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Yorodumi- EMDB-10383: A structure of the EIAV CA-SP hexamer (C2) from Gag-deltaMA tubes... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10383 | |||||||||||||||||||||||||||||||||
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Title | A structure of the EIAV CA-SP hexamer (C2) from Gag-deltaMA tubes assembled at pH6 | |||||||||||||||||||||||||||||||||
Map data | A 3.8 Angstrom structure of the EIAV CA-SP hexamer (C2) from Gag-dMA tubes assembled at pH6 | |||||||||||||||||||||||||||||||||
Sample |
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Function / homology | Function and homology information viral budding via host ESCRT complex / viral nucleocapsid / structural constituent of virion / nucleic acid binding / zinc ion binding Similarity search - Function | |||||||||||||||||||||||||||||||||
Biological species | Equine infectious anemia virus | |||||||||||||||||||||||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 3.8 Å | |||||||||||||||||||||||||||||||||
Authors | Dick RA / Xu C / Morado DR / Kravchuk V / Ricana CL / Lyddon TD / Broad AM / Feathers JR / Johnson MC / Vogt VM ...Dick RA / Xu C / Morado DR / Kravchuk V / Ricana CL / Lyddon TD / Broad AM / Feathers JR / Johnson MC / Vogt VM / Perilla JR / Briggs JAG / Schur FKM | |||||||||||||||||||||||||||||||||
Funding support | Austria, United States, United Kingdom, Germany, 10 items
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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. | |||||||||||||||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10383.map.gz | 46.7 MB | EMDB map data format | |
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Header (meta data) | emd-10383-v30.xml emd-10383.xml | 21.8 KB 21.8 KB | Display Display | EMDB header |
Images | emd_10383.png | 196 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10383 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10383 | HTTPS FTP |
-Related structure data
Related structure data | 6t63MC 6t61C 6t64C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10383.map.gz / Format: CCP4 / Size: 50.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | A 3.8 Angstrom structure of the EIAV CA-SP hexamer (C2) from Gag-dMA tubes assembled at pH6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.041 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Equine infectious anemia virus
Entire | Name: Equine infectious anemia virus |
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Components |
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-Supramolecule #1: Equine infectious anemia virus
Supramolecule | Name: Equine infectious anemia virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all 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 |
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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 |
-Macromolecule #1: Gag polyprotein
Macromolecule | Name: Gag polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO |
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Source (natural) | Organism: Equine infectious anemia virus |
Molecular weight | Theoretical: 54.881535 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGDPLTWSKA LKKLEKVTVQ GSQKLTTGNC NWALSLVDLF HDTNFVKEKD WQLRDVIPLL EDVTQTLSGQ EREAFERTWW AISAVKMGL QINNVVDGKA SFQLLRAKYE KKTANKKQSE PSEEYPIMID GAGNRNFRPL TPRGYTTWVN TIQTNGLLNE A SQNLFGIL ...String: MGDPLTWSKA LKKLEKVTVQ GSQKLTTGNC NWALSLVDLF HDTNFVKEKD WQLRDVIPLL EDVTQTLSGQ EREAFERTWW AISAVKMGL QINNVVDGKA SFQLLRAKYE KKTANKKQSE PSEEYPIMID GAGNRNFRPL TPRGYTTWVN TIQTNGLLNE A SQNLFGIL SVDCTSEEMN AFLDVVPGQA GQKQILLDAI DKIADDWDNR HPLPNAPLVA PPQGPIPMTA RFIRGLGVPR ER QMEPAFD QFRQTYRQWI IEAMSEGIKV MIGKPKAQNI RQGAKEPYPE FVDRLLSQIK SEGHPQEISK FLTDTLTIQN ANE ECRNAM RHLRPEDTLE EKMYACRDIG TTKQKMMLLA KALQTGLAGP FKGGALKGGP LKAAQTCYNC GKPGHLSSQC RAPK VCFKC KQPGHFSKQC RSVPKNGKQG AQGRPQKQTF PIQQKSQHNK SVVQETPQTQ NLYPDLSEIK KEYNVKEKDQ VEDLN LDSL WE |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6 Component:
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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. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: -3.5 µm / Nominal defocus min: -1.5 µm / Nominal magnification: 130000 |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Extraction | Number tomograms: 56 / Number images used: 357324 Method: Subvolumes were defined according to their position on the VLPs Software - Name: MATLAB / Software - details: partially based on the TOM toolbox Details: Subtomogram extraction positions were defined in Amira using the electron microscopy toolbox by determing the radii and the spline of the VLPs. Initially, positions were oversampled and ...Details: Subtomogram extraction positions were defined in Amira using the electron microscopy toolbox by determing the radii and the spline of the VLPs. Initially, positions were oversampled and subsequently cleaned during alignments using cross-correlation and distance thresholds. |
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CTF correction | Software: (Name: CTFFIND (ver. 4), NOVACTF) / Details: CTF-correction was performed using NOVACTF |
Final angle assignment | Type: PROJECTION MATCHING Projection matching processing - Number reference projections: 1 Projection matching processing - Merit function: CC / Software: (Name: AV3, TOM Toolbox) Details: Subtomogram alignment was performed as described in the published manuscript. |
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: AV3, TOM Toolbox) / Number subtomograms used: 112929 |
Details | 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. |
-Atomic model buiding 1
Initial model | PDB ID: |
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Details | Rigid body fitting was done in Chimera. Missing residues were built de novo in Coot. Refinement was performed iteratively in Phenix and Coot. |
Refinement | Space: REAL / Protocol: OTHER / Target criteria: Cross-correlation coefficient |
Output model | PDB-6t63: |