[English] 日本語
Yorodumi
- EMDB-1576: Structural analysis of the interaction of human adenovirus 5 with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1576
TitleStructural analysis of the interaction of human adenovirus 5 with erythrocytes.
Map dataThis is a map of the adenovirus fivefold vertex interacting directly with the surface of a human red blood cell ghost.
Sample
  • Sample: Human adenovirus serotype 5 interacting with the surface of human erythrocyte-derived ghosts.
  • Virus: Adenovirus serotype 5
  • Organelle or cellular component: Erythrocyte ghost
KeywordsAdenovirus / erythrocyte / complement receptor / coxsackie-adenovirus receptor / penton base
Biological speciesHomo sapiens (human) / Adenovirus serotype 5
Methodsingle particle reconstruction / cryo EM / Resolution: 40.0 Å
AuthorsCarlisle RC / Di Y / Cerny AM / Sonnen AF-P / Sim RB / Green NK / Subr V / Ulbrich K / Gilbert RJC / Fisher KD ...Carlisle RC / Di Y / Cerny AM / Sonnen AF-P / Sim RB / Green NK / Subr V / Ulbrich K / Gilbert RJC / Fisher KD / Finberg RW / Seymour LW
CitationJournal: Blood / Year: 2009
Title: Human erythrocytes bind and inactivate type 5 adenovirus by presenting Coxsackie virus-adenovirus receptor and complement receptor 1.
Authors: Robert C Carlisle / Ying Di / Anna M Cerny / Andreas F-P Sonnen / Robert B Sim / Nicola K Green / Vladimir Subr / Karel Ulbrich / Robert J C Gilbert / Kerry D Fisher / Robert W Finberg / Leonard W Seymour /
Abstract: Type 5 adenovirus (Ad5) is a human pathogen that has been widely developed for therapeutic uses, with only limited success to date. We report here the novel finding that human erythrocytes present ...Type 5 adenovirus (Ad5) is a human pathogen that has been widely developed for therapeutic uses, with only limited success to date. We report here the novel finding that human erythrocytes present Coxsackie virus-adenovirus receptor (CAR) providing an Ad5 sequestration mechanism that protects against systemic infection. Interestingly, erythrocytes from neither mice nor rhesus macaques present CAR. Excess Ad5 fiber protein or anti-CAR antibody inhibits the binding of Ad5 to human erythrocytes and cryo-electron microscopy shows attachment via the fiber protein of Ad5, leading to close juxtaposition with the erythrocyte membrane. Human, but not murine, erythrocytes also present complement receptor (CR1), which binds Ad5 in the presence of antibodies and complement. Transplantation of human erythrocytes into nonobese diabetic/severe combined immunodeficiency mice extends blood circulation of intravenous Ad5 but decreases its extravasation into human xenograft tumors. Ad5 also shows extended circulation in transgenic mice presenting CAR on their erythrocytes, although it clears rapidly in transgenic mice presenting erythrocyte CR1. Hepatic infection is inhibited in both transgenic models. Erythrocytes may therefore restrict Ad5 infection (natural and therapeutic) in humans, independent of antibody status, presenting a formidable challenge to Ad5 therapeutics. "Stealthing" of Ad5 using hydrophilic polymers may enable circumvention of these natural virus traps.
History
DepositionOct 29, 2008-
Header (metadata) releaseNov 5, 2008-
Map releaseJun 10, 2009-
UpdateOct 27, 2009-
Current statusOct 27, 2009Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 35
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 35
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1576.gif

emd_1576_1.tif

emd_1576_2.tif

emd_1576_3.tif

emd_1576_4.tif

emd_1576_5.tif

emd_1576_6.tif

emd_1576_7.tif

Downloads & links

-
Map

FileDownload / File: emd_1576.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a map of the adenovirus fivefold vertex interacting directly with the surface of a human red blood cell ghost.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
2.6 Å/pix.
x 200 pix.
= 520. Å		2.6 Å/pix.
x 200 pix.
= 520. Å		2.6 Å/pix.
x 200 pix.
= 520. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 26.800000000000001 / Movie #1: 35
Minimum - Maximum-169.669999999999987 - 172.360000000000014
Average (Standard dev.)4.53112 (±19.277000000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-100-100-99
Dimensions200200200
Spacing200200200
CellA=B=C: 520 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.62.62.6
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z520.000520.000520.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-100-100-99
NX/NY/NZ200200200
MAP C/R/S213
start NC/NR/NS-100-100-99
NC/NR/NS200200200
D min/max/mean-169.670172.3604.531

-
Supplemental data

-
Others

Details[IMAGE_DETAILS]
First six images are of the interaction, and will be published in the Blood manuscript
with the reconstruction. The last one is an aligned average, showing the virus, membrane
and fibre attaching.
The images are of Ad5 interacting with erythrocyte ghost
membranes via its fibre that projects from the fivefold vertex represent the stage
in virus-membrane interaction prior to the one reconstructed in the deposited map.
The interaction is via the coxsackie-adenovirus receptor (CAR), which binds to the
end of the fibre. The main focus of the manuscript describing this work was the
demonstration that CAR is found on human erythrocytes, along with complement
receptor 1 (CR1) and that this has major implications for the use of Ad5 as a
vector in immunisation.
Image

File: emd_1576_1.tif
Image

File: emd_1576_2.tif
Image

File: emd_1576_3.tif
Image

File: emd_1576_4.tif
Image

File: emd_1576_5.tif
Image

File: emd_1576_6.tif
Image

File: emd_1576_7.tif

-
Sample components

-
Entire : Human adenovirus serotype 5 interacting with the surface of human...

EntireName: Human adenovirus serotype 5 interacting with the surface of human erythrocyte-derived ghosts.
Components
  • Sample: Human adenovirus serotype 5 interacting with the surface of human erythrocyte-derived ghosts.
  • Virus: Adenovirus serotype 5
  • Organelle or cellular component: Erythrocyte ghost

-
Supramolecule #1000: Human adenovirus serotype 5 interacting with the surface of human...

SupramoleculeName: Human adenovirus serotype 5 interacting with the surface of human erythrocyte-derived ghosts.
type: sample / ID: 1000
Oligomeric state: One penton vertex binds to the erythrocyte surface
Number unique components: 2

-
Supramolecule #1: Adenovirus serotype 5

SupramoleculeName: Adenovirus serotype 5 / type: virus / ID: 1 / Name.synonym: Adenovirus
Details: The adenovirus was mixed with erythrocyte ghosts, to which they bound.
Sci species name: Adenovirus serotype 5 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: Yes / Syn species name: Adenovirus
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES

-
Supramolecule #2: Erythrocyte ghost

SupramoleculeName: Erythrocyte ghost / type: organelle_or_cellular_component / ID: 2 / Name.synonym: red blood cell ghost
Details: The ghosts were prepared from fresh human blood using osmotic shock and sonication.
Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Blood / Cell: Erythrocyte / Location in cell: Plasma membrane

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4 / Details: PBS
GridDetails: 300 mesh copper grid with lacey carbon film
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Homemade plunger / Method: Blot for 1-2 seconds before plunging.

-
Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 4 / Bits/pixel: 8
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 27000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: Per micrograph
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 40.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER
Details: Final map was calculated using imposed fivefold symmetry orthogonal to the axis of view.
Number images used: 27
Final angle assignmentDetails: Angles around y axis, since viewed perpendicular to fivefold vertex, using Euler convention of SPIDER and XPLOR

+
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