[English] 日本語
Yorodumi
- EMDB-1057: The structure of echovirus type 12 bound to a two-domain fragment... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1057
TitleThe structure of echovirus type 12 bound to a two-domain fragment of its cellular attachment protein decay-accelerating factor (CD 55).
Map dataThree dimensional reconstruction of echovirus type 12 bound to domains three and four of its cellular receptor decay-accelerating factor. Calculated from cryo-negative stain images
Sample
  • Sample: Echovirus type 12 bound to decay accelerating factor domains 3 and 4
  • Virus: Human echovirus 12
  • Organelle or cellular component: Decay accelerating factor domains 3 and 4
Function / homology
Function and homology information


regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / 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) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ficolin-1-rich granule membrane ...regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / 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) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ficolin-1-rich granule membrane / complement activation, classical pathway / COPI-mediated anterograde transport / side of membrane / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / secretory granule membrane / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / Regulation of Complement cascade / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / RNA-protein covalent cross-linking / cytoplasmic vesicle membrane / host cell cytoplasmic vesicle membrane / positive regulation of T cell cytokine production / nucleoside-triphosphate phosphatase / channel activity / virus receptor activity / positive regulation of cytosolic calcium ion concentration / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / membrane raft / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / Golgi membrane / cysteine-type endopeptidase activity / viral RNA genome replication / innate immune response / RNA-directed RNA polymerase activity / : / DNA-templated transcription / lipid binding / Neutrophil degranulation / host cell nucleus / virion attachment to host cell / structural molecule activity / cell surface / ATP hydrolysis activity / 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) / Sushi/SCR/CCP domain / Picornavirus coat protein VP4 superfamily / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein ...: / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Picornavirus coat protein VP4 superfamily / 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) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / 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
Complement decay-accelerating factor / Genome polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human) / Human echovirus 12
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 16.0 Å
AuthorsBhella D / Goodfellow IG / Roversi P / Pettigrew D / Chaudhry Y / Evans DJ / Lea SM
CitationJournal: J Biol Chem / Year: 2004
Title: The structure of echovirus type 12 bound to a two-domain fragment of its cellular attachment protein decay-accelerating factor (CD 55).
Authors: David Bhella / Ian G Goodfellow / Pietro Roversi / David Pettigrew / Yasmin Chaudhry / David J Evans / Susan M Lea /
Abstract: Echovirus type 12 (EV12), an Enterovirus of the Picornaviridae family, uses the complement regulator decay-accelerating factor (DAF, CD55) as a cellular receptor. We have calculated a three- ...Echovirus type 12 (EV12), an Enterovirus of the Picornaviridae family, uses the complement regulator decay-accelerating factor (DAF, CD55) as a cellular receptor. We have calculated a three-dimensional reconstruction of EV12 bound to a fragment of DAF consisting of short consensus repeat domains 3 and 4 from cryo-negative stain electron microscopy data (EMD code 1057). This shows that, as for an earlier reconstruction of the related echovirus type 7 bound to DAF, attachment is not within the viral canyon but occurs close to the 2-fold symmetry axes. Despite this general similarity our reconstruction reveals a receptor interaction that is quite different from that observed for EV7. Fitting of the crystallographic co-ordinates for DAF(34) and EV11 into the reconstruction shows a close agreement between the crystal structure of the receptor fragment and the density for the virus-bound receptor, allowing unambiguous positioning of the receptor with respect to the virion (PDB code 1UPN). Our finding that the mode of virus-receptor interaction in EV12 is distinct from that seen for EV7 raises interesting questions regarding the evolution and biological significance of the DAF binding phenotype in these viruses.
History
DepositionOct 8, 2003-
Header (metadata) releaseOct 8, 2003-
Map releaseNov 25, 2003-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 65
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 65
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-1upn
  • Surface level: 65
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1upn
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1057.gif

Downloads & links

-
Map

FileDownload / File: emd_1057.map.gz / Format: CCP4 / Size: 20 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThree dimensional reconstruction of echovirus type 12 bound to domains three and four of its cellular receptor decay-accelerating factor. Calculated from cryo-negative stain images
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.42 Å/pix.
x 175 pix.
= 598.5 Å		3.42 Å/pix.
x 175 pix.
= 598.5 Å		3.42 Å/pix.
x 175 pix.
= 598.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.42 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 169.0 / Movie #1: 65
Minimum - Maximum0.0 - 255.0
Average (Standard dev.)66.186300000000003 (±31.677700000000002)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-87-87-87
Dimensions175175175
Spacing175175175
CellA=B=C: 598.5 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.423.423.42
M x/y/z175175175
origin x/y/z0.0000.0000.000
length x/y/z598.500598.500598.500
α/β/γ90.00090.00090.000
start NX/NY/NZ0052
NX/NY/NZ12812855
MAP C/R/S123
start NC/NR/NS-87-87-87
NC/NR/NS175175175
D min/max/mean0.000255.00066.186

-
Supplemental data

-
Sample components

-
Entire : Echovirus type 12 bound to decay accelerating factor domains 3 and 4

EntireName: Echovirus type 12 bound to decay accelerating factor domains 3 and 4
Components
  • Sample: Echovirus type 12 bound to decay accelerating factor domains 3 and 4
  • Virus: Human echovirus 12
  • Organelle or cellular component: Decay accelerating factor domains 3 and 4

-
Supramolecule #1000: Echovirus type 12 bound to decay accelerating factor domains 3 and 4

SupramoleculeName: Echovirus type 12 bound to decay accelerating factor domains 3 and 4
type: sample / ID: 1000 / Number unique components: 2

-
Supramolecule #1: Human echovirus 12

SupramoleculeName: Human echovirus 12 / type: virus / ID: 1 / Name.synonym: EV12 / NCBI-ID: 35293 / Sci species name: Human echovirus 12 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No / Syn species name: EV12
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES

-
Supramolecule #2: Decay accelerating factor domains 3 and 4

SupramoleculeName: Decay accelerating factor domains 3 and 4 / type: organelle_or_cellular_component / ID: 2 / Name.synonym: DAF34 / Number of copies: 60 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Komagataella pastoris (fungus)

-
Experimental details

-
Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.4 / Details: PBS A
StainingType: NEGATIVE
Details: Protein absorbed to grid, floated onto 20% ammonium molybdate (pH 7.4), blotted and plunged into liquid ethane
GridDetails: 400 mesh Quantifoils
VitrificationCryogen name: ETHANE / Method: blot for 2 seconds, wait for 2 seconds plunge

-
Electron microscopy

MicroscopeJEOL 1200EXII
Alignment procedureLegacy - Astigmatism: objective astigmatism corrected at 200k x
DetailsMICROSCOPE JEOL 1200 EX with OXFORD INSTRUMENTS CRYO-TRANSFER STAGE
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 3.42 µm / Number real images: 16 / Details: Images scanned on a Dunvegan HiScan / Bits/pixel: 16
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 29200 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 3.4 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 30000
Sample stageSpecimen holder: side entry / Specimen holder model: OTHER

-
Image processing

CTF correctionDetails: Merged individual particles from focal pairs
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EM3DR2, PFT2, CTFMIX
Details: Particles were aligned using a model based strategy starting with a model derived from the crystallographic co-ordinates of EV-1, filtered to 16 Angstroms resolution. The program is called ...Details: Particles were aligned using a model based strategy starting with a model derived from the crystallographic co-ordinates of EV-1, filtered to 16 Angstroms resolution. The program is called PFT (Polar Fourier Transform). The reconstructions were calculated using the EM3DR2 program which is based on the standard method of calculating icosahedral reconstructions as described by Crowther,'Fourier-Bessel'.
Number images used: 903

-
Atomic model buiding 1

Details3D crystal structure fitting details lodged with PDB 1UPN
Output model

PDB-1upn:
COMPLEX OF ECHOVIRUS TYPE 12 WITH DOMAINS 3 AND 4 OF ITS RECEPTOR DECAY ACCELERATING FACTOR (CD55) BY CRYO ELECTRON MICROSCOPY AT 16 A

+
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