[English] 日本語
Yorodumi
- EMDB-0164: Immature CA domain from HIV-1 MA-SP1 Gag proteolytic cleavage mut... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0164
TitleImmature CA domain from HIV-1 MA-SP1 Gag proteolytic cleavage mutant virus particles
Map dataStructure of the immature CA domain from HIV-1 MA-SP1 Gag proteolytic cleavage mutant virus particles
Sample
  • Virus: Human immunodeficiency virus 1
    • Protein or peptide: Gag polyproteinGroup-specific antigen
Biological speciesHomo sapiens (human) / Human immunodeficiency virus 1
Methodsubtomogram averaging / cryo EM / Resolution: 4.0 Å
AuthorsMattei S / Tan AWK / Glass B / Mueller B / Kraeusslich HG / Briggs JAG
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
Title: High-resolution structures of HIV-1 Gag cleavage mutants determine structural switch for virus maturation.
Authors: Simone Mattei / Aaron Tan / Bärbel Glass / Barbara Müller / Hans-Georg Kräusslich / John A G Briggs /
Abstract: HIV-1 maturation occurs via multiple proteolytic cleavages of the Gag polyprotein, causing rearrangement of the virus particle required for infectivity. Cleavage results in beta-hairpin formation at ...HIV-1 maturation occurs via multiple proteolytic cleavages of the Gag polyprotein, causing rearrangement of the virus particle required for infectivity. Cleavage results in beta-hairpin formation at the N terminus of the CA (capsid) protein and loss of a six-helix bundle formed by the C terminus of CA and the neighboring SP1 peptide. How individual cleavages contribute to changes in protein structure and interactions, and how the mature, conical capsid forms, are poorly understood. Here, we employed cryoelectron tomography to determine morphology and high-resolution CA lattice structures for HIV-1 derivatives in which Gag cleavage sites are mutated. These analyses prompt us to revise current models for the crucial maturation switch. Unlike previously proposed, cleavage on either terminus of CA was sufficient, in principle, for lattice maturation, while complete processing was needed for conical capsid formation. We conclude that destabilization of the six-helix bundle, rather than beta-hairpin formation, represents the main determinant of structural maturation.
History
DepositionJul 31, 2018-
Header (metadata) releaseSep 5, 2018-
Map releaseSep 26, 2018-
UpdateOct 10, 2018-
Current statusOct 10, 2018Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.299
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.299
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0164.png

Downloads & links

-
Map

FileDownload / File: emd_0164.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the immature CA domain from HIV-1 MA-SP1 Gag proteolytic cleavage mutant virus particles
Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.299 / Movie #1: 0.299
Minimum - Maximum-0.48887178 - 0.9003156
Average (Standard dev.)0.00044535988 (±0.11472652)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 259.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z259.200259.200259.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.4890.9000.000

-
Supplemental data

-
Sample components

-
Entire : Human immunodeficiency virus 1

EntireName: Human immunodeficiency virus 1
Components
  • Virus: Human immunodeficiency virus 1
    • Protein or peptide: Gag polyproteinGroup-specific antigen

-
Supramolecule #1: Human immunodeficiency virus 1

SupramoleculeName: Human immunodeficiency virus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 11676 / Sci species name: Human immunodeficiency virus 1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Host systemOrganism: Homo sapiens (human) / Recombinant cell: HEK293T / Recombinant plasmid: pCHIV

-
Macromolecule #1: Gag polyprotein

MacromoleculeName: Gag polyprotein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MGARASVLSG GELDRWEKIR LRPGGKKKYK LKHIVWASRE LERFAVNPGL LETSEGCRQI LGQLQPSLQ TGSEELRSLY NTVATLYCVH QRIEIKDTKE ALDKIEEEQN KSKKKAQQAA A DTGHSNQV SQNIPIVQNI QGQMVHQAIS PRTLNAWVKV VEEKAFSPEV ...String:
MGARASVLSG GELDRWEKIR LRPGGKKKYK LKHIVWASRE LERFAVNPGL LETSEGCRQI LGQLQPSLQ TGSEELRSLY NTVATLYCVH QRIEIKDTKE ALDKIEEEQN KSKKKAQQAA A DTGHSNQV SQNIPIVQNI QGQMVHQAIS PRTLNAWVKV VEEKAFSPEV IPMFSALSEG AT PQDLNTM LNTVGGHQAA MQMLKETINE EAAEWDRVHP VHAGPIAPGQ MREPRGSDIA GTT STLQEQ IGWMTNNPPI PVGEIYKRWI ILGLNKIVRM YSPTSILDIR QGPKEPFRDY VDRF YKTLR AEQASQEVKN WMTETLLVQN ANPDCKTILK ALGPAATLEE MMTACQGVGG PGHKA RVIA EAISQVTNSA TIMMQRGNFR NQRKIVKCFN CGKEGHTARN CRAPRKKGCW KCGKEG HQM KDCTERQANF LGKIWPSYKG RPGNFLQSRP EPTAPPEESF RSGVETTTPP QKQEPID KE LYPLTSLRSL FGNDPSSQ

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
Details: The grid was glow discharged with a current of 20 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 288.15 K / Instrument: FEI VITROBOT MARK II

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.5 µm
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-10 / Average electron dose: 3.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

ExtractionNumber tomograms: 65 / Number images used: 610037
Method: Volumes picked on spherical mesh matching centre and radius of virions
Software: (Name: AV3, TOM Toolbox, UCSF Chimera, MATLAB)
Details: Volumes were picked by defining a spherical mesh to match the centre and radius of each virion, and randomising the in-plane Euler angle of particles seeded along the mesh.
CTF correctionSoftware: (Name: CTFFIND (ver. 4), CTFPHASEFLIP, NOVACTF)
Details: CTF correction was initially performed by phase-flipping using CTFFIND4, and these tomograms were used for subtomogram alignment. The final reconstruction was generated from tomograms CTF ...Details: CTF correction was initially performed by phase-flipping using CTFFIND4, and these tomograms were used for subtomogram alignment. The final reconstruction was generated from tomograms CTF corrected by CTF multiplication with astigmatism correction using novaCTF (Turonova et al, 2017).
Final angle assignmentType: OTHER / Software: (Name: AV3, TOM Toolbox)
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: AV3, TOM Toolbox) / Number subtomograms used: 88574
DetailsImages were collected in super-resolution mode and Fourier cropped to 3708 by 3708 pixels in SerialEM

+
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