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Yorodumi- EMDB-2625: Negative stain reconstruction of 8ANC195 Fab in complex with BG50... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2625 | |||||||||
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Title | Negative stain reconstruction of 8ANC195 Fab in complex with BG505 SOSIP.664 trimer | |||||||||
Map data | Reconstruction of 8ANC195 Fab bound to soluble Env trimer BG505.SOSIP | |||||||||
Sample |
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Keywords | HIV-1 / broadly neutralizing antibodies / bnAb / 8ANC195 / SOSIP | |||||||||
Biological species | Human Immunodeficiency Virus-1 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 18.7 Å | |||||||||
Authors | Lee JH / Scharf L / Bjorkman PJ / Ward AB | |||||||||
Citation | Journal: Cell Rep / Year: 2014 Title: Antibody 8ANC195 reveals a site of broad vulnerability on the HIV-1 envelope spike. Authors: Louise Scharf / Johannes F Scheid / Jeong Hyun Lee / Anthony P West / Courtney Chen / Han Gao / Priyanthi N P Gnanapragasam / René Mares / Michael S Seaman / Andrew B Ward / Michel C ...Authors: Louise Scharf / Johannes F Scheid / Jeong Hyun Lee / Anthony P West / Courtney Chen / Han Gao / Priyanthi N P Gnanapragasam / René Mares / Michael S Seaman / Andrew B Ward / Michel C Nussenzweig / Pamela J Bjorkman / Abstract: Broadly neutralizing antibodies (bNAbs) to HIV-1 envelope glycoprotein (Env) can prevent infection in animal models. Characterized bNAb targets, although key to vaccine and therapeutic strategies, ...Broadly neutralizing antibodies (bNAbs) to HIV-1 envelope glycoprotein (Env) can prevent infection in animal models. Characterized bNAb targets, although key to vaccine and therapeutic strategies, are currently limited. We defined a new site of vulnerability by solving structures of bNAb 8ANC195 complexed with monomeric gp120 by X-ray crystallography and trimeric Env by electron microscopy. The site includes portions of gp41 and N-linked glycans adjacent to the CD4-binding site on gp120, making 8ANC195 the first donor-derived anti-HIV-1 bNAb with an epitope spanning both Env subunits. Rather than penetrating the glycan shield by using a single variable-region CDR loop, 8ANC195 inserted its entire heavy-chain variable domain into a gap to form a large interface with gp120 glycans and regions of the gp120 inner domain not contacted by other bNAbs. By isolating additional 8ANC195 clonal variants, we identified a more potent variant, which may be valuable for therapeutic approaches using bNAb combinations with nonoverlapping epitopes. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2625.map.gz | 13.8 MB | EMDB map data format | |
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Header (meta data) | emd-2625-v30.xml emd-2625.xml | 12 KB 12 KB | Display Display | EMDB header |
Images | emd_2625.png | 133 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2625 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2625 | HTTPS FTP |
-Validation report
Summary document | emd_2625_validation.pdf.gz | 203.5 KB | Display | EMDB validaton report |
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Full document | emd_2625_full_validation.pdf.gz | 202.6 KB | Display | |
Data in XML | emd_2625_validation.xml.gz | 5.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2625 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2625 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2625.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of 8ANC195 Fab bound to soluble Env trimer BG505.SOSIP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Sample components
-Entire : 8ANC195 Fab in complex with BG505 SOSIP.664 gp140 trimer
Entire | Name: 8ANC195 Fab in complex with BG505 SOSIP.664 gp140 trimer |
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Components |
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-Supramolecule #1000: 8ANC195 Fab in complex with BG505 SOSIP.664 gp140 trimer
Supramolecule | Name: 8ANC195 Fab in complex with BG505 SOSIP.664 gp140 trimer type: sample / ID: 1000 / Oligomeric state: One Fab binds per gp140 monomer / Number unique components: 2 |
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Molecular weight | Theoretical: 500 KDa |
-Macromolecule #1: Soluble HIV-1 Envelope glycoprotein
Macromolecule | Name: Soluble HIV-1 Envelope glycoprotein / 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: Human Immunodeficiency Virus-1 / Strain: BG505 / synonym: HIV-1 |
Molecular weight | Theoretical: 350 KDa |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293T |
-Macromolecule #2: Fab 8ANC195
Macromolecule | Name: Fab 8ANC195 / type: protein_or_peptide / ID: 2 / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 50 KDa |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293T |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.03 mg/mL |
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Buffer | pH: 7.4 / Details: 150 mM NaCl, 50 mM Tris |
Staining | Type: NEGATIVE Details: Grids with adsorbed sample stained with 2% UF for 30 seconds |
Grid | Details: 400 mesh Cu with thin carbon support, glow discharged |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI 12 |
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Temperature | Max: 293 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism corrected at 52,000x mag |
Details | Data collected from 0 to -40 degrees in 10 degree increments |
Date | May 13, 2013 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 195 / Average electron dose: 25 e/Å2 / Details: Data collected on CCD |
Tilt angle min | 0 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Calibrated magnification: 52000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.8 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 52000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
-Image processing
CTF correction | Details: not corrected |
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Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 18.7 Å / Resolution method: OTHER / Software - Name: EMAN2, Sparx / Number images used: 11637 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: E / Chain - #3 - Chain ID: F / Chain - #4 - Chain ID: I / Chain - #5 - Chain ID: J |
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Software | Name: Chimera |
Details | The models were fit using the Fit function in Chimera. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
-Atomic model buiding 2
Initial model | PDB ID: Chain - #0 - Chain ID: G / Chain - #1 - Chain ID: H / Chain - #2 - Chain ID: L |
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Software | Name: Chimera |
Details | This structure was fit by either superimposing the gp120 onto gp120 of the SOSIP trimer, or by using the Fit function in Chimera. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |