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Yorodumi- PDB-7lbf: CryoEM structure of the HCMV Trimer gHgLgO in complex with human ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lbf | ||||||
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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 | ||||||
Components |
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Keywords | VIRAL PROTEIN/Immune System / virus / receptor / complex / neutralizing antibody / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex | ||||||
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 / embryonic skeletal system morphogenesis / vascular endothelial growth factor binding / retina vasculature development in camera-type eye / cardiac myofibril assembly / embryonic digestive tract morphogenesis / vascular endothelial growth factor receptor activity / Leydig cell differentiation / cell activation / male genitalia development / Signaling by PDGF / positive regulation of chemotaxis / signal transduction involved in regulation of gene expression / embryonic cranial skeleton morphogenesis / platelet-derived growth factor receptor binding / face morphogenesis / estrogen metabolic process / white fat cell differentiation / adrenal gland development / roof of mouth development / odontogenesis of dentin-containing tooth / microvillus / platelet-derived growth factor receptor signaling pathway / negative regulation of platelet activation / transmembrane receptor protein tyrosine kinase activity / hematopoietic progenitor cell differentiation / : / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / positive regulation of calcium-mediated signaling / Downstream signal transduction / HCMV Late Events / cellular response to amino acid stimulus / extracellular matrix organization / cell chemotaxis / lung development / host cell endosome membrane / receptor protein-tyrosine kinase / regulation of actin cytoskeleton organization / HCMV Early Events / wound healing / cellular response to reactive oxygen species / peptidyl-tyrosine phosphorylation / cilium / Constitutive Signaling by Aberrant PI3K in Cancer / platelet aggregation / positive regulation of fibroblast proliferation / cell junction / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / host cell Golgi apparatus / protein autophosphorylation / in utero embryonic development / receptor complex / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / entry receptor-mediated virion attachment to host cell / positive regulation of cell migration / protein kinase activity / symbiont entry into host cell / external side of plasma membrane / fusion of virus membrane with host plasma membrane / positive regulation of cell population proliferation / viral envelope / endoplasmic reticulum membrane / protein-containing complex binding / 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) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
Authors | Kschonsak, M. / Rouge, L. / Arthur, C.P. / Hoangdung, H. / Patel, N. / Kim, I. / Johnson, M. / Kraft, E. / Rohou, A.L. / Gill, A. ...Kschonsak, M. / Rouge, L. / Arthur, C.P. / Hoangdung, H. / Patel, N. / Kim, I. / Johnson, M. / Kraft, E. / Rohou, A.L. / 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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7lbf.cif.gz | 372.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lbf.ent.gz | 298.5 KB | Display | PDB format |
PDBx/mmJSON format | 7lbf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lbf_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7lbf_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7lbf_validation.xml.gz | 52.4 KB | Display | |
Data in CIF | 7lbf_validation.cif.gz | 79.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lb/7lbf ftp://data.pdbj.org/pub/pdb/validation_reports/lb/7lbf | HTTPS FTP |
-Related structure data
Related structure data | 23253MC 7lbeC 7lbgC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Envelope glycoprotein ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 87311.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human cytomegalovirus (strain Merlin) / Strain: Merlin / Gene: gH, UL75 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: Q6SW67 |
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#2: Protein | Mass: 30846.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human cytomegalovirus (strain Merlin) / Strain: Merlin / Gene: gL, UL115 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: F5HCH8 |
#3: Protein | Mass: 58298.504 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human cytomegalovirus / Gene: UL74 / Production host: Homo sapiens (human) / References: UniProt: Q8BCU3 |
-Protein , 1 types, 1 molecules D
#4: Protein | Mass: 59154.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDGFRA, PDGFR2, RHEPDGFRA / Production host: Homo sapiens (human) References: UniProt: P16234, receptor protein-tyrosine kinase |
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-Antibody , 4 types, 4 molecules EFGH
#5: Antibody | Mass: 25780.020 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
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#6: Antibody | Mass: 26600.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
#7: Antibody | Mass: 28355.809 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
#8: Antibody | Mass: 27547.818 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
-Sugars , 3 types, 21 molecules
#9: Polysaccharide | Source method: isolated from a genetically manipulated source #10: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #11: Sugar | ChemComp-NAG / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight | Value: 0.335 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 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 | ||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse. | ||||||||||||||||||||||||
Specimen support | Details: The grid was coated with Au/Pd 80/20 prior use. / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3 | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot for 2.5 seconds before plunging |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 165000 X / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 10 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 34829 / Details: Images were collected in 50 frames every 0.2 s |
Image scans | Movie frames/image: 50 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 4151085 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3560620 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 Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL |