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- EMDB-5418: Subunit organization of the membrane-bound HIV-1 envelope glycopr... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-5418 | |||||||||
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Title | Subunit organization of the membrane-bound HIV-1 envelope glycoprotein trimer | |||||||||
![]() | Reconstruction of the membrane-bound HIV-1 envelope glycoprotein trimer precursor | |||||||||
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![]() | HIV-1 / envelope glycoprotein / virus entry | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 10.8 Å | |||||||||
![]() | Mao Y / Wang L / Gu C / Herschhorn A / Xiang SH / Haim H / Yang X / Sodroski J | |||||||||
![]() | ![]() Title: Subunit organization of the membrane-bound HIV-1 envelope glycoprotein trimer. Authors: Youdong Mao / Liping Wang / Christopher Gu / Alon Herschhorn / Shi-Hua Xiang / Hillel Haim / Xinzhen Yang / Joseph Sodroski / ![]() Abstract: The trimeric human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env) spike is a molecular machine that mediates virus entry into host cells and is the sole target for virus- ...The trimeric human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env) spike is a molecular machine that mediates virus entry into host cells and is the sole target for virus-neutralizing antibodies. The mature Env spike results from cleavage of a trimeric glycoprotein precursor, gp160, into three gp120 and three gp41 subunits. Here, we describe an ~11-Å cryo-EM structure of the trimeric HIV-1 Env precursor in its unliganded state. The three gp120 and three gp41 subunits form a cage-like structure with an interior void surrounding the trimer axis. Interprotomer contacts are limited to the gp41 transmembrane region, the torus-like gp41 ectodomain and a trimer-association domain of gp120 composed of the V1, V2 and V3 variable regions. The cage-like architecture, which is unique among characterized viral envelope proteins, restricts antibody access, reflecting requirements imposed by HIV-1 persistence in the host. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 166.9 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.5 KB 10.5 KB | Display Display | ![]() |
Images | ![]() | 28.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of the membrane-bound HIV-1 envelope glycoprotein trimer precursor | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.99 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : The membrane-bound HIV-1 envelope glycoprotein trimer precursor
Entire | Name: The membrane-bound HIV-1 envelope glycoprotein trimer precursor |
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Components |
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-Supramolecule #1000: The membrane-bound HIV-1 envelope glycoprotein trimer precursor
Supramolecule | Name: The membrane-bound HIV-1 envelope glycoprotein trimer precursor type: sample / ID: 1000 Details: The membrane glycoprotein was monodisperse and solubilized in detergents. Oligomeric state: trimer / Number unique components: 1 |
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Molecular weight | Experimental: 440 KDa / Theoretical: 435 KDa / Method: Sedimentation, SDS-PAGE |
-Macromolecule #1: HIV-1 envelope glycoprotein trimer precursor
Macromolecule | Name: HIV-1 envelope glycoprotein trimer precursor / type: protein_or_peptide / ID: 1 / Name.synonym: Env trimer, gp160 trimer Details: The membrane glycoprotein is solubilized in detergents. Number of copies: 3 / Oligomeric state: trimer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 440 KDa / Theoretical: 435 KDa |
Recombinant expression | Organism: ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2.0 mg/mL |
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Buffer | pH: 7.4 / Details: 20 mM Tris-HCl, 300 mM NaCl, 0.01% Cymal-6 |
Grid | Details: 200 or 400 mesh copper grid with thin holey carbon support, glow discharged |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 93 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Min: 89 K / Max: 93 K / Average: 91 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 150,000 times magnification |
Date | Aug 1, 2009 |
Image recording | Category: CCD / Film or detector model: GENERIC GATAN (4k x 4k) / Average electron dose: 10 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 200835 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 150000 |
Sample stage | Specimen holder: CT3500 / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER, XIMPP / Number images used: 90306 |