[English] 日本語
Yorodumi- EMDB-3093: BG505 SOSIP.664 N137A trimer in complex with PGT124 Fab with 3H h... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3093 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | BG505 SOSIP.664 N137A trimer in complex with PGT124 Fab with 3H heavy chain | |||||||||
Map data | Reconstruction of PGT124 H3 Fab in complex with BG505 SOSIP.664 N137A | |||||||||
Sample |
| |||||||||
Keywords | PGT124 / HIV-1 / broadly neutralizing antibody / Env | |||||||||
Biological species | Human Immunodeficiency Virus-1 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 17.0 Å | |||||||||
Authors | Lee JH / Garces F / Wilson IA / Ward AB | |||||||||
Citation | Journal: Immunity / Year: 2015 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3093.map.gz | 13.9 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-3093-v30.xml emd-3093.xml | 10.6 KB 10.6 KB | Display Display | EMDB header |
Images | emd_3093.png | 339.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3093 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3093 | HTTPS FTP |
-Validation report
Summary document | emd_3093_validation.pdf.gz | 207.5 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_3093_full_validation.pdf.gz | 206.6 KB | Display | |
Data in XML | emd_3093_validation.xml.gz | 5.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3093 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3093 | HTTPS FTP |
-Related structure data
Related structure data | 3092C 6379C 6380C 5cexC 5ceyC 5cezC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_3093.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Reconstruction of PGT124 H3 Fab in complex with BG505 SOSIP.664 N137A | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : PGT124 3H+3L Fab in complex with BG505 SOSIP.664 N137A
Entire | Name: PGT124 3H+3L Fab in complex with BG505 SOSIP.664 N137A |
---|---|
Components |
|
-Supramolecule #1000: PGT124 3H+3L Fab in complex with BG505 SOSIP.664 N137A
Supramolecule | Name: PGT124 3H+3L Fab in complex with BG505 SOSIP.664 N137A type: sample / ID: 1000 / Oligomeric state: 3 Fabs bind one SOSIP trimer / Number unique components: 2 |
---|---|
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 / Details: Has N137A mutation / Number of copies: 1 / Oligomeric state: Trimer / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Human Immunodeficiency Virus-1 / Strain: BG505 / synonym: HIV-1 |
Molecular weight | Theoretical: 420 MDa |
Recombinant expression | Organism: Mammalian (mammals) / Recombinant cell: HEK293S |
-Macromolecule #2: PGT124 Antibody
Macromolecule | Name: PGT124 Antibody / type: protein_or_peptide / ID: 2 / Name.synonym: PGT124 Details: The Fab has a heavy chain (H3) and light chain (L3) pairing, from the PGT124 lineage. Number of copies: 3 / Oligomeric state: heterodimer / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Theoretical: 50 MDa |
Recombinant expression | Organism: Mammalian (mammals) / Recombinant cell: HEK293F |
-Experimental details
-Structure determination
Method | negative staining |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.01 mg/mL |
---|---|
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 |
-Electron microscopy
Microscope | FEI TECNAI 12 |
---|---|
Temperature | Average: 298 K |
Alignment procedure | Legacy - Astigmatism: Corrected at 52,000x mag |
Date | Aug 31, 2014 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 343 / 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 max: 0.9 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 52000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
-Image processing
Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: OTHER / Software - Name: Sparx / Number images used: 27577 |
---|
-Atomic model buiding 1
Initial model | PDB ID: |
---|---|
Software | Name: Chimera |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |