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Yorodumi- EMDB-6432: RCT reconstruction of glycoprotein gHgLgO in complex with neutral... -
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-Basic information
Entry | Database: EMDB / ID: EMD-6432 | |||||||||
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Title | RCT reconstruction of glycoprotein gHgLgO in complex with neutralizing Fab fragments 3G16 and 13H11 | |||||||||
Map data | RCT reconstruction of glycoprotein gHgLgO in complex with neutralizing Fab fragments 3G16 and 13H11 | |||||||||
Sample |
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Keywords | CMV / Pentameric gHgLgO entry virus | |||||||||
Biological species | Cytomegalovirus / unidentified (others) | |||||||||
Method | single particle reconstruction / Resolution: 19.0 Å | |||||||||
Authors | Ciferri C / Cianfrocco MA / Chandramouli S / Carfi A | |||||||||
Citation | Journal: PLoS Pathog / Year: 2015 Title: Antigenic Characterization of the HCMV gH/gL/gO and Pentamer Cell Entry Complexes Reveals Binding Sites for Potently Neutralizing Human Antibodies. Authors: Claudio Ciferri / Sumana Chandramouli / Alexander Leitner / Danilo Donnarumma / Michael A Cianfrocco / Rachel Gerrein / Kristian Friedrich / Yukti Aggarwal / Giuseppe Palladino / Ruedi ...Authors: Claudio Ciferri / Sumana Chandramouli / Alexander Leitner / Danilo Donnarumma / Michael A Cianfrocco / Rachel Gerrein / Kristian Friedrich / Yukti Aggarwal / Giuseppe Palladino / Ruedi Aebersold / Nathalie Norais / Ethan C Settembre / Andrea Carfi / Abstract: Human Cytomegalovirus (HCMV) is a major cause of morbidity and mortality in transplant patients and in fetuses following congenital infection. The glycoprotein complexes gH/gL/gO and ...Human Cytomegalovirus (HCMV) is a major cause of morbidity and mortality in transplant patients and in fetuses following congenital infection. The glycoprotein complexes gH/gL/gO and gH/gL/UL128/UL130/UL131A (Pentamer) are required for HCMV entry in fibroblasts and endothelial/epithelial cells, respectively, and are targeted by potently neutralizing antibodies in the infected host. Using purified soluble forms of gH/gL/gO and Pentamer as well as a panel of naturally elicited human monoclonal antibodies, we determined the location of key neutralizing epitopes on the gH/gL/gO and Pentamer surfaces. Mass Spectrometry (MS) coupled to Chemical Crosslinking or to Hydrogen Deuterium Exchange was used to define residues that are either in proximity or part of neutralizing epitopes on the glycoprotein complexes. We also determined the molecular architecture of the gH/gL/gO- and Pentamer-antibody complexes by Electron Microscopy (EM) and 3D reconstructions. The EM analysis revealed that the Pentamer specific neutralizing antibodies bind to two opposite surfaces of the complex, suggesting that they may neutralize infection by different mechanisms. Together, our data identify the location of neutralizing antibodies binding sites on the gH/gL/gO and Pentamer complexes and provide a framework for the development of antibodies and vaccines against HCMV. | |||||||||
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_6432.map.gz | 3.3 MB | EMDB map data format | |
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Header (meta data) | emd-6432-v30.xml emd-6432.xml | 10.8 KB 10.8 KB | Display Display | EMDB header |
Images | 400_6432.gif 80_6432.gif | 30.8 KB 3.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6432 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6432 | HTTPS FTP |
-Validation report
Summary document | emd_6432_validation.pdf.gz | 78.1 KB | Display | EMDB validaton report |
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Full document | emd_6432_full_validation.pdf.gz | 77.3 KB | Display | |
Data in XML | emd_6432_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6432 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6432 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6432.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | RCT reconstruction of glycoprotein gHgLgO in complex with neutralizing Fab fragments 3G16 and 13H11 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.3 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 : Glycoprotein gH/gL/gO Complex bound to 13H11 and 3G16 Fab Fragment
Entire | Name: Glycoprotein gH/gL/gO Complex bound to 13H11 and 3G16 Fab Fragment |
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Components |
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-Supramolecule #1000: Glycoprotein gH/gL/gO Complex bound to 13H11 and 3G16 Fab Fragment
Supramolecule | Name: Glycoprotein gH/gL/gO Complex bound to 13H11 and 3G16 Fab Fragment type: sample / ID: 1000 / Details: Glycosylation increases size. / Number unique components: 5 |
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Molecular weight | Experimental: 300 KDa / Theoretical: 250 KDa / Method: Size Exclusion Chromatography |
-Macromolecule #1: Glycoprotein H
Macromolecule | Name: Glycoprotein H / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: Cytomegalovirus |
Molecular weight | Experimental: 300 KDa / Theoretical: 250 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #2: Glycoprotein L
Macromolecule | Name: Glycoprotein L / type: protein_or_peptide / ID: 2 / Recombinant expression: Yes |
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Source (natural) | Organism: Cytomegalovirus |
Molecular weight | Experimental: 300 KDa / Theoretical: 250 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #3: Glycoprotein O
Macromolecule | Name: Glycoprotein O / type: protein_or_peptide / ID: 3 / Recombinant expression: Yes |
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Source (natural) | Organism: Cytomegalovirus |
Molecular weight | Experimental: 300 KDa / Theoretical: 250 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #4: 3G16 antibody Fab fragment
Macromolecule | Name: 3G16 antibody Fab fragment / type: protein_or_peptide / ID: 4 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: unidentified (others) |
Molecular weight | Experimental: 300 KDa / Theoretical: 250 KDa |
-Macromolecule #5: 13H11 antibody Fab fragment
Macromolecule | Name: 13H11 antibody Fab fragment / type: protein_or_peptide / ID: 5 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: unidentified (others) |
Molecular weight | Experimental: 300 KDa / Theoretical: 250 KDa |
-Experimental details
-Structure determination
Processing | single particle reconstruction |
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Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: NONE / Instrument: OTHER |
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-Electron microscopy
Microscope | FEI TECNAI 12 |
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Date | Apr 4, 2014 |
Image recording | Category: CCD / Film or detector model: FEI EAGLE (4k x 4k) / Number real images: 50 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
-Image processing
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: OTHER / Number images used: 3000 |
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