[English] 日本語
Yorodumi
- EMDB-1450: Human T-lymphotropic virus-1 visualized at the virological synaps... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1450
TitleHuman T-lymphotropic virus-1 visualized at the virological synapse by electron tomography.
Map dataThe tomogram shows a virological synapse between a naturally HTVL-1 infected CD4+ T lymphocyte (right) and a target cell (left). Two electron dense (anti-gag labeled) HTLV-1 particles can be seen in the synaptic cleft.
Sample
  • Sample: HTLV-1 virological snapse formed between CD4 T lymphocytes of HTLV-1 infeceted individual
  • Organelle or cellular component: virological synapse
Biological speciesHomo sapiens (human)
Methodelectron tomography / negative staining / Resolution: 50.0 Å
AuthorsMajorovits E / Nejmeddine M / Tanaka Y / Taylor GP / Fuller SD / Bangham CRM
CitationJournal: PLoS One / Year: 2008
Title: Human T-lymphotropic virus-1 visualized at the virological synapse by electron tomography.
Authors: Endre Majorovits / Mohamed Nejmeddine / Yuetsu Tanaka / Graham P Taylor / Stephen D Fuller / Charles R M Bangham /
Abstract: Human T-lymphotropic virus 1 (HTLV-1) is transmitted directly between cells via an organized cell-cell contact called a virological synapse (VS). The VS has been studied by light microscopy, but the ...Human T-lymphotropic virus 1 (HTLV-1) is transmitted directly between cells via an organized cell-cell contact called a virological synapse (VS). The VS has been studied by light microscopy, but the ultrastructure of the VS and the nature of the transmitted viral particle have remained unknown. Cell-free enveloped virions of HTLV-1 are undetectable in the serum of individuals infected with the human T-lymphotropic virus 1 (HTLV-1) and during in vitro culture of naturally infected lymphocytes. However, the viral envelope protein is required for infectivity of HTLV-1, suggesting that complete, enveloped HTLV-1 virions are transferred across the synapse. Here, we use electron tomography combined with immunostaining of viral protein to demonstrate the presence of enveloped HTLV-1 particles within the VS formed between naturally infected lymphocytes. We show in 3D that HTLV-1 particles can be detected in multiple synaptic clefts at different locations simultaneously within the same VS. The synaptic clefts are surrounded by the tightly apposed plasma membranes of the two cells. HTLV-1 virions can contact the recipient cell membrane before detaching from the infected cell. The results show that the HTLV-1 virological synapse that forms spontaneously between lymphocytes of HTLV-1 infected individuals allows direct cell-cell transmission of the virus by triggered, directional release of enveloped HTLV-1 particles into confined intercellular spaces.
History
DepositionNov 1, 2007-
Header (metadata) releaseNov 6, 2007-
Map releaseJun 6, 2008-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_1450.map.gz / Format: CCP4 / Size: 156.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe tomogram shows a virological synapse between a naturally HTVL-1 infected CD4+ T lymphocyte (right) and a target cell (left). Two electron dense (anti-gag labeled) HTLV-1 particles can be seen in the synaptic cleft.
Voxel sizeX: 33.6 Å / Y: 33.6 Å / Z: 25.9 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)17.9574 (±4.31085)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions1300600215
Spacing1300600215
CellA: 43680 Å / B: 20160 Å / C: 5568.5 Å
α=β=γ: 90 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z33.59999692307733.625.9
M x/y/z1300600215
origin x/y/z0.0000.0000.000
length x/y/z43679.99620160.0005568.500
α/β/γ90.00090.00090.000
start NX/NY/NZ-60-60-59
NX/NY/NZ120120120
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS6001300215
D min/max/mean-128.000127.00017.957

-
Supplemental data

-
Sample components

-
Entire : HTLV-1 virological snapse formed between CD4 T lymphocytes of HTL...

EntireName: HTLV-1 virological snapse formed between CD4 T lymphocytes of HTLV-1 infeceted individual
Components
  • Sample: HTLV-1 virological snapse formed between CD4 T lymphocytes of HTLV-1 infeceted individual
  • Organelle or cellular component: virological synapse

-
Supramolecule #1000: HTLV-1 virological snapse formed between CD4 T lymphocytes of HTL...

SupramoleculeName: HTLV-1 virological snapse formed between CD4 T lymphocytes of HTLV-1 infeceted individual
type: sample / ID: 1000 / Number unique components: 1

-
Supramolecule #1: virological synapse

SupramoleculeName: virological synapse / type: organelle_or_cellular_component / ID: 1 / Number of copies: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Homo sapiens (human) / synonym: human being / Cell: CD4 T lymphocyte / Organelle: Plasma membrane / Location in cell: Plasma membrane

-
Experimental details

-
Structure determination

Methodnegative staining
Processingelectron tomography

-
Sample preparation

BufferpH: 7.2 / Details: sodium cacodylate buffer 0.1M
StainingType: NEGATIVE / Details: 1% OsO4 staining
GridDetails: Formvar coated 2x1mm Cu slot grid
VitrificationCryogen name: NONE

-
Electron microscopy

MicroscopeFEI TECNAI F30
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 10800 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.2 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 9300
Specialist opticsEnergy filter - Name: GIF / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 25.0 eV
Sample stageSpecimen holder: Gatan flip-flop holder / Specimen holder model: OTHER / Tilt series - Axis1 - Min angle: 65.0 ° / Tilt series - Axis1 - Max angle: 65 ° / Tilt series - Axis1 - Angle increment: 1 °
TemperatureAverage: 290 K
DateFeb 26, 2007
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN (2k x 2k)
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

-
Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 50.0 Å / Software - Name: IMOD / Number images used: 130

+
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