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Yorodumi- EMDB-1247: Distribution and three-dimensional structure of AIDS virus envelo... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1247 | |||||||||
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Title | Distribution and three-dimensional structure of AIDS virus envelope spikes. | |||||||||
Map data | 3D map of SIVmac239 viral membrane. It is acquired by subtracting the 3D averaged volume of "top/bottom view" spikes from averaged volume of the "side view" spikes (supplementary method of the reference) . Author's threshold 2.25. It should be loaded together with the associated SIVmac239 envelope spike map (SIVmac239_Env_spike.map, EMD-1246, author's threshold 2.65 ). | |||||||||
Sample |
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Biological species | Simian immunodeficiency virus | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 32.0 Å | |||||||||
Authors | Zhu P / Liu J / Bess J / Chertova E / Lifson JD / Grise H / Ofek GA / Taylor KA / Roux KH | |||||||||
Citation | Journal: Nature / Year: 2006 Title: Distribution and three-dimensional structure of AIDS virus envelope spikes. Authors: Ping Zhu / Jun Liu / Julian Bess / Elena Chertova / Jeffrey D Lifson / Henry Grisé / Gilad A Ofek / Kenneth A Taylor / Kenneth H Roux / Abstract: Envelope glycoprotein (Env) spikes on AIDS retroviruses initiate infection of host cells and are therefore targets for vaccine development. Though crystal structures for partial Env subunits are ...Envelope glycoprotein (Env) spikes on AIDS retroviruses initiate infection of host cells and are therefore targets for vaccine development. Though crystal structures for partial Env subunits are known, the structure and distribution of native Env spikes on virions is obscure. We applied cryoelectron microscopy tomography to define ultrastructural details of spikes. Virions of wild-type human immunodeficiency virus 1 (HIV-1) and a mutant simian immunodeficiency virus (SIV) had approximately 14 and approximately 73 spikes per particle, respectively, with some clustering of HIV-1 spikes. Three-dimensional averaging showed that the surface glycoprotein (gp120) 'head' of each subunit of the trimeric SIV spike contains a primary mass, with two secondary lobes. The transmembrane glycoprotein 'stalk' of each trimer is composed of three independent legs that project obliquely from the trimer head, tripod-like. Reconciling available atomic structures with the three-dimensional whole spike density map yields insights into the orientation of Env spike structural elements and possible structural bases of their functions. | |||||||||
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_1247.map.gz | 687.2 KB | EMDB map data format | |
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Header (meta data) | emd-1247-v30.xml emd-1247.xml | 11 KB 11 KB | Display Display | EMDB header |
Images | 1247.gif | 35.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1247 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1247 | HTTPS FTP |
-Validation report
Summary document | emd_1247_validation.pdf.gz | 194.1 KB | Display | EMDB validaton report |
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Full document | emd_1247_full_validation.pdf.gz | 193.3 KB | Display | |
Data in XML | emd_1247_validation.xml.gz | 5.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1247 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1247 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1247.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 3D map of SIVmac239 viral membrane. It is acquired by subtracting the 3D averaged volume of "top/bottom view" spikes from averaged volume of the "side view" spikes (supplementary method of the reference) . Author's threshold 2.25. It should be loaded together with the associated SIVmac239 envelope spike map (SIVmac239_Env_spike.map, EMD-1246, author's threshold 2.65 ). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 5.56 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 : Membrane of SIVmac239 virus with truncated cytoplasmic tail
Entire | Name: Membrane of SIVmac239 virus with truncated cytoplasmic tail |
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Components |
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-Supramolecule #1000: Membrane of SIVmac239 virus with truncated cytoplasmic tail
Supramolecule | Name: Membrane of SIVmac239 virus with truncated cytoplasmic tail type: sample / ID: 1000 Details: The virus was AT-2 treated to eliminate the infectivity. Number unique components: 1 |
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-Supramolecule #1: Simian immunodeficiency virus
Supramolecule | Name: Simian immunodeficiency virus / type: virus / ID: 1 / Name.synonym: SIVmac239 membrane / NCBI-ID: 11723 / Sci species name: Simian immunodeficiency virus / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: SIVmac239 membrane |
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Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
-Sample preparation
Buffer | Details: PBS |
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Grid | Details: 200 mesh Quantifoil R2/1 copper grid |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Home made plunger |
-Electron microscopy
Microscope | FEI/PHILIPS CM300FEG/ST |
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Details | Minimum tilt angle was -70 |
Date | Aug 30, 2004 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F224 (2k x 2k) / Number real images: 80 / Average electron dose: 60 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 43200 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm |
Sample stage | Specimen holder: Gatan 626 cryoholder / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: 70 ° / Tilt series - Axis1 - Max angle: 70 ° |
-Image processing
Details | The tomographic tilt angle increment was determined by cosine rule, i.e., ~2-3 degrees increment around low tilt angles and <1 degree increment in the high tilt angles. Average number of tilts used in the 3D reconstructions: 80. Average tomographic tilt angle increment: 2. |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 32.0 Å / Resolution method: OTHER / Software - Name: Protomo Details: The resolution of the final averaged map, determined by Fourier shell correlation (based on a cutoff value of 0.5)is 2.5 nm and, after low pass filtering to the estimated first node in the ...Details: The resolution of the final averaged map, determined by Fourier shell correlation (based on a cutoff value of 0.5)is 2.5 nm and, after low pass filtering to the estimated first node in the contrast transfer function, 3.2 nm. |
-Atomic model buiding 1
Initial model |
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Software | Name: Chimera | ||||||||
Details | PDBEntryID_givenInChain. The gp120 core and 2F5 and 4E10 peptides structure were fittted by manual docking using program chimera and then applied 3-fold symmetry around Z axis. | ||||||||
Refinement | Protocol: RIGID BODY FIT |