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Yorodumi- EMDB-1814: Structural Comparison of HIV-1 Envelope Spikes with and without t... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1814 | |||||||||
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Title | Structural Comparison of HIV-1 Envelope Spikes with and without the V1V2 Loop | |||||||||
Map data | This is a map for HIV-1 Envelope spike with the v1v2 loop deleted | |||||||||
Sample |
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Keywords | Structural classification | |||||||||
Biological species | Human immunodeficiency virus 1 | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 33.0 Å | |||||||||
Authors | Hu G / Liu J / Taylor KA / Roux KH | |||||||||
Citation | Journal: J Virol / Year: 2011 Title: Structural comparison of HIV-1 envelope spikes with and without the V1/V2 loop. Authors: Guiqing Hu / Jun Liu / Kenneth A Taylor / Kenneth H Roux / Abstract: We have used cryoelectron tomography of vitreous-ice-embedded HIV-1 virions to compare the envelope (Env) spikes of a wild-type strain with those of a mutant strain in which the V1/V2 loop has been ...We have used cryoelectron tomography of vitreous-ice-embedded HIV-1 virions to compare the envelope (Env) spikes of a wild-type strain with those of a mutant strain in which the V1/V2 loop has been deleted. Deletion of V1/V2 results in a spike with far more structural heterogeneity than is observed in the wild type, likely reflecting greatly enhanced gp120 protomer flexibility. A major difference between the two forms is a pronounced loss of mass from the "peak" of the native Env spike. The apparent loss of contact among three gp120 protomers likely accounts for the more open structure, heterogeneity in configuration, and previous observations that broadly neutralizing epitopes and reactive sites on other structural elements are more exposed in such constructs. | |||||||||
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_1814.map.gz | 214.5 KB | EMDB map data format | |
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Header (meta data) | emd-1814-v30.xml emd-1814.xml | 7.3 KB 7.3 KB | Display Display | EMDB header |
Images | emd_1814.png | 90 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1814 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1814 | HTTPS FTP |
-Validation report
Summary document | emd_1814_validation.pdf.gz | 187.3 KB | Display | EMDB validaton report |
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Full document | emd_1814_full_validation.pdf.gz | 186.4 KB | Display | |
Data in XML | emd_1814_validation.xml.gz | 4.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1814 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1814 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1814.map.gz / Format: CCP4 / Size: 230.5 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a map for HIV-1 Envelope spike with the v1v2 loop deleted | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.6 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 : HIV-1 R3A deleteV1V2 virus
Entire | Name: HIV-1 R3A deleteV1V2 virus |
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Components |
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-Supramolecule #1000: HIV-1 R3A deleteV1V2 virus
Supramolecule | Name: HIV-1 R3A deleteV1V2 virus / type: sample / ID: 1000 / Details: Sample is ice-embeded / Number unique components: 1 |
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-Supramolecule #1: Envelope glycoprotein
Supramolecule | Name: Envelope glycoprotein / type: organelle_or_cellular_component / ID: 1 / Name.synonym: HIV-1 virus / Recombinant expression: Yes / Database: NCBI |
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Source (natural) | Organism: Human immunodeficiency virus 1 / Strain: R3A |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
-Sample preparation
Vitrification | Cryogen name: ETHANE / Instrument: OTHER |
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-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Category: CCD / Film or detector model: GENERIC CCD / Average electron dose: 100 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder: Multi-specimen holer / Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 33.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Protomo and I3 |
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-Atomic model buiding 1
Initial model | PDB ID: |
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Refinement | Space: REAL |