[English] 日本語
Yorodumi
- EMDB-1155: The mechanism of HIV-1 core assembly: insights from three-dimensi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1155
TitleThe mechanism of HIV-1 core assembly: insights from three-dimensional reconstructions of authentic virions.
Map dataTomographic reconstruction of HIV-1 virions
Sample
  • Sample: HIV-1 virions
  • Virus: Human immunodeficiency virus
Biological speciesHuman immunodeficiency virus
Methodelectron tomography / cryo EM / negative staining
AuthorsBriggs JAG / Grunewald K / Glass B / Forster F
CitationJournal: Structure / Year: 2006
Title: The mechanism of HIV-1 core assembly: insights from three-dimensional reconstructions of authentic virions.
Authors: John A G Briggs / Kay Grünewald / Bärbel Glass / Friedrich Förster / Hans-Georg Kräusslich / Stephen D Fuller /
Abstract: Infectious HIV particles contain a characteristic cone-shaped core encasing the viral RNA and replication proteins. The core exhibits significant heterogeneity in size and shape, yet consistently ...Infectious HIV particles contain a characteristic cone-shaped core encasing the viral RNA and replication proteins. The core exhibits significant heterogeneity in size and shape, yet consistently forms a well-defined structure. The mechanism by which the core is assembled in the maturing virion remains poorly understood. Using cryo-electron tomography, we have produced three-dimensional reconstructions of authentic, unstained HIV-1. These reveal the viral morphology with unprecedented clarity and suggest the following mechanism for core formation inside the extracellular virion: core growth initiates at the narrow end of the cone and proceeds toward the distal side of the virion until limited by the viral membrane. Curvature and closure of the broad end of the core are then directed by the inner surface of the viral membrane. This mechanism accommodates significant flexibility in lattice growth while ensuring the closure of cores of variable size and shape.
History
DepositionAug 30, 2005-
Header (metadata) releaseAug 30, 2005-
Map releaseJan 16, 2006-
UpdateSep 2, 2011-
Current statusSep 2, 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

1155.gif

Downloads & links

-
Map

FileDownload / File: emd_1155.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationTomographic reconstruction of HIV-1 virions
Voxel sizeX=Y=Z: 16.4 Å
Density
Contour LevelBy EMDB: 21.0
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)5.03894 (±12.399900000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions91141281
Spacing91141281
CellA: 1492.4 Å / B: 2312.4 Å / C: 4608.4 Å
α=β=γ: 90 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z16.416.416.4
M x/y/z91141281
origin x/y/z0.0000.0000.000
length x/y/z1492.4002312.4004608.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-70-70-69
NX/NY/NZ140140140
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS14191281
D min/max/mean-128.000127.0005.039

-
Supplemental data

-
Supplemental map: 1155 inverted int16.map

File1155_inverted_int16.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : HIV-1 virions

EntireName: HIV-1 virions
Components
  • Sample: HIV-1 virions
  • Virus: Human immunodeficiency virus

-
Supramolecule #1000: HIV-1 virions

SupramoleculeName: HIV-1 virions / type: sample / ID: 1000 / Number unique components: 1

-
Supramolecule #1: Human immunodeficiency virus

SupramoleculeName: Human immunodeficiency virus / type: virus / ID: 1 / Name.synonym: HIV-1 / NCBI-ID: 12721 / Sci species name: Human immunodeficiency virus / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: HIV-1
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES

-
Experimental details

-
Structure determination

Methodnegative staining, cryo EM
Processingelectron tomography

-
Sample preparation

BufferpH: 7.2 / Details: PBS
StainingType: NEGATIVE / Details: unstained
GridDetails: holey carbon film
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 36500 / Illumination mode: FLOOD BEAM / Imaging mode: OTHER / Cs: 2.0 mm / Nominal defocus max: 6.5 µm / Nominal defocus min: 5.5 µm
Specialist opticsEnergy filter - Name: GIF2000 / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: 68 ° / Tilt series - Axis1 - Max angle: 68 ° / Tilt series - Axis1 - Angle increment: 2 °
DateOct 22, 2004
Image recordingAverage electron dose: 50 e/Å2

-
Image processing

Final reconstructionAlgorithm: OTHER / Software - Name: IMOD

+
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