[English] 日本語
Yorodumi- EMDB-2331: Negative stain reconstruction of BG505 SOSIP gp140 HIV-1 trimer i... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2331 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Negative stain reconstruction of BG505 SOSIP gp140 HIV-1 trimer in complex with PGT135 Fab | |||||||||
Map data | Reconstruction of PGT135-BG505 SOSIP complex | |||||||||
Sample |
| |||||||||
Keywords | HIV / SOSIP / broadly neutralizing antibodies | |||||||||
Biological species | Human immunodeficiency virus 1 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 20.0 Å | |||||||||
Authors | Lee JH / Kong L / Murin CD / Cupo A / Moore JP / Wilson IA / Ward AB | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2013 Title: Supersite of immune vulnerability on the glycosylated face of HIV-1 envelope glycoprotein gp120. Authors: Leopold Kong / Jeong Hyun Lee / Katie J Doores / Charles D Murin / Jean-Philippe Julien / Ryan McBride / Yan Liu / Andre Marozsan / Albert Cupo / Per-Johan Klasse / Simon Hoffenberg / ...Authors: Leopold Kong / Jeong Hyun Lee / Katie J Doores / Charles D Murin / Jean-Philippe Julien / Ryan McBride / Yan Liu / Andre Marozsan / Albert Cupo / Per-Johan Klasse / Simon Hoffenberg / Michael Caulfield / C Richter King / Yuanzi Hua / Khoa M Le / Reza Khayat / Marc C Deller / Thomas Clayton / Henry Tien / Ten Feizi / Rogier W Sanders / James C Paulson / John P Moore / Robyn L Stanfield / Dennis R Burton / Andrew B Ward / Ian A Wilson / Abstract: A substantial proportion of the broadly neutralizing antibodies (bnAbs) identified in certain HIV-infected donors recognize glycan-dependent epitopes on HIV-1 gp120. Here we elucidate how the bnAb ...A substantial proportion of the broadly neutralizing antibodies (bnAbs) identified in certain HIV-infected donors recognize glycan-dependent epitopes on HIV-1 gp120. Here we elucidate how the bnAb PGT 135 binds its Asn332 glycan-dependent epitope from its 3.1-Å crystal structure with gp120, CD4 and Fab 17b. PGT 135 interacts with glycans at Asn332, Asn392 and Asn386, using long CDR loops H1 and H3 to penetrate the glycan shield and access the gp120 protein surface. EM reveals that PGT 135 can accommodate the conformational and chemical diversity of gp120 glycans by altering its angle of engagement. Combined structural studies of PGT 135, PGT 128 and 2G12 show that this Asn332-dependent antigenic region is highly accessible and much more extensive than initially appreciated, which allows for multiple binding modes and varied angles of approach; thereby it represents a supersite of vulnerability for antibody neutralization. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2331.map.gz | 11.1 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-2331-v30.xml emd-2331.xml | 11.6 KB 11.6 KB | Display Display | EMDB header |
Images | emd_2331.png | 112 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2331 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2331 | HTTPS FTP |
-Validation report
Summary document | emd_2331_validation.pdf.gz | 192.6 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_2331_full_validation.pdf.gz | 191.7 KB | Display | |
Data in XML | emd_2331_validation.xml.gz | 5.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2331 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2331 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_2331.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Reconstruction of PGT135-BG505 SOSIP complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.18 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : PGT135 Fab fragment bound to HIV-1 clade A BG505 background SOSIP...
Entire | Name: PGT135 Fab fragment bound to HIV-1 clade A BG505 background SOSIP gp140 trimer. |
---|---|
Components |
|
-Supramolecule #1000: PGT135 Fab fragment bound to HIV-1 clade A BG505 background SOSIP...
Supramolecule | Name: PGT135 Fab fragment bound to HIV-1 clade A BG505 background SOSIP gp140 trimer. type: sample / ID: 1000 / Oligomeric state: One Fab binds one gp140 monomer / Number unique components: 2 |
---|---|
Molecular weight | Theoretical: 500 KDa |
-Macromolecule #1: HIV-1 SOSIP.664 gp140
Macromolecule | Name: HIV-1 SOSIP.664 gp140 / type: protein_or_peptide / ID: 1 / Details: co-expressed with Furin / Number of copies: 3 / Oligomeric state: trimer / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Human immunodeficiency virus 1 / Strain: BG505 |
Molecular weight | Theoretical: 350 KDa |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant strain: human / Recombinant cell: HEK293S / Recombinant plasmid: pPPI4 |
-Macromolecule #2: PGT135 broadly neutralizing antibody
Macromolecule | Name: PGT135 broadly neutralizing antibody / type: protein_or_peptide / ID: 2 / Name.synonym: bnAb PGT135 / Number of copies: 3 / Oligomeric state: monomer / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Cell: B-Cell |
Molecular weight | Theoretical: 50 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: SF9 |
-Experimental details
-Structure determination
Method | negative staining |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.03 mg/mL |
---|---|
Buffer | pH: 7.4 / Details: 1x TBS |
Staining | Type: NEGATIVE / Details: Stained with 2% UF |
Grid | Details: 400 Cu mesh grid glow discharged at 20 mA |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI F20 |
---|---|
Alignment procedure | Legacy - Astigmatism: objective astigmatism corrected at 100,000 mag Legacy - Electron beam tilt params: -2 |
Details | Images collected in 5 degree increments from 0 to -55 |
Date | Jun 12, 2012 |
Image recording | Category: CCD / Film or detector model: GENERIC GATAN (4k x 4k) / Digitization - Sampling interval: 0.109 µm / Number real images: 1095 / Average electron dose: 20 e/Å2 / Details: Data collected on CCD / Bits/pixel: 16 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 0.92 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 100000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC / Tilt angle min: -50 |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Not corrected |
---|---|
Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN Details: Particles picked automatically using DoG-picker and cleaned up with reference free 2D class averaging Number images used: 8831 |