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- EMDB-5019: Molecular Structure of Unliganded Native HIV-1 gp120 trimer: Spik... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-5019 | |||||||||
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Title | Molecular Structure of Unliganded Native HIV-1 gp120 trimer: Spike region | |||||||||
![]() | unliganded HIV-1 BaL spike | |||||||||
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![]() | HIV-1 / envelope glycoprotein. immunodeficiency virus / gp120 | |||||||||
Function / homology | ![]() Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / membrane Similarity search - Function | |||||||||
Biological species | envelope glycoprotein (unknown) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 20.0 Å | |||||||||
![]() | Bartesaghi A / Borgnia M / Liu J / Sapiro G / Subramaniam S | |||||||||
![]() | ![]() Title: Molecular architecture of native HIV-1 gp120 trimers. Authors: Jun Liu / Alberto Bartesaghi / Mario J Borgnia / Guillermo Sapiro / Sriram Subramaniam / ![]() Abstract: The envelope glycoproteins (Env) of human and simian immunodeficiency viruses (HIV and SIV, respectively) mediate virus binding to the cell surface receptor CD4 on target cells to initiate infection. ...The envelope glycoproteins (Env) of human and simian immunodeficiency viruses (HIV and SIV, respectively) mediate virus binding to the cell surface receptor CD4 on target cells to initiate infection. Env is a heterodimer of a transmembrane glycoprotein (gp41) and a surface glycoprotein (gp120), and forms trimers on the surface of the viral membrane. Using cryo-electron tomography combined with three-dimensional image classification and averaging, we report the three-dimensional structures of trimeric Env displayed on native HIV-1 in the unliganded state, in complex with the broadly neutralizing antibody b12 and in a ternary complex with CD4 and the 17b antibody. By fitting the known crystal structures of the monomeric gp120 core in the b12- and CD4/17b-bound conformations into the density maps derived by electron tomography, we derive molecular models for the native HIV-1 gp120 trimer in unliganded and CD4-bound states. We demonstrate that CD4 binding results in a major reorganization of the Env trimer, causing an outward rotation and displacement of each gp120 monomer. This appears to be coupled with a rearrangement of the gp41 region along the central axis of the trimer, leading to closer contact between the viral and target cell membranes. Our findings elucidate the structure and conformational changes of trimeric HIV-1 gp120 relevant to antibody neutralization and attachment to target cells. | |||||||||
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 | ![]() | 134.8 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.9 KB 9.9 KB | Display Display | ![]() |
Images | ![]() | 606.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3dnnMC ![]() 5018C ![]() 5020C ![]() 5021C ![]() 5022C ![]() 5023C ![]() 3dnlC ![]() 3dnoC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | unliganded HIV-1 BaL spike | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.1 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 : HIV-1 BaL virus
Entire | Name: HIV-1 BaL virus |
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Components |
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-Supramolecule #1000: HIV-1 BaL virus
Supramolecule | Name: HIV-1 BaL virus / type: sample / ID: 1000 Details: Structures determined by cryo-electron tomography combined with 3D averaging Number unique components: 1 |
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-Supramolecule #1: envelope glycoprotein
Supramolecule | Name: envelope glycoprotein / type: virus / ID: 1 / Name.synonym: envelope glycoprotein / Sci species name: envelope glycoprotein / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: envelope glycoprotein |
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Host (natural) | Organism: ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
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Sample preparation
Buffer | pH: 7.2 / Details: 0.01 M Tris, 0.1 M NaCl, 1 mM EDTA |
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Grid | Details: home-made holey carbon |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 77 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: Blot and plunge |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Average: 77 K |
Specialist optics | Energy filter - Name: Gatan / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Image recording | Category: CCD / Film or detector model: GENERIC CCD / Average electron dose: 80 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 34000 |
Sample stage | Specimen holder: Cartridge / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -70 ° / Tilt series - Axis1 - Max angle: 70 ° |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Image processing
Details | Average number of tilts used in the 3D reconstructions: 400. Average tomographic tilt angle increment: 1. |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMOD and in-house procedures |