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- EMDB-3092: BG505 SOSIP.664 trimer in complex with PGT124 Fab with 32H heavy chain -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-3092 | |||||||||
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Title | BG505 SOSIP.664 trimer in complex with PGT124 Fab with 32H heavy chain | |||||||||
![]() | BG505 SOSIP.664 in complex with a PGT124 precursor Fab | |||||||||
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![]() | PGT124 / HIV-1 / broadly neutralizing antibody / Env | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 22.0 Å | |||||||||
![]() | Lee JH / Garces F / Wilson IA / Ward AB | |||||||||
![]() | ![]() Title: Affinity Maturation of a Potent Family of HIV Antibodies Is Primarily Focused on Accommodating or Avoiding Glycans. Authors: Fernando Garces / Jeong Hyun Lee / Natalia de Val / Alba Torrents de la Pena / Leopold Kong / Cristina Puchades / Yuanzi Hua / Robyn L Stanfield / Dennis R Burton / John P Moore / Rogier W ...Authors: Fernando Garces / Jeong Hyun Lee / Natalia de Val / Alba Torrents de la Pena / Leopold Kong / Cristina Puchades / Yuanzi Hua / Robyn L Stanfield / Dennis R Burton / John P Moore / Rogier W Sanders / Andrew B Ward / Ian A Wilson / ![]() ![]() Abstract: The high-mannose patch on the HIV-1 envelope (Env) glycoprotein is the epicenter for binding of the potent broadly neutralizing PGT121 family of antibodies, but strategies for generating such ...The high-mannose patch on the HIV-1 envelope (Env) glycoprotein is the epicenter for binding of the potent broadly neutralizing PGT121 family of antibodies, but strategies for generating such antibodies by vaccination have not been defined. We generated structures of inferred antibody intermediates by X-ray crystallography and electron microscopy to elucidate the molecular events that occurred during evolution of this family. Binding analyses revealed that affinity maturation was primarily focused on avoiding, accommodating, or binding the N137 glycan. The overall antibody approach angle to Env was defined very early in the maturation process, yet some variation evolved in the PGT121 family branches that led to differences in glycan specificities in their respective epitopes. Furthermore, we determined a crystal structure of the recombinant BG505 SOSIP.664 HIV-1 trimer with a PGT121 family member at 3.0 Å that, in concert with these antibody intermediate structures, provides insights to advance design of HIV vaccine candidates. | |||||||||
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 | ![]() | 14 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.3 KB 10.3 KB | Display Display | ![]() |
Images | ![]() | 354.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3093C ![]() 6379C ![]() 6380C ![]() 5cexC ![]() 5ceyC ![]() 5cezC C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | BG505 SOSIP.664 in complex with a PGT124 precursor Fab | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.05 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 : PGT124 32H+3L Fab in complex with BG505 SOSIP.664
Entire | Name: PGT124 32H+3L Fab in complex with BG505 SOSIP.664 |
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Components |
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-Supramolecule #1000: PGT124 32H+3L Fab in complex with BG505 SOSIP.664
Supramolecule | Name: PGT124 32H+3L Fab in complex with BG505 SOSIP.664 / type: sample / ID: 1000 / Oligomeric state: 3 Fabs bind one SOSIP trimer / Number unique components: 2 |
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Molecular weight | Theoretical: 570 MDa |
-Macromolecule #1: BG505 SOSIP.664 Env trimer
Macromolecule | Name: BG505 SOSIP.664 Env trimer / type: protein_or_peptide / ID: 1 / Name.synonym: BG505 SOSIP.664 / Number of copies: 1 / Oligomeric state: Trimer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 420 MDa |
Recombinant expression | Organism: Mammalian (mammals) / Recombinant cell: HEK293S |
-Macromolecule #2: PGT124 Fab with 32H heavy chain
Macromolecule | Name: PGT124 Fab with 32H heavy chain / type: protein_or_peptide / ID: 2 / Name.synonym: PGT124 32H-3L Details: One light and one heavy chain forms the Fab heterodimer Number of copies: 3 / Oligomeric state: Heterodimer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 50 KDa |
Recombinant expression | Organism: ![]() |
-Experimental details
-Structure determination
Method | negative staining |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.01 mg/mL |
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Buffer | pH: 7.4 / Details: 20 mM Tris, 150 mM NaCl |
Staining | Type: NEGATIVE Details: Grids adsorbed with protein then stained with 2% w/v uranyl formate |
Grid | Details: 400 mesh Cu grid with carbon support, plasma cleaned |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
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Electron microscopy
Microscope | FEI TECNAI 12 |
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Temperature | Average: 298 K |
Alignment procedure | Legacy - Astigmatism: Corrected at 52,000x mag |
Date | Jun 14, 2014 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 460 / Average electron dose: 25 e/Å2 |
Tilt angle min | 0 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus min: 0.7 µm / Nominal magnification: 52000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
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Image processing
Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: OTHER / Software - Name: Sparx / Number images used: 8719 |
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-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: ![]() |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |