[English] 日本語
Yorodumi
- EMDB-5523: Protease Cleavage Leads to Formation of Mature Trimer Interface i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5523
TitleProtease Cleavage Leads to Formation of Mature Trimer Interface in HIV-1 Capsid
Map dataReconstruction of CA in HIV-1 CA-SP1-NC assembly
Sample
  • Sample: CA in HIV-1 CA-SP1-NC assembly
  • Protein or peptide: HIV-1 CA-SP1-NC
KeywordsHIV-1 / capsid / nucleocapsid / maturation / cryoEM / cross-linking / interface
Biological speciesHuman immunodeficiency virus 1
Methodhelical reconstruction / cryo EM / Resolution: 13.0 Å
AuthorsMeng X / Zhao G / Yufenyuy E / Ke D / Ning J / DeLucia M / Ahn J / Gronenborn AM / Aiken C / Zhang P
CitationJournal: PLoS Pathog / Year: 2012
Title: Protease cleavage leads to formation of mature trimer interface in HIV-1 capsid.
Authors: Xin Meng / Gongpu Zhao / Ernest Yufenyuy / Danxia Ke / Jiying Ning / Maria Delucia / Jinwoo Ahn / Angela M Gronenborn / Christopher Aiken / Peijun Zhang /
Abstract: During retrovirus particle maturation, the assembled Gag polyprotein is cleaved by the viral protease into matrix (MA), capsid (CA), and nucleocapsid (NC) proteins. To form the mature viral capsid, ...During retrovirus particle maturation, the assembled Gag polyprotein is cleaved by the viral protease into matrix (MA), capsid (CA), and nucleocapsid (NC) proteins. To form the mature viral capsid, CA rearranges, resulting in a lattice composed of hexameric and pentameric CA units. Recent structural studies of assembled HIV-1 CA revealed several inter-subunit interfaces in the capsid lattice, including a three-fold interhexamer interface that is critical for proper capsid stability. Although a general architecture of immature particles has been provided by cryo-electron tomographic studies, the structural details of the immature particle and the maturation pathway remain unknown. Here, we used cryo-electron microscopy (cryoEM) to determine the structure of tubular assemblies of the HIV-1 CA-SP1-NC protein. Relative to the mature assembled CA structure, we observed a marked conformational difference in the position of the CA-CTD relative to the NTD in the CA-SP1-NC assembly, involving the flexible hinge connecting the two domains. This difference was verified via engineered disulfide crosslinking, revealing that inter-hexamer contacts, in particular those at the pseudo three-fold axis, are altered in the CA-SP1-NC assemblies compared to the CA assemblies. Results from crosslinking analyses of mature and immature HIV-1 particles containing the same Cys substitutions in the Gag protein are consistent with these findings. We further show that cleavage of preassembled CA-SP1-NC by HIV-1 protease in vitro leads to release of SP1 and NC without disassembly of the lattice. Collectively, our results indicate that the proteolytic cleavage of Gag leads to a structural reorganization of the polypeptide and creates the three-fold interhexamer interface, important for the formation of infectious HIV-1 particles.
History
DepositionOct 12, 2012-
Header (metadata) releaseOct 24, 2012-
Map releaseOct 24, 2012-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.024
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.024
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.024
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5523_1.tif

Downloads & links

-
Map

FileDownload / File: emd_5523.map.gz / Format: CCP4 / Size: 79.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of CA in HIV-1 CA-SP1-NC assembly
Voxel sizeX=Y=Z: 2.66 Å
Density
Contour LevelBy AUTHOR: 0.024 / Movie #1: 0.024
Minimum - Maximum-0.11270955 - 0.13998687
Average (Standard dev.)-0.0009129 (±0.02129342)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-118-140
Dimensions320236281
Spacing320236281
CellA: 627.76 Å / B: 851.2 Å / C: 747.46 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.662.662.66
M x/y/z236320281
origin x/y/z0.0000.0000.000
length x/y/z627.760851.200747.460
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-118-160-140
NC/NR/NS236320281
D min/max/mean-0.1130.140-0.001

-
Supplemental data

-
Sample components

-
Entire : CA in HIV-1 CA-SP1-NC assembly

EntireName: CA in HIV-1 CA-SP1-NC assembly
Components
  • Sample: CA in HIV-1 CA-SP1-NC assembly
  • Protein or peptide: HIV-1 CA-SP1-NC

-
Supramolecule #1000: CA in HIV-1 CA-SP1-NC assembly

SupramoleculeName: CA in HIV-1 CA-SP1-NC assembly / type: sample / ID: 1000 / Number unique components: 1

-
Macromolecule #1: HIV-1 CA-SP1-NC

MacromoleculeName: HIV-1 CA-SP1-NC / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: NL4-3
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pr55Gag

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

Concentration10 mg/mL
BufferpH: 8 / Details: 250 mM NaCl, 50 mM Tris-HCl
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

-
Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
DateDec 10, 2009
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 6 / Average electron dose: 15 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: CTF correction of each particle
Final reconstructionApplied symmetry - Helical parameters - Δz: 5.9 Å
Applied symmetry - Helical parameters - Δ&Phi: 129.2 °
Applied symmetry - Helical parameters - Axial symmetry: D2 (2x2 fold dihedral)
Resolution.type: BY AUTHOR / Resolution: 13.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider, IHRSR
DetailsIHRSR and Spider scripts from the Grigorieff lab were used for helical processing.

-
Atomic model buiding 1

Initial modelPDB ID:

2kod

SoftwareName: Chimera, Situs
RefinementSpace: REAL

-
Atomic model buiding 2

Initial modelPDB ID:

3h47

SoftwareName: Chimera, Situs
RefinementSpace: REAL

+
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