxsackievirus B3 passaged through rhabdomysarcoma cells rhabdomy...

SupramoleculeName: coxsackievirus B3 passaged through rhabdomysarcoma cells rhabdomyosarcoma cells
type: virus / ID: 1 / Name.synonym: CVB3-RD
Details: virus are saturated with one DAF bound at each possible site
Sci species name: coxsackievirus B3 passaged through rhabdomysarcoma cells rhabdomyosarcoma cells
Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No / Syn species name: CVB3-RD
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Molecular weightExperimental: 7.0 MDa / Theoretical: 7.0 MDa
Virus shellShell ID: 1 / Name: VP1 / Diameter: 300 Å / T number (triangulation number): 1
Virus shellShell ID: 2 / Name: VP2 / Diameter: 300 Å / T number (triangulation number): 1
Virus shellShell ID: 3 / Name: VP3 / Diameter: 300 Å / T number (triangulation number): 1

-
Macromolecule #1: decay-accelerating factor

MacromoleculeName: decay-accelerating factor / type: protein_or_peptide / ID: 1 / Name.synonym: DAF
Details: each molecule of DAF 70kD; DAF has His6 tag at c-terminus
Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightExperimental: 1.0 MDa / Theoretical: 1.0 MDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2 mg/mL
BufferpH: 6 / Details: 50mM MES
GridDetails: quantifoils
VitrificationCryogen name: ETHANE / Chamber temperature: 120 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: plunger / Method: blot before plunging

-
Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
Electron beamAcceleration voltage: 300 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsCalibrated magnification: 47000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 4.6 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 45000
Sample stageSpecimen holder: side mounted nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureMin: 83 K / Max: 83 K / Average: 93 K
Alignment procedureLegacy - Astigmatism: lens astigmatism was corrected at 98,000 times mag
DateAug 6, 2004
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 44 / Average electron dose: 24 e/Å2 / Details: scanned at 7 microns and bin averaged to 14 / Od range: 1 / Bits/pixel: 8
Tilt angle min0

-
Image processing

CTF correctionDetails: robEM
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMPFT, EM3DR / Number images used: 2269
DetailsVirion were incubated with DAF at ratio of 4 DAF molecules per every potential binding site.

+
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