[English] 日本語
Yorodumi
- EMDB-46620: Human adenovirus 6 (Ad6) in complex with coagulation Factor FX at... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-46620
TitleHuman adenovirus 6 (Ad6) in complex with coagulation Factor FX at 5.0A resolution.
Map dataRDAd6_FX_new_virion_5.0A
Sample
  • Complex: Human adenovirus 6 (Ad6) in complex with coagulation Factor FX
KeywordsHuman adenovirus 6 Hexon Coagulation Factor X Binding Complex / VIRUS
Biological speciesHuman adenovirus 6
Methodsingle particle reconstruction / cryo EM / Resolution: 5.0 Å
AuthorsReddy VS / Ma OX
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI161367 United States
CitationJournal: Nat Commun / Year: 2024
Title: Structure-derived insights from blood factors binding to the surfaces of different adenoviruses.
Authors: Haley E Mudrick / Shao-Chia Lu / Janarjan Bhandari / Mary E Barry / Jack R Hemsath / Felix G M Andres / Olivia X Ma / Michael A Barry / Vijay S Reddy /
Abstract: The tropism of adenoviruses (Ads) is significantly influenced by the binding of various blood factors. To investigate differences in their binding, we conducted cryo-EM analysis on complexes of ...The tropism of adenoviruses (Ads) is significantly influenced by the binding of various blood factors. To investigate differences in their binding, we conducted cryo-EM analysis on complexes of several human adenoviruses with human platelet factor-4 (PF4), coagulation factors FII (Prothrombin), and FX. While we observed EM densities for FII and FX bound to all the species-C adenoviruses examined, no densities were seen for PF4, even though PF4 can co-pellet with various Ads. Similar to FX, the γ-carboxyglutamic acid (Gla) domain of FII binds within the surface cavity of hexon trimers. While FII binds equally to species-C Ads: Ad5, Ad6, and Ad657, FX exhibits significantly better binding to Ad5 and Ad657 compared to Ad6. Although only the FX-Gla domain is observed at high-resolution (3.7 Å), the entire FX is visible at low-resolution bound to Ad5 in three equivalent binding modes consistent with the 3-fold symmetric hexon. Only the Gla and kringle-1 domains of FII are visible on all the species-C adenoviruses, where the rigid FII binds in an upright fashion, in contrast to the flexible and bent FX. These data suggest that differential binding of FII and FX may shield certain species-C adenoviruses differently against immune molecules, thereby modulating their tropism.
History
DepositionAug 17, 2024-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_46620.png

Downloads & links

-
Map

FileDownload / File: emd_46620.map.gz / Format: CCP4 / Size: 976.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRDAd6_FX_new_virion_5.0A
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.79 Å/pix.
x 400 pix.
= 716.8 Å		1.79 Å/pix.
x 800 pix.
= 1433.6 Å		1.79 Å/pix.
x 800 pix.
= 1433.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.792 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009
Minimum - Maximum-0.01900195 - 0.05431882
Average (Standard dev.)0.00083915744 (±0.0041921507)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00400
Dimensions800800400
Spacing800800400
CellA: 1433.6001 Å / B: 1433.6001 Å / C: 716.80005 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: RDAd6 FX new virion 5.0A

Fileemd_46620_half_map_1.map
AnnotationRDAd6_FX_new_virion_5.0A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: RDAd6 FX new virion 5.0A

Fileemd_46620_half_map_2.map
AnnotationRDAd6_FX_new_virion_5.0A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human adenovirus 6 (Ad6) in complex with coagulation Factor FX

EntireName: Human adenovirus 6 (Ad6) in complex with coagulation Factor FX
Components
  • Complex: Human adenovirus 6 (Ad6) in complex with coagulation Factor FX

-
Supramolecule #1: Human adenovirus 6 (Ad6) in complex with coagulation Factor FX

SupramoleculeName: Human adenovirus 6 (Ad6) in complex with coagulation Factor FX
type: complex / ID: 1 / Parent: 0 / Details: Icosahedral (I1) reconstruction
Source (natural)Organism: Human adenovirus 6
Molecular weightTheoretical: 150 MDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2 mg/mL
BufferpH: 7.2
Details: 50mM HEPES pH 7.2, 300mM NaCl, 10mM CaCl2 and 5mM MgCl2
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K
DetailsHuman adenovirus 6 in complex with coagulation Factor II (Prothrombin)

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number grids imaged: 2 / Number real images: 4226 / Average exposure time: 5.0 sec. / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 24310
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 1769
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT / Target criteria: Cross-correlation Coefficient

+
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