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Yorodumi- EMDB-6431: RCT reconstruction of CMV gHgLgO and pentameric complexes bound t... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6431 | |||||||||
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Title | RCT reconstruction of CMV gHgLgO and pentameric complexes bound to highly neutralizing antibodies | |||||||||
Map data | RCT reconstruction of gHgLgO-3G16 complex | |||||||||
Sample |
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Keywords | CMV / Herpesviruses / neutralizing antibodies gH gL gO Pentameric Pentamer | |||||||||
Biological species | Cytomegalovirus / unidentified (others) | |||||||||
Method | single particle reconstruction / Resolution: 18.0 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_6431.map.gz | 930.5 KB | EMDB map data format | |
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Header (meta data) | emd-6431-v30.xml emd-6431.xml | 9.3 KB 9.3 KB | Display Display | EMDB header |
Images | 400_6431.gif 80_6431.gif | 18.5 KB 2.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6431 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6431 | HTTPS FTP |
-Validation report
Summary document | emd_6431_validation.pdf.gz | 77.6 KB | Display | EMDB validaton report |
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Full document | emd_6431_full_validation.pdf.gz | 76.7 KB | Display | |
Data in XML | emd_6431_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6431 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6431 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6431.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | RCT reconstruction of gHgLgO-3G16 complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : gHgLgO bound to 3G16 neutralizing Antibody
Entire | Name: gHgLgO bound to 3G16 neutralizing Antibody |
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Components |
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-Supramolecule #1000: gHgLgO bound to 3G16 neutralizing Antibody
Supramolecule | Name: gHgLgO bound to 3G16 neutralizing Antibody / type: sample / ID: 1000 / Details: Sample is glycosylated. / Oligomeric state: heterotetramer / Number unique components: 4 |
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Molecular weight | Experimental: 200 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 |
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 |
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 |
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) |
-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 | Mar 3, 2014 |
Image recording | Category: CCD / Film or detector model: FEI CETA (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: 18.0 Å / Resolution method: OTHER / Number images used: 3000 |
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