[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleThe structure and flexibility of conical HIV-1 capsids determined within intact virions.
Journal, issue, pagesScience, Vol. 354, Issue 6318, Page 1434-1437, Year 2016
Publish dateDec 16, 2016
AuthorsSimone Mattei / Bärbel Glass / Wim J H Hagen / Hans-Georg Kräusslich / John A G Briggs /
PubMed AbstractHIV-1 contains a cone-shaped capsid encasing the viral genome. This capsid is thought to follow fullerene geometry-a curved hexameric lattice of the capsid protein, CA, closed by incorporating 12 CA ...HIV-1 contains a cone-shaped capsid encasing the viral genome. This capsid is thought to follow fullerene geometry-a curved hexameric lattice of the capsid protein, CA, closed by incorporating 12 CA pentamers. Current models for core structure are based on crystallography of hexameric and cross-linked pentameric CA, electron microscopy of tubular CA arrays, and simulations. Here, we report subnanometer-resolution cryo-electron tomography structures of hexameric and pentameric CA within intact HIV-1 particles. Whereas the hexamer structure is compatible with crystallography studies, the pentamer forms using different interfaces. Determining multiple structures revealed how CA flexes to form the variably curved core shell. We show that HIV-1 CA assembles both aberrant and perfect fullerene cones, supporting models in which conical cores assemble de novo after maturation.
External linksScience / PubMed:27980210
MethodsEM (tomography) / EM (subtomogram averaging)
Resolution6.8 - 8.8 Å
Structure data

EMDB-3464:
Cryo-electron tomogram containing mature HIV-1 particles
Method: EM (tomography)

EMDB-3465, PDB-5mcx:
The structure of the mature HIV-1 CA hexamer in intact virus particles
Method: EM (subtomogram averaging) / Resolution: 6.8 Å

EMDB-3466, PDB-5mcy:
The structure of the mature HIV-1 CA pentamer in intact virus particles
Method: EM (subtomogram averaging) / Resolution: 8.8 Å

EMDB-3467, PDB-5mcz:
The structure of the mature HIV-1 CA hexameric lattice with curvature parameters: tilt=-1, twist=0
Method: EM (subtomogram averaging) / Resolution: 8.2 Å

EMDB-3468, PDB-5md0:
The structure of the mature HIV-1 CA hexameric lattice with curvature parameters: tilt=5, twist=6
Method: EM (subtomogram averaging) / Resolution: 8.4 Å

EMDB-3469, PDB-5md1:
The structure of the mature HIV-1 CA hexameric lattice with curvature parameters: tilt=5, twist=0
Method: EM (subtomogram averaging) / Resolution: 8.2 Å

EMDB-3470, PDB-5md2:
The structure of the mature HIV-1 CA hexameric lattice with curvature parameters: tilt=5, twist=-6
Method: EM (subtomogram averaging) / Resolution: 8.6 Å

EMDB-3471, PDB-5md3:
The structure of the mature HIV-1 CA hexameric lattice with curvature parameters: tilt=11, twist=12
Method: EM (subtomogram averaging) / Resolution: 8.5 Å

EMDB-3472, PDB-5md4:
The structure of the mature HIV-1 CA hexameric lattice with curvature parameters: tilt=11, twist=6
Method: EM (subtomogram averaging) / Resolution: 8.4 Å

EMDB-3473, PDB-5md5:
The structure of the mature HIV-1 CA hexameric lattice with curvature parameters: tilt=11, twist=0
Method: EM (subtomogram averaging) / Resolution: 8.2 Å

EMDB-3474, PDB-5md6:
The structure of the mature HIV-1 CA hexameric lattice with curvature parameters: tilt=11, twist=-6
Method: EM (subtomogram averaging) / Resolution: 8.1 Å

EMDB-3475, PDB-5md7:
The structure of the mature HIV-1 CA hexameric lattice with curvature parameters: tilt=11, twist=-12
Method: EM (subtomogram averaging) / Resolution: 8.4 Å

EMDB-3477, PDB-5md8:
The structure of the mature HIV-1 CA hexameric lattice with curvature parameters: tilt=17, twist=12
Method: EM (subtomogram averaging) / Resolution: 8.6 Å

EMDB-3478, PDB-5md9:
The structure of the mature HIV-1 CA hexameric lattice with curvature parameters: tilt=17, twist=6
Method: EM (subtomogram averaging) / Resolution: 8.0 Å

EMDB-3479, PDB-5mda:
The structure of the mature HIV-1 CA hexameric lattice with curvature parameters: tilt=17, twist=0
Method: EM (subtomogram averaging) / Resolution: 8.4 Å

EMDB-3480, PDB-5mdb:
The structure of the mature HIV-1 CA hexameric lattice with curvature parameters: tilt=17, twist=-6
Method: EM (subtomogram averaging) / Resolution: 8.4 Å

EMDB-3481, PDB-5mdc:
The structure of the mature HIV-1 CA hexameric lattice with curvature parameters: tilt=17, twist=-12
Method: EM (subtomogram averaging) / Resolution: 8.4 Å

EMDB-3482, PDB-5mdd:
The structure of the mature HIV-1 CA hexameric lattice with curvature parameters: tilt=23, twist=6
Method: EM (subtomogram averaging) / Resolution: 8.5 Å

EMDB-3483, PDB-5mde:
The structure of the mature HIV-1 CA hexameric lattice with curvature parameters: tilt=23, twist=0
Method: EM (subtomogram averaging) / Resolution: 8.4 Å

EMDB-3484, PDB-5mdf:
The structure of the mature HIV-1 CA hexameric lattice with curvature parameters: tilt=23, twist=-6
Method: EM (subtomogram averaging) / Resolution: 8.5 Å

EMDB-3485, PDB-5mdg:
The structure of the mature HIV-1 CA hexameric lattice with curvature parameters: tilt=29, twist=0
Method: EM (subtomogram averaging) / Resolution: 8.7 Å

Source
  • human immunodeficiency virus 1
KeywordsVIRAL PROTEIN / retrovirus / HIV-1 / capsid / hexamer / pentamer / lattice curvature

+
About Yorodumi Papers

-
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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more