[English] 日本語
Yorodumi
- EMDB-4016: A 4.5 Angstrom structure of HIV-1 CA-SP1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4016
TitleA 4.5 Angstrom structure of HIV-1 CA-SP1
Map data
Sample
  • Virus: Human immunodeficiency virus 1
    • Protein or peptide: HIV-1 deltaMACANCSP2
Biological speciesHuman immunodeficiency virus 1
Methodsubtomogram averaging / cryo EM / Resolution: 4.5 Å
AuthorsSchur FKM / Obr M / Hagen WJH / Wan W / Arjen JJ / Kirkpatrick JM / Sachse C / Kraeusslich H-G / Briggs JAG
CitationJournal: Science / Year: 2016
Title: An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation.
Authors: Florian K M Schur / Martin Obr / Wim J H Hagen / William Wan / Arjen J Jakobi / Joanna M Kirkpatrick / Carsten Sachse / Hans-Georg Kräusslich / John A G Briggs /
Abstract: Immature HIV-1 assembles at and buds from the plasma membrane before proteolytic cleavage of the viral Gag polyprotein induces structural maturation. Maturation can be blocked by maturation ...Immature HIV-1 assembles at and buds from the plasma membrane before proteolytic cleavage of the viral Gag polyprotein induces structural maturation. Maturation can be blocked by maturation inhibitors (MIs), thereby abolishing infectivity. The CA (capsid) and SP1 (spacer peptide 1) region of Gag is the key regulator of assembly and maturation and is the target of MIs. We applied optimized cryo-electron tomography and subtomogram averaging to resolve this region within assembled immature HIV-1 particles at 3.9 angstrom resolution and built an atomic model. The structure reveals a network of intra- and intermolecular interactions mediating immature HIV-1 assembly. The proteolytic cleavage site between CA and SP1 is inaccessible to protease. We suggest that MIs prevent CA-SP1 cleavage by stabilizing the structure, and MI resistance develops by destabilizing CA-SP1.
History
DepositionJun 9, 2016-
Header (metadata) releaseJul 13, 2016-
Map releaseJul 20, 2016-
UpdateNov 28, 2018-
Current statusNov 28, 2018Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.331
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.331
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_4016.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.331 / Movie #1: 0.331
Minimum - Maximum-0.7111671 - 1.2737906
Average (Standard dev.)0.014012828 (±0.12550773)
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-0.7111.2740.014

-
Supplemental data

-
Sample components

-
Entire : Human immunodeficiency virus 1

EntireName: Human immunodeficiency virus 1
Components
  • Virus: Human immunodeficiency virus 1
    • Protein or peptide: HIV-1 deltaMACANCSP2

-
Supramolecule #1: Human immunodeficiency virus 1

SupramoleculeName: Human immunodeficiency virus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Virus-like particles were obtained by in vitro assembly of a truncated Gag construct (deltaMACANCSP2)
NCBI-ID: 11676 / Sci species name: Human immunodeficiency virus 1 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Host systemOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET11C

-
Macromolecule #1: HIV-1 deltaMACANCSP2

MacromoleculeName: HIV-1 deltaMACANCSP2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: SPRTLNAWVK VVEEKAFSPE VIPMFSALSE GATPQDLNTM LNTVGGHQAA MQMLKETINE EAAEWDRLH PVHAGPIAPG QMREPRGSDI AGTTSTLQEQ IGWMTHNPPI PVGEIYKRWI I LGLNKIVR MYSPTSILDI RQGPKEPFRD YVDRFYKTLR AEQASQEVKN ...String:
SPRTLNAWVK VVEEKAFSPE VIPMFSALSE GATPQDLNTM LNTVGGHQAA MQMLKETINE EAAEWDRLH PVHAGPIAPG QMREPRGSDI AGTTSTLQEQ IGWMTHNPPI PVGEIYKRWI I LGLNKIVR MYSPTSILDI RQGPKEPFRD YVDRFYKTLR AEQASQEVKN WMTETLLVQN AN PDCKTIL KALGPGATLE EMMTACQGVG GPGHKARVLA EAMSQVT

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

-
Sample preparation

Concentration5 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
50.0 mMHEPES
100.0 mMSodium ChlorideNaClSodium chloride
1.0 mMEDTAEthylenediaminetetraacetic acid
1.0 mMTCEP

Details: Virus-like particles were assembled in the presence of nucleic acid (73mer oligonucleotide, 1:10 molar ratio oligonucleotide:protein).
GridModel: C-flat / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Details: at 20 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 15 K / Instrument: FEI VITROBOT MARK II
Details: 10nM colloidal gold was added to the sample prior to plunge freezing..
DetailsVirus-like particles were assembled in vitro

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
DetailsNanoprobe
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 6-10 / Number grids imaged: 1 / Average exposure time: 1.0 sec. / Average electron dose: 5.0 e/Å2
Details: Number of frames ranged from 6-10 Exposure time per tilt ranged from 0.6 to 1.0 seconds
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

ExtractionNumber tomograms: 93 / Number images used: 461868
Details: Subtomograms were extracted from the surface of each particle according to the determined radius of the particle.
CTF correctionSoftware:
Namedetails
CTFFIND (ver. 4)CTF determination
CTFPHASEFLIPCTF correction within IMOD

Details: CTF correction was performed using the ctfphaseflip program in IMOD prior to backprojection.
Final angle assignmentType: OTHER / Software: (Name: AV3, TOM Toolbox) / Details: Cross-correlation based template matching
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: AV3, TOM Toolbox) / Number subtomograms used: 88236
DetailsFrames were aligned using MotionCorr. Tilts in a tilt series were exposure filtered for cumulative electron dose. Tomograms were reconstructed using 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