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Yorodumi- EMDB-23253: CryoEM structure of the HCMV Trimer gHgLgO in complex with human ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23253 | |||||||||
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Title | CryoEM structure of the HCMV Trimer gHgLgO in complex with human Platelet-derived growth factor receptor alpha and neutralizing fabs 13H11 and MSL-109 | |||||||||
Map data | Composite map of HCMV Trimer-PDGFRa with fabs 13H11 and Msl-109 used for model building | |||||||||
Sample |
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Function / homology | Function and homology information platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor receptor-alpha signaling pathway / Imatinib-resistant PDGFR mutants / Sunitinib-resistant PDGFR mutants / Regorafenib-resistant PDGFR mutants / Sorafenib-resistant PDGFR mutants / PDGFR mutants bind TKIs / metanephric glomerular capillary formation / regulation of mesenchymal stem cell differentiation / luteinization ...platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor receptor-alpha signaling pathway / Imatinib-resistant PDGFR mutants / Sunitinib-resistant PDGFR mutants / Regorafenib-resistant PDGFR mutants / Sorafenib-resistant PDGFR mutants / PDGFR mutants bind TKIs / metanephric glomerular capillary formation / regulation of mesenchymal stem cell differentiation / luteinization / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / platelet-derived growth factor binding / retina vasculature development in camera-type eye / embryonic skeletal system morphogenesis / vascular endothelial growth factor binding / cardiac myofibril assembly / embryonic digestive tract morphogenesis / vascular endothelial growth factor receptor activity / Leydig cell differentiation / male genitalia development / cell activation / positive regulation of chemotaxis / signal transduction involved in regulation of gene expression / Signaling by PDGF / embryonic cranial skeleton morphogenesis / platelet-derived growth factor receptor binding / face morphogenesis / estrogen metabolic process / adrenal gland development / roof of mouth development / odontogenesis of dentin-containing tooth / microvillus / negative regulation of platelet activation / platelet-derived growth factor receptor signaling pathway / white fat cell differentiation / hematopoietic progenitor cell differentiation / positive regulation of phospholipase C activity / positive regulation of calcium-mediated signaling / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / transmembrane receptor protein tyrosine kinase activity / extracellular matrix organization / cell chemotaxis / Downstream signal transduction / host cell endosome membrane / HCMV Late Events / regulation of actin cytoskeleton organization / cellular response to amino acid stimulus / lung development / wound healing / cilium / receptor protein-tyrosine kinase / platelet aggregation / cellular response to reactive oxygen species / HCMV Early Events / peptidyl-tyrosine phosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of fibroblast proliferation / PIP3 activates AKT signaling / cell junction / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / host cell Golgi apparatus / RAF/MAP kinase cascade / in utero embryonic development / entry receptor-mediated virion attachment to host cell / protein autophosphorylation / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / protein kinase activity / positive regulation of cell migration / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / external side of plasma membrane / viral envelope / positive regulation of cell population proliferation / protein-containing complex binding / endoplasmic reticulum membrane / host cell plasma membrane / virion membrane / Golgi apparatus / protein homodimerization activity / protein-containing complex / nucleoplasm / ATP binding / membrane / nucleus / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Human cytomegalovirus / Homo sapiens (human) / Human cytomegalovirus (strain Merlin) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 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_23253.map.gz | 65.2 MB | EMDB map data format | |
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Header (meta data) | emd-23253-v30.xml emd-23253.xml | 41.1 KB 41.1 KB | Display Display | EMDB header |
Images | emd_23253.png | 88 KB | ||
Others | emd_23253_additional_1.map.gz emd_23253_additional_2.map.gz emd_23253_additional_3.map.gz emd_23253_additional_4.map.gz emd_23253_additional_5.map.gz emd_23253_additional_6.map.gz emd_23253_additional_7.map.gz | 65.1 MB 65 MB 65.1 MB 65.1 MB 65.1 MB 65 MB 65.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23253 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23253 | HTTPS FTP |
-Related structure data
Related structure data | 7lbfMC 7lbeC 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_23253.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 HCMV Trimer-PDGFRa with fabs 13H11 and Msl-109 used for model building | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: Focussed map of gL and part. gH region,...
File | emd_23253_additional_1.map | ||||||||||||
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Annotation | Focussed map of gL and part. gH region, sharpened used for composite map generation | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focussed map of PDGFRa and gO region, sharpened...
File | emd_23253_additional_2.map | ||||||||||||
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Annotation | Focussed map of PDGFRa and gO region, sharpened used for composite map generation | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Overall map of Trimer-PDGFRa bound to 2 fabs...
File | emd_23253_additional_3.map | ||||||||||||
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Annotation | Overall map of Trimer-PDGFRa bound to 2 fabs non-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_23253_additional_4.map | ||||||||||||
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Annotation | Focussed map of part. gH and Fv regions of both 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 both fabs, non-sharpened
File | emd_23253_additional_5.map | ||||||||||||
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Annotation | Focussed map of part. gH and Fv regions of both fabs, non-sharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focussed map of gL and part. gH region, non-sharpened
File | emd_23253_additional_6.map | ||||||||||||
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Annotation | Focussed map of gL and part. gH region, non-sharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focussed map of PDGFRa and gO region, non-sharpened
File | emd_23253_additional_7.map | ||||||||||||
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Annotation | Focussed map of PDGFRa and gO region, non-sharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : HCMV Trimer gHgLgO bound to human receptor PDGFRa and neutralizin...
+Supramolecule #1: HCMV Trimer gHgLgO bound to human receptor PDGFRa and neutralizin...
+Supramolecule #2: HCMV Trimer gHgLgO
+Supramolecule #3: PDGFRa and neutralizing fabs 13H11 and MSL-109
+Macromolecule #1: Envelope glycoprotein H
+Macromolecule #2: Envelope glycoprotein L
+Macromolecule #3: Envelope glycoprotein O
+Macromolecule #4: Isoform 3 of Platelet-derived growth factor receptor alpha
+Macromolecule #5: Fab 13H11 light chain
+Macromolecule #6: Fab 13H11 heavy chain
+Macromolecule #7: Fab MSL-109 light chain
+Macromolecule #8: Fab MSL-109 heavy chain
+Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose
-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 was monodisperse. |
-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: 2 / Number real images: 34829 / 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: 4151085 |
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CTF correction | Software - Name: CTFFIND / Software - details: 4.1.13 |
Startup model | Type of model: OTHER Details: EM map of HCMV Trimer-13H11-Msl109 used as starting reference |
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 50 of 100 classes |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: cisTEM (ver. 1.02) |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.8 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 refinements is a composite map after combining 3 focussed maps with PHENIX Number images used: 3560620 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-7lbf: |