Germany, Austria, United States, United Kingdom, 10 items
Organization
Grant number
Country
German Research Foundation
BR 3635/2-1
Germany
Austrian Science Fund
P31445
Austria
National Institutes of Health/National Institute of General Medical Sciences
R01-GM107013
United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases
R01-AI147890
United States
National Institutes of Health/National Institute of General Medical Sciences
P30-GM110758
United States
National Science Foundation (United States)
1659534
United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases
AI142263
United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases
P50AI150481
United States
Medical Research Council (United Kingdom)
MC_UP_1201/16
United Kingdom
European Research Council
ERC-2014-CoG 648432 - MEMBRANEFUSION
United Kingdom
Citation
Journal: PLoS Pathog / Year: 2020 Title: Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. Authors: Robert A Dick / Chaoyi Xu / Dustin R Morado / Vladyslav Kravchuk / Clifton L Ricana / Terri D Lyddon / Arianna M Broad / J Ryan Feathers / Marc C Johnson / Volker M Vogt / Juan R Perilla / ...Authors: Robert A Dick / Chaoyi Xu / Dustin R Morado / Vladyslav Kravchuk / Clifton L Ricana / Terri D Lyddon / Arianna M Broad / J Ryan Feathers / Marc C Johnson / Volker M Vogt / Juan R Perilla / John A G Briggs / Florian K M Schur / Abstract: Retrovirus assembly is driven by the multidomain structural protein Gag. Interactions between the capsid domains (CA) of Gag result in Gag multimerization, leading to an immature virus particle that ...Retrovirus assembly is driven by the multidomain structural protein Gag. Interactions between the capsid domains (CA) of Gag result in Gag multimerization, leading to an immature virus particle that is formed by a protein lattice based on dimeric, trimeric, and hexameric protein contacts. Among retroviruses the inter- and intra-hexamer contacts differ, especially in the N-terminal sub-domain of CA (CANTD). For HIV-1 the cellular molecule inositol hexakisphosphate (IP6) interacts with and stabilizes the immature hexamer, and is required for production of infectious virus particles. We have used in vitro assembly, cryo-electron tomography and subtomogram averaging, atomistic molecular dynamics simulations and mutational analyses to study the HIV-related lentivirus equine infectious anemia virus (EIAV). In particular, we sought to understand the structural conservation of the immature lentivirus lattice and the role of IP6 in EIAV assembly. Similar to HIV-1, IP6 strongly promoted in vitro assembly of EIAV Gag proteins into virus-like particles (VLPs), which took three morphologically highly distinct forms: narrow tubes, wide tubes, and spheres. Structural characterization of these VLPs to sub-4Å resolution unexpectedly showed that all three morphologies are based on an immature lattice with preserved key structural components, highlighting the structural versatility of CA to form immature assemblies. A direct comparison between EIAV and HIV revealed that both lentiviruses maintain similar immature interfaces, which are established by both conserved and non-conserved residues. In both EIAV and HIV-1, IP6 regulates immature assembly via conserved lysine residues within the CACTD and SP. Lastly, we demonstrate that IP6 stimulates in vitro assembly of immature particles of several other retroviruses in the lentivirus genus, suggesting a conserved role for IP6 in lentiviral assembly.
Download / File: emd_10386.map.gz / Format: CCP4 / Size: 135.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
Cryo-electron tomogram containing EIAV Gag-deltaMA spheres and tubes assembled at pH6
Voxel size
X=Y=Z: 8.328 Å
Density
Minimum - Maximum
-3434.792 - 3399.958
Average (Standard dev.)
103.01864 (±83.679924)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
0
0
50
Dimensions
464
464
165
Spacing
464
464
165
Cell
A: 3864.1921 Å / B: 3864.1921 Å / C: 1374.12 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
8.328
8.328
8.328
M x/y/z
464
464
165
origin x/y/z
0.000
0.000
0.000
length x/y/z
3864.192
3864.192
1374.120
α/β/γ
90.000
90.000
90.000
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
50
NC/NR/NS
464
464
165
D min/max/mean
-3434.792
3399.958
103.019
-
Supplemental data
-
Sample components
-
Entire : Equine infectious anemia virus
Entire
Name: Equine infectious anemia virus
Components
Virus: Equine infectious anemia virus
-
Supramolecule #1: Equine infectious anemia virus
Supramolecule
Name: Equine infectious anemia virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: Gag construct was expressed in E.coli and purified using the SUMO-tag system. Assembly was performed at pH6. NCBI-ID: 11665 / Sci species name: Equine infectious anemia virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host (natural)
Organism: Equus caballus (horse)
Host system
Organism: Escherichia coli (E. coli) / Recombinant strain: BL21
Virus shell
Shell ID: 1 / Name: Capsid / Diameter: 350.0 Å
-
Experimental details
-
Structure determination
Method
cryo EM
Processing
electron tomography
Aggregation state
particle
-
Sample preparation
Buffer
pH: 6 Component:
Concentration
Formula
Name
50.0 mM
MES
2-(N-morpholino)ethanesulfonic acid
100.0 mM
NaCl
Sodium chloride
2.0 mM
TCEP
tris(2-carboxyethyl)phosphine
Grid
Model: C-flat-2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: 20mA
Vitrification
Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 15 K / Instrument: FEI VITROBOT MARK II / Details: 1-2 seconds blot time, offset -3mm.
Details
Virus-like-particles (tubular) of EIAV Gag deltaMAdeltap9 (referred to as Gag deltaMA) assembled at pH6.
Sectioning
Other: NO SECTIONING
Fiducial marker
Manufacturer: BBI / Diameter: 10 nm
-
Electron microscopy
Microscope
FEI TITAN KRIOS
Specialist optics
Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Details
nanoprobe
Image recording
Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3708 pixel / Digitization - Dimensions - Height: 3838 pixel / Number grids imaged: 1 / Average exposure time: 1.4 sec. / Average electron dose: 3.4 e/Å2 Details: Data was acquired using a dose-symmetric tilt acquisition scheme, as described in Hagen et al, 2017, J. Struct. Biol, 197(2):191-8
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Tilt series were low-pass filtered according to their cumulative dose using exposure filters that were calculated using an exposure-dependent amplitude attenuation function and critical exposure constants (as published in Grant & Grigorieff, Elife, 2015). Tilt series were aligned and reconstructed in IMOD.
Final reconstruction
Algorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 41
CTF correction
Software: (Name: CTFFIND (ver. 4), NOVACTF) / Details: CTF-correction was performed using NOVACTF
+
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.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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
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