[English] 日本語
Yorodumi
- EMDB-1464: Adenovirus serotype 5 hexon mediates liver gene transfer. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1464
TitleAdenovirus serotype 5 hexon mediates liver gene transfer.
Map dataThree-dimensional reconstruction of Adenovirus type 5 bound to Factor X
Sample
  • Sample: Adenovirus type 5 bound to Factor X
  • Virus: Human adenovirus 5
  • Ligand: Factor X
Biological speciesHuman adenovirus 5
Methodsingle particle reconstruction / cryo EM / Resolution: 23.0 Å
AuthorsWaddington SN / McVey JH / Bhella D / Parker AL / Barker K / Atoda H / Pink R / Buckley SM / Greig JA / Denby L ...Waddington SN / McVey JH / Bhella D / Parker AL / Barker K / Atoda H / Pink R / Buckley SM / Greig JA / Denby L / Custers J / Morita T / Francischetti IM / Monteiro RQ / Barouch DH / van Rooijen N / Napoli C / Havenga MJ / Nicklin SA / Baker AH
CitationJournal: Cell / Year: 2008
Title: Adenovirus serotype 5 hexon mediates liver gene transfer.
Authors: Simon N Waddington / John H McVey / David Bhella / Alan L Parker / Kristeen Barker / Hideko Atoda / Rebecca Pink / Suzanne M K Buckley / Jenny A Greig / Laura Denby / Jerome Custers / ...Authors: Simon N Waddington / John H McVey / David Bhella / Alan L Parker / Kristeen Barker / Hideko Atoda / Rebecca Pink / Suzanne M K Buckley / Jenny A Greig / Laura Denby / Jerome Custers / Takashi Morita / Ivo M B Francischetti / Robson Q Monteiro / Dan H Barouch / Nico van Rooijen / Claudio Napoli / Menzo J E Havenga / Stuart A Nicklin / Andrew H Baker /
Abstract: Adenoviruses are used extensively as gene transfer agents, both experimentally and clinically. However, targeting of liver cells by adenoviruses compromises their potential efficacy. In cell culture, ...Adenoviruses are used extensively as gene transfer agents, both experimentally and clinically. However, targeting of liver cells by adenoviruses compromises their potential efficacy. In cell culture, the adenovirus serotype 5 fiber protein engages the coxsackievirus and adenovirus receptor (CAR) to bind cells. Paradoxically, following intravascular delivery, CAR is not used for liver transduction, implicating alternate pathways. Recently, we demonstrated that coagulation factor (F)X directly binds adenovirus leading to liver infection. Here, we show that FX binds to the Ad5 hexon, not fiber, via an interaction between the FX Gla domain and hypervariable regions of the hexon surface. Binding occurs in multiple human adenovirus serotypes. Liver infection by the FX-Ad5 complex is mediated through a heparin-binding exosite in the FX serine protease domain. This study reveals an unanticipated function for hexon in mediating liver gene transfer in vivo.
History
DepositionJan 10, 2008-
Header (metadata) releaseJan 10, 2008-
Map releaseFeb 22, 2008-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 262.697161173
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 262.697161173
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1464.gif

Downloads & links

-
Map

FileDownload / File: emd_1464.map.gz / Format: CCP4 / Size: 42.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThree-dimensional reconstruction of Adenovirus type 5 bound to Factor X
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.54 Å/pix.
x 225 pix.
= 1471.5 Å		6.54 Å/pix.
x 225 pix.
= 1471.5 Å		6.54 Å/pix.
x 225 pix.
= 1471.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.54 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 293.0 / Movie #1: 262.6971612
Minimum - Maximum-963.807999999999993 - 1253.8900000000001
Average (Standard dev.)25.505600000000001 (±124.706999999999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-112-112-112
Dimensions225225225
Spacing225225225
CellA=B=C: 1471.5 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.546.546.54
M x/y/z225225225
origin x/y/z0.0000.0000.000
length x/y/z1471.5001471.5001471.500
α/β/γ90.00090.00090.000
start NX/NY/NZ29-50166
NX/NY/NZ106122134
MAP C/R/S123
start NC/NR/NS-112-112-112
NC/NR/NS225225225
D min/max/mean-963.8081253.89225.506

-
Supplemental data

-
Sample components

-
Entire : Adenovirus type 5 bound to Factor X

EntireName: Adenovirus type 5 bound to Factor X
Components
  • Sample: Adenovirus type 5 bound to Factor X
  • Virus: Human adenovirus 5
  • Ligand: Factor X

-
Supramolecule #1000: Adenovirus type 5 bound to Factor X

SupramoleculeName: Adenovirus type 5 bound to Factor X / type: sample / ID: 1000 / Number unique components: 2

-
Supramolecule #1: Human adenovirus 5

SupramoleculeName: Human adenovirus 5 / type: virus / ID: 1 / Name.synonym: Ad5 / NCBI-ID: 28285 / Sci species name: Human adenovirus 5 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No / Syn species name: Ad5
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Name: Ad5 / Diameter: 900 Å / T number (triangulation number): 25

-
Macromolecule #1: Factor X

MacromoleculeName: Factor X / type: ligand / ID: 1 / Name.synonym: FX
Details: Commercially purified Factor X from Haematologic Technologies Inc.
Number of copies: 240 / Oligomeric state: monomer / Recombinant expression: No
Source (natural)Tissue: blood/liver

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4 / Details: 10 nM Tris 100 mM NaCl 5 mM CaCl
GridDetails: 400 mesh copper R2/2 quantifoils
VitrificationCryogen name: ETHANE
Method: 5 ul of virus-ligand complex was loaded onto a freshly glow-discharged grid and blotted until the filter paper detached.

-
Electron microscopy

MicroscopeJEOL 1200EXII
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 29128 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 3.4 mm / Nominal defocus max: 3.9 µm / Nominal defocus min: 0.668 µm / Nominal magnification: 30000
Sample stageSpecimen holder: side entry, liquid nitrogen cooled / Specimen holder model: OTHER
TemperatureAverage: 108 K
Alignment procedureLegacy - Astigmatism: Astigmatism corrected at 100,000 times magnification
DetailsDefocus Pairs were recorded
DateJun 1, 2007
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 6.35 µm / Number real images: 21 / Average electron dose: 10 e/Å2 / Details: Images were binned by a factor of 3 / Bits/pixel: 16

-
Image processing

CTF correctionDetails: each particle was corrected and defocus paired particles merged
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: OTHER / Software - Name: PFT3DR2, MRC / Number images used: 305

+
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