+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2863 | |||||||||
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Title | Surface rendered vitrified native Env | |||||||||
Map data | Surface rendered vitrified native Env | |||||||||
Sample |
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Keywords | Cryo-electron microscopy / Env trimers / image processing / isomerization arrested state / receptor binding domain | |||||||||
Biological species | Moloney murine leukemia virus | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 19.0 Å | |||||||||
Authors | Wu S-R / Sjoberg M / Wallin M / Lindqvist B / Ekstrom M / Hebert H / Koeck P / Garoff H | |||||||||
Citation | Journal: EMBO J / Year: 2008 Title: Turning of the receptor-binding domains opens up the murine leukaemia virus Env for membrane fusion. Authors: Shang-Rung Wu / Mathilda Sjöberg / Michael Wallin / Birgitta Lindqvist / Maria Ekström / Hans Hebert / Philip J B Koeck / Henrik Garoff / Abstract: The activity of the membrane fusion protein Env of Moloney mouse leukaemia virus is controlled by isomerization of the disulphide that couples its transmembrane (TM) and surface (SU) subunits. We ...The activity of the membrane fusion protein Env of Moloney mouse leukaemia virus is controlled by isomerization of the disulphide that couples its transmembrane (TM) and surface (SU) subunits. We have arrested Env activation at a stage prior to isomerization by alkylating the active thiol in SU and compared the structure of isomerization-arrested Env with that of native Env. Env trimers of respective form were isolated from solubilized particles by sedimentation and their structures were reconstructed from electron microscopic images of both vitrified and negatively stained samples. We found that the protomeric unit of both trimers formed three protrusions, a top, middle and a lower one. The atomic structure of the receptor-binding domain of SU fitted into the upper protrusion. This was formed similar to a bent finger. Significantly, in native Env the tips of the fingers were directed against each other enclosing a cavity below, whereas they had turned outward in isomerization-arrested Env transforming the cavity into an open well. This might subsequently guide the fusion peptides in extended TM subunits into the target membrane. | |||||||||
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_2863.map.gz | 369.9 KB | EMDB map data format | |
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Header (meta data) | emd-2863-v30.xml emd-2863.xml | 9.9 KB 9.9 KB | Display Display | EMDB header |
Images | emd-2863.gif | 45.9 KB | ||
Others | emd_2863_additional_1.map.gz | 376.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2863 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2863 | HTTPS FTP |
-Validation report
Summary document | emd_2863_validation.pdf.gz | 207.5 KB | Display | EMDB validaton report |
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Full document | emd_2863_full_validation.pdf.gz | 206.7 KB | Display | |
Data in XML | emd_2863_validation.xml.gz | 4.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2863 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2863 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2863.map.gz / Format: CCP4 / Size: 422.9 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Surface rendered vitrified native Env | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.76835 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Supplemental map: emd 2863 additional 1.map
File | emd_2863_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Native Env
Entire | Name: Native Env |
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Components |
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-Supramolecule #1000: Native Env
Supramolecule | Name: Native Env / type: sample / ID: 1000 / Oligomeric state: Trimer / Number unique components: 1 |
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Molecular weight | Experimental: 200 KDa / Method: Gel electrophoresis |
-Macromolecule #1: Moloney murine leukemia virus
Macromolecule | Name: Moloney murine leukemia virus / type: protein_or_peptide / ID: 1 / Name.synonym: Mo-MLV Env Details: Moloney murine leukemia virus ICTvDb ID 00.061.1.02.014.00.001. Number of copies: 3 / Oligomeric state: Trimer / Recombinant expression: No |
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Source (natural) | Organism: Moloney murine leukemia virus / Tissue: Virus / Cell: MOV-3, NIH 3T3 |
Molecular weight | Experimental: 200 KDa |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 Details: 20 mM HEPES, 135 mM NaCl, pH 7.45, 1.8 mM CaCl2, 0.15 % Triton X-100, 12 % (w/w) sucrose |
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Staining | Type: NEGATIVE / Details: No staining |
Grid | Details: 400 mesh grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 77 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: Blot for 3 seconds twice before plunging |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Min: 93 K / Max: 96 K / Average: 95 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected using online FFT |
Date | May 10, 2008 |
Image recording | Category: CCD / Film or detector model: GENERIC CCD / Digitization - Sampling interval: 30 µm / Number real images: 80 / Average electron dose: 9 e/Å2 / Bits/pixel: 8 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 86000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 7057 |
Final two d classification | Number classes: 131 |