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- EMDB-5779: Cryo-EM structure of the BG505 SOSIP.664 HIV-1 Env trimer with 3 ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-5779 | |||||||||
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Title | Cryo-EM structure of the BG505 SOSIP.664 HIV-1 Env trimer with 3 PGV04 Fabs | |||||||||
![]() | Cryo-EM structure of a fully glycosylated SOSIP.664 Env trimer with 3 broadly neutralizing PGV04 Fabs | |||||||||
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![]() | HIV-1 trimeric spike / gp140 / SOSIP / broadly neutralizing antibody / PGV04 / Env / Envelope glycoprotein | |||||||||
Function / homology | ![]() positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / 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 ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / 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 / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.8 Å | |||||||||
![]() | Lyumkis D / Julien JP / de Val N / Cupo A / Potter CS / Klasse PJ / Burton DR / Sanders RW / Moore JP / Carragher B ...Lyumkis D / Julien JP / de Val N / Cupo A / Potter CS / Klasse PJ / Burton DR / Sanders RW / Moore JP / Carragher B / Wilson IA / Ward AB | |||||||||
![]() | ![]() Title: Cryo-EM structure of a fully glycosylated soluble cleaved HIV-1 envelope trimer. Authors: Dmitry Lyumkis / Jean-Philippe Julien / Natalia de Val / Albert Cupo / Clinton S Potter / Per-Johan Klasse / Dennis R Burton / Rogier W Sanders / John P Moore / Bridget Carragher / Ian A ...Authors: Dmitry Lyumkis / Jean-Philippe Julien / Natalia de Val / Albert Cupo / Clinton S Potter / Per-Johan Klasse / Dennis R Burton / Rogier W Sanders / John P Moore / Bridget Carragher / Ian A Wilson / Andrew B Ward / ![]() Abstract: The HIV-1 envelope glycoprotein (Env) trimer contains the receptor binding sites and membrane fusion machinery that introduce the viral genome into the host cell. As the only target for broadly ...The HIV-1 envelope glycoprotein (Env) trimer contains the receptor binding sites and membrane fusion machinery that introduce the viral genome into the host cell. As the only target for broadly neutralizing antibodies (bnAbs), Env is a focus for rational vaccine design. We present a cryo-electron microscopy reconstruction and structural model of a cleaved, soluble Env trimer (termed BG505 SOSIP.664 gp140) in complex with a CD4 binding site (CD4bs) bnAb, PGV04, at 5.8 angstrom resolution. The structure reveals the spatial arrangement of Env components, including the V1/V2, V3, HR1, and HR2 domains, as well as shielding glycans. The structure also provides insights into trimer assembly, gp120-gp41 interactions, and the CD4bs epitope cluster for bnAbs, which covers a more extensive area and defines a more complex site of vulnerability than previously described. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 56.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.7 KB 13.7 KB | Display Display | ![]() |
Images | ![]() | 175.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3j5mMC ![]() 5780C ![]() 5781C ![]() 5782C 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 | Cryo-EM structure of a fully glycosylated SOSIP.664 Env trimer with 3 broadly neutralizing PGV04 Fabs | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.21 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 : Fully glycosylated BG505 SOSIP.664 Envelope trimer with 3 broadly...
Entire | Name: Fully glycosylated BG505 SOSIP.664 Envelope trimer with 3 broadly neutralizing PGV04 Fabs |
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Components |
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-Supramolecule #1000: Fully glycosylated BG505 SOSIP.664 Envelope trimer with 3 broadly...
Supramolecule | Name: Fully glycosylated BG505 SOSIP.664 Envelope trimer with 3 broadly neutralizing PGV04 Fabs type: sample / ID: 1000 Oligomeric state: three SOSIP.664 gp140 subunits (trimeric HIV-1 spike) with 3 PGV04 Fabs Number unique components: 2 |
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Molecular weight | Theoretical: 600 KDa |
-Macromolecule #1: BG505 SOSIP.664 HIV-1 Envelope glycoprotein gp140
Macromolecule | Name: BG505 SOSIP.664 HIV-1 Envelope glycoprotein gp140 / type: protein_or_peptide / ID: 1 / Name.synonym: Env / Number of copies: 3 / Oligomeric state: trimer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 600 KDa |
Recombinant expression | Organism: ![]() |
-Macromolecule #2: Fragment antigen binding
Macromolecule | Name: Fragment antigen binding / type: protein_or_peptide / ID: 2 / Name.synonym: Fab / Number of copies: 3 / Oligomeric state: heterodimer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() |
Molecular weight | Experimental: 50 KDa / Theoretical: 50 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 | 0.72 mg/mL |
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Buffer | pH: 7.6 / Details: 20 mM Tris, 150 mM NaCl, 0.085 mM DDM |
Grid | Details: 400 mesh C-Flat CF-22-4C, plasma treated for 5 seconds |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER Method: Specimen was prepared for cryo-EM by applying 3 microliters of sample to a freshly plasma cleaned holey carbon C-flat grid (Protochips, Inc.), allowing the sample to adsorb to the grid for 30 ...Method: Specimen was prepared for cryo-EM by applying 3 microliters of sample to a freshly plasma cleaned holey carbon C-flat grid (Protochips, Inc.), allowing the sample to adsorb to the grid for 30 seconds, followed by blotting with a small piece of filter paper and plunge-freezing into liquid ethane using a manual cryo-plunger in an ambient environment (4 degrees C). |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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Alignment procedure | Legacy - Astigmatism: objective lens astigmatism was corrected by observing Thon rings with the Leginon software |
Details | electron counting mode |
Date | Feb 21, 2013 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Digitization - Sampling interval: 5.0 µm / Number real images: 6355 / Average electron dose: 32 e/Å2 Details: The dose was fractionated over 20 raw frames collected over a 5-second exposure time (250 ms per frame) on the Gatan K2 Summit direct detection device, with each frame receiving a dose of ~9. ...Details: The dose was fractionated over 20 raw frames collected over a 5-second exposure time (250 ms per frame) on the Gatan K2 Summit direct detection device, with each frame receiving a dose of ~9.4 e-/pixel/sec. The individual frames were aligned using a GPU-enabled frame-alignment program that was generously provided by Yifan Cheng and Xueming Li. This program was used to track the global shifts between individual frames. |
Tilt angle min | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 29000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 29000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Image processing
Details | Reconstructed using resolution-limited refinement procedure implemented in Xmipp and Frealign. |
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CTF correction | Details: Frealign |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Xmipp, Frealign Details: Final maps were calculated after sorting for the presence of sub-stoichiometrically labeled trimers. Number images used: 49572 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Refinement | Space: REAL |
Output model | ![]() PDB-3j5m: |
-Atomic model buiding 2
Initial model | PDB ID: |
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Refinement | Space: REAL |
Output model | ![]() PDB-3j5m: |
-Atomic model buiding 3
Initial model | PDB ID: |
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Refinement | Space: REAL |
Output model | ![]() PDB-3j5m: |