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Yorodumi- EMDB-23252: CryoEM structure of the HCMV Trimer gHgLgO in complex with neutra... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23252 | |||||||||
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Title | CryoEM structure of the HCMV Trimer gHgLgO in complex with neutralizing fabs 13H11 and MSL-109 | |||||||||
Map data | Composite map of Trimer gHgLgO bound to fabs 13H11 and Msl-109 used for model refinement | |||||||||
Sample |
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Function / homology | Function and homology information host cell endosome membrane / HCMV Late Events / HCMV Early Events / host cell Golgi apparatus / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Human cytomegalovirus / Homo sapiens (human) / Human cytomegalovirus (strain Merlin) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Kschonsak M / Rouge L / Arthur CP / Hoangdung H / Patel N / Kim I / Johnson M / Kraft E / Rohou AL / Gill A ...Kschonsak M / Rouge L / Arthur CP / Hoangdung H / Patel N / Kim I / Johnson M / Kraft E / Rohou AL / Gill A / Martinez-Martin N / Payandeh J / Ciferri C | |||||||||
Citation | Journal: Cell / Year: 2021 Title: Structures of HCMV Trimer reveal the basis for receptor recognition and cell entry. Authors: Marc Kschonsak / Lionel Rougé / Christopher P Arthur / Ho Hoangdung / Nidhi Patel / Ingrid Kim / Matthew C Johnson / Edward Kraft / Alexis L Rohou / Avinash Gill / Nadia Martinez-Martin / ...Authors: Marc Kschonsak / Lionel Rougé / Christopher P Arthur / Ho Hoangdung / Nidhi Patel / Ingrid Kim / Matthew C Johnson / Edward Kraft / Alexis L Rohou / Avinash Gill / Nadia Martinez-Martin / Jian Payandeh / Claudio Ciferri / Abstract: Human cytomegalovirus (HCMV) infects the majority of the human population and represents the leading viral cause of congenital birth defects. HCMV utilizes the glycoproteins gHgLgO (Trimer) to bind ...Human cytomegalovirus (HCMV) infects the majority of the human population and represents the leading viral cause of congenital birth defects. HCMV utilizes the glycoproteins gHgLgO (Trimer) to bind to platelet-derived growth factor receptor alpha (PDGFRα) and transforming growth factor beta receptor 3 (TGFβR3) to gain entry into multiple cell types. This complex is targeted by potent neutralizing antibodies and represents an important candidate for therapeutics against HCMV. Here, we determine three cryogenic electron microscopy (cryo-EM) structures of the trimer and the details of its interactions with four binding partners: the receptor proteins PDGFRα and TGFβR3 as well as two broadly neutralizing antibodies. Trimer binding to PDGFRα and TGFβR3 is mutually exclusive, suggesting that they function as independent entry receptors. In addition, Trimer-PDGFRα interaction has an inhibitory effect on PDGFRα signaling. Our results provide a framework for understanding HCMV receptor engagement, neutralization, and the development of anti-viral strategies 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_23252.map.gz | 65.2 MB | EMDB map data format | |
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Header (meta data) | emd-23252-v30.xml emd-23252.xml | 39.5 KB 39.5 KB | Display Display | EMDB header |
Images | emd_23252.png | 81.4 KB | ||
Others | emd_23252_additional_1.map.gz emd_23252_additional_2.map.gz emd_23252_additional_3.map.gz emd_23252_additional_4.map.gz emd_23252_additional_5.map.gz emd_23252_additional_6.map.gz emd_23252_additional_7.map.gz | 65 MB 65 MB 65 MB 65 MB 65 MB 65 MB 65 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23252 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23252 | HTTPS FTP |
-Related structure data
Related structure data | 7lbeMC 7lbfC 7lbgC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23252.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Composite map of Trimer gHgLgO bound to fabs 13H11 and Msl-109 used for model refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.3514 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Overall map of Trimer bound to fabs 13H11...
File | emd_23252_additional_1.map | ||||||||||||
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Annotation | Overall map of Trimer bound to fabs 13H11 and Msl-109, non-sharpened used for composite map generation | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focussed map of gO and part. gL, sharpened...
File | emd_23252_additional_2.map | ||||||||||||
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Annotation | Focussed map of gO and part. gL, sharpened used for composite map generation | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focussed map of part. gL and part. gH,...
File | emd_23252_additional_3.map | ||||||||||||
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Annotation | Focussed map of part. gL and part. gH, sharpened used for composite map generation | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focussed map of part gH and Fv regions...
File | emd_23252_additional_4.map | ||||||||||||
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Annotation | Focussed map of part gH and Fv regions of fabs, sharpened used for composite map generation | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focussed map of part gH and Fv regions of fabs, non-sharpened
File | emd_23252_additional_5.map | ||||||||||||
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Annotation | Focussed map of part gH and Fv regions of fabs, non-sharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focussed map of part. gL and part. gH, non-sharpened
File | emd_23252_additional_6.map | ||||||||||||
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Annotation | Focussed map of part. gL and part. gH, non-sharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focussed map of gO and part. gL, non-sharpened
File | emd_23252_additional_7.map | ||||||||||||
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Annotation | Focussed map of gO and part. gL, non-sharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : HCMV Trimer gHgLgO bound to neutralizing fabs 13H11 and MSL-109
+Supramolecule #1: HCMV Trimer gHgLgO bound to neutralizing fabs 13H11 and MSL-109
+Supramolecule #2: HCMV Trimer gHgLgO
+Supramolecule #3: neutralizing fabs 13H11 and MSL-109
+Macromolecule #1: Envelope glycoprotein H
+Macromolecule #2: Envelope glycoprotein L
+Macromolecule #3: Envelope glycoprotein O
+Macromolecule #4: Fab 13H11 light chain
+Macromolecule #5: Fab 13H11 heavy chain
+Macromolecule #6: Fab MSL-109 light chain
+Macromolecule #7: Fab MSL-109 heavy chain
+Macromolecule #10: 2-acetamido-2-deoxy-beta-D-glucopyranose
+Macromolecule #11: alpha-D-mannopyranose
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | 2D array |
-Sample preparation
Concentration | 0.4 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
Details: The sample was gently cross-linked with 0.025% (v/v) EM-grade glutaraldehyde for 10 min at RT and quenched with 9 mM Tris pH 7.5 | |||||||||
Grid | Model: C-flat-1.2/1.3 / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Details: The grid was coated with Au/Pd 80/20 prior use. | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 2.5 seconds before plunging. | |||||||||
Details | This sample contained monomeric and dimeric protein complexes. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Number real images: 14717 / Average exposure time: 10.0 sec. / Average electron dose: 50.0 e/Å2 / Details: Images were collected in 50 frames every 0.2 s |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 1478640 |
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CTF correction | Software - Name: CTFFIND / Software - details: 4.1.13 |
Startup model | Type of model: OTHER / Details: ab-initio reconstruction using cisTEM |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: cisTEM (ver. 1.02) |
Final 3D classification | Number classes: 100 / Software - Name: RELION (ver. 3.1) / Details: selected 52 of 100 classes |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: cisTEM (ver. 1.02) |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1.02) Details: Used score threshold of 0.25 for final 3D reconstruction. Map used for model building and refinements is a composite map after combining 3 focussed maps with PHENIX Number images used: 1350211 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-7lbe: |