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Yorodumi- EMDB-24369: Cryo-EM Structure of the HCMV gHgLgO Trimer Derived from AD169 an... -
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-Basic information
Entry | Database: EMDB / ID: EMD-24369 | |||||||||
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Title | Cryo-EM Structure of the HCMV gHgLgO Trimer Derived from AD169 and TR strains in complex with PDGFRalpha | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information platelet-derived growth factor alpha-receptor activity / Imatinib-resistant PDGFR mutants / Sunitinib-resistant PDGFR mutants / Regorafenib-resistant PDGFR mutants / Sorafenib-resistant PDGFR mutants / PDGFR mutants bind TKIs / platelet-derived growth factor receptor-alpha signaling pathway / metanephric glomerular capillary formation / regulation of mesenchymal stem cell differentiation / luteinization ...platelet-derived growth factor alpha-receptor activity / Imatinib-resistant PDGFR mutants / Sunitinib-resistant PDGFR mutants / Regorafenib-resistant PDGFR mutants / Sorafenib-resistant PDGFR mutants / PDGFR mutants bind TKIs / platelet-derived growth factor receptor-alpha signaling pathway / 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 digestive tract morphogenesis / embryonic skeletal system morphogenesis / vascular endothelial growth factor binding / retina vasculature development in camera-type eye / cardiac myofibril assembly / vascular endothelial growth factor receptor activity / Leydig cell differentiation / cell activation / male genitalia development / positive regulation of chemotaxis / Signaling by PDGF / signal transduction involved in regulation of gene expression / 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 / platelet-derived growth factor receptor signaling pathway / white fat cell differentiation / negative regulation of platelet activation / hematopoietic progenitor cell differentiation / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / transmembrane receptor protein tyrosine kinase activity / positive regulation of calcium-mediated signaling / Downstream signal transduction / extracellular matrix organization / cell chemotaxis / host cell endosome membrane / platelet aggregation / regulation of actin cytoskeleton organization / cellular response to amino acid stimulus / membrane => GO:0016020 / lung development / wound healing / receptor protein-tyrosine kinase / cilium / peptidyl-tyrosine phosphorylation / cellular response to reactive oxygen species / 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 / RAF/MAP kinase cascade / host cell Golgi apparatus / in utero embryonic development / protein autophosphorylation / entry receptor-mediated virion attachment to host cell / 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 / external side of plasma membrane / fusion of virus membrane with host plasma membrane / viral envelope / positive regulation of cell population proliferation / 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 herpesvirus 5 strain AD169 / Homo sapiens (human) / Human betaherpesvirus 5 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.43 Å | |||||||||
Authors | Liu J / Vanarsdall AL / Chen D / Johnson DC / Jardetzky TS | |||||||||
Funding support | United States, 1 items
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Citation | Journal: mBio / Year: 2021 Title: Cryo-Electron Microscopy Structure and Interactions of the Human Cytomegalovirus gHgLgO Trimer with Platelet-Derived Growth Factor Receptor Alpha. Authors: Jing Liu / Adam Vanarsdall / Dong-Hua Chen / Andrea Chin / David Johnson / Theodore S Jardetzky / Abstract: Human cytomegalovirus (HCMV) is a herpesvirus that produces disease in transplant patients and newborn children. Entry of HCMV into cells relies on gH/gL trimer (gHgLgO) and pentamer (gHgLUL128-131) ...Human cytomegalovirus (HCMV) is a herpesvirus that produces disease in transplant patients and newborn children. Entry of HCMV into cells relies on gH/gL trimer (gHgLgO) and pentamer (gHgLUL128-131) complexes that bind cellular receptors. Here, we studied the structure and interactions of the HCMV trimer, formed by AD169 strain gH and gL and TR strain gO proteins, with the human platelet-derived growth factor receptor alpha (PDGFRα). Three trimer surfaces make extensive contacts with three PDGFRα N-terminal domains, causing PDGFRα to wrap around gO in a structure similar to a human hand, explaining the high-affinity interaction. gO is among the least conserved HCMV proteins, with 8 distinct genotypes. We observed high conservation of residues mediating gO-gL interactions but more extensive gO variability in the PDGFRα interface. Comparisons between our trimer structure and a previously determined structure composed of different subunit genotypes indicate that gO variability is accommodated by adjustments in the gO-PDGFRα interface. We identified two loops within gO that were disordered and apparently glycosylated, which could be deleted without disrupting PDGFRα binding. We also identified four gO residues that contact PDGFRα, which when mutated produced markedly reduced receptor binding. These residues fall within conserved contact sites of gO with PDGFRα and may represent key targets for anti-trimer neutralizing antibodies and HCMV vaccines. Finally, we observe that gO mutations distant from the gL interaction site impact trimer expression, suggesting that the intrinsic folding or stability of gO can impact the efficiency of trimer assembly. HCMV is a herpesvirus that infects a large percentage of the adult population and causes significant levels of disease in immunocompromised individuals and birth defects in the developing fetus. The virus encodes a complex protein machinery that coordinates infection of different cell types in the body, including a trimer formed of gH, gL, and gO subunits. Here, we studied the interactions of the HCMV trimer with its receptor on cells, the platelet derived growth factor receptor α (PDGFRα), to better understand how HCMV coordinates virus entry into cells. Our results add to our understanding of HCMV strain-specific differences and identify sites on the trimer that represent potential targets for therapeutic antibodies or vaccine development. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_24369.map.gz | 168.2 MB | EMDB map data format | |
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Header (meta data) | emd-24369-v30.xml emd-24369.xml | 26.8 KB 26.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_24369_fsc.xml | 14.4 KB | Display | FSC data file |
Images | emd_24369.png | 85.5 KB | ||
Others | emd_24369_additional_1.map.gz emd_24369_additional_2.map.gz emd_24369_additional_3.map.gz emd_24369_half_map_1.map.gz emd_24369_half_map_2.map.gz | 168.1 MB 168.1 MB 160.5 MB 165.1 MB 165.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24369 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24369 | HTTPS FTP |
-Validation report
Summary document | emd_24369_validation.pdf.gz | 844.6 KB | Display | EMDB validaton report |
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Full document | emd_24369_full_validation.pdf.gz | 844.1 KB | Display | |
Data in XML | emd_24369_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | emd_24369_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24369 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24369 | HTTPS FTP |
-Related structure data
Related structure data | 7ramMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_24369.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #3
File | emd_24369_additional_1.map | ||||||||||||
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Density Histograms |
-Additional map: #2
File | emd_24369_additional_2.map | ||||||||||||
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-Additional map: #1
File | emd_24369_additional_3.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_24369_half_map_1.map | ||||||||||||
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-Half map: #1
File | emd_24369_half_map_2.map | ||||||||||||
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Density Histograms |
-Sample components
-Entire : HCMV trimer in complex with receptor PDGFRalpha
Entire | Name: HCMV trimer in complex with receptor PDGFRalpha |
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Components |
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-Supramolecule #1: HCMV trimer in complex with receptor PDGFRalpha
Supramolecule | Name: HCMV trimer in complex with receptor PDGFRalpha / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Human herpesvirus 5 strain AD169 |
Recombinant expression | Organism: Homo sapiens (human) |
-Supramolecule #2: human platelet-derived growth factor receptor alpha extracellular...
Supramolecule | Name: human platelet-derived growth factor receptor alpha extracellular domain type: complex / ID: 2 / Parent: 1 / Macromolecule list: #4 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #1: Envelope glycoprotein H
Macromolecule | Name: Envelope glycoprotein H / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Human herpesvirus 5 strain AD169 / Strain: AD169 |
Molecular weight | Theoretical: 80.43543 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: LLLNTYGRPI RFLRENTTQC TYNSSLRNST VVRENAISFN FFQSYNQYYV FHMPRCLFAG PLAEQFLNQV DLTETLERYQ QRLNTYALV SKDLASYRSF SQQLKAQDSL GQQPTTVPPP IDLSIPHVWM PPQTTPHDWK GSHTTSGLHR PHFNQTCILF D GHDLLFST ...String: LLLNTYGRPI RFLRENTTQC TYNSSLRNST VVRENAISFN FFQSYNQYYV FHMPRCLFAG PLAEQFLNQV DLTETLERYQ QRLNTYALV SKDLASYRSF SQQLKAQDSL GQQPTTVPPP IDLSIPHVWM PPQTTPHDWK GSHTTSGLHR PHFNQTCILF D GHDLLFST VTPCLHQGFY LMDELRYVKI TLTEDFFVVT VSIDDDTPML LIFGHLPRVL FKAPYQRDNF ILRQTEKHEL LV LVKKAQL NRHSYLKDSD FLDAALDFNY LDLSALLRNS FHRYAVDVLK SGRCQMLDRR TVEMAFAYAL ALFAAARQEE AGT EISIPR ALDRQAALLQ IQEFMITCLS QTPPRTTLLL YPTAVDLAKR ALWTPDQITD ITSLVRLVYI LSKQNQQHLI PQWA LRQIA DFALQLHKTH LASFLSAFAR QELYLMGSLV HSMLVHTTER REIFIVETGL CSLAELSHFT QLLAHPHHEY LSDLY TPCS SSGRRDHSLE RLTRLFPDAT VPATVPAALS ILSTMQPSTL ETFPDLFCLP LGESFSALTV SEHVSYVVTN QYLIKG ISY PVSTTVVGQS LIITQTDSQT KCELTRNMHT THSITAALNI SLENCAFCQS ALLEYDDTQG VINIMYMHDS DDVLFAL DP YNEVVVSSPR THYLMLLKNG TVLEVTDVVV DATDSRGSLV PRGSSAWSHP QFEKAGHHHH HHHH |
-Macromolecule #2: Envelope glycoprotein L
Macromolecule | Name: Envelope glycoprotein L / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Human herpesvirus 5 strain AD169 / Strain: AD169 |
Molecular weight | Theoretical: 27.138018 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: PTAAEKVPAE CPELTRRCLL GEVFQGDKYE SWLRPLVNVT RRDGPLSQLI RYRPVTPEAA NSVLLDDAFL DTLALLYNNP DQLRALLTL LSSDTAPRWM TVMRGYSECG DGSPAVYTCV DDLCRGYDLT RLSYGRSIFT EHVLGFELVP PSLFNVVVAI R NEATRTNR ...String: PTAAEKVPAE CPELTRRCLL GEVFQGDKYE SWLRPLVNVT RRDGPLSQLI RYRPVTPEAA NSVLLDDAFL DTLALLYNNP DQLRALLTL LSSDTAPRWM TVMRGYSECG DGSPAVYTCV DDLCRGYDLT RLSYGRSIFT EHVLGFELVP PSLFNVVVAI R NEATRTNR AVRLPVSTAA APEGITLFYG LYNAVKEFCL RHQLDPPLLR HLDKYYAGLP PELKQTRVNL PAHSRYGPQA VD AR |
-Macromolecule #3: Envelope glycoprotein O
Macromolecule | Name: Envelope glycoprotein O / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Human betaherpesvirus 5 |
Molecular weight | Theoretical: 53.937715 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGRKGEMRGV FNLFFLMSLT FLLFSFINCR AAVRLSVGRY WSGKVLSTIG KQRLDKFKLE ILKQLEKDIY TKYFNMTRQH IKNLTMNMT EFPRYYILAG PIQNNSVTYL WFDFYSTQLR KPAKYVFSEY NHTAKTITFR PPSCGTVPSM TCLSEMLNVS K RNDTGEQG ...String: MGRKGEMRGV FNLFFLMSLT FLLFSFINCR AAVRLSVGRY WSGKVLSTIG KQRLDKFKLE ILKQLEKDIY TKYFNMTRQH IKNLTMNMT EFPRYYILAG PIQNNSVTYL WFDFYSTQLR KPAKYVFSEY NHTAKTITFR PPSCGTVPSM TCLSEMLNVS K RNDTGEQG CGNFTTFNPM FFNVPRWNTK LYVGSKKVNV DSQTIYFLGL TALLLRYAQR NCTHSFYLVN AMSRNLFRVP KY INGTKLK NTMRKLKRKQ APVKEQSEKK SKKSQSTTTP YSPYTTSTAL NVTTNATYSV TTTARRVSTS TIAYRPDSSF MKS IMTTQL RDLATWVYTT LRYRQNPFCE SSRNRTAVSE FMKNTHVLIR NETPYTIYGT LDMSSLYYNE TMFVENKTAS ETTP TSPST GFQRTFIDPL WDYLDSLLFL DEIRNFSLQS PTYGNLTPPE HRRAVNLSTL NSLWWWLQ |
-Macromolecule #4: Platelet-derived growth factor receptor alpha
Macromolecule | Name: Platelet-derived growth factor receptor alpha / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: receptor protein-tyrosine kinase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 59.370016 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGTSHPAFLV LGCLLTGLSL ILCQLSLPSI LPNENEKVVQ LNSSFSLRCF GESEVSWQYP MSEEESSDVE IRNEENNSGL FVTVLEVSS ASAAHTGLYT CYYNHTQTEE NELEGRHIYI YVPDPDVAFV PLGMTDYLVI VEDDDSAIIP CRTTDPETPV T LHNSEGVV ...String: MGTSHPAFLV LGCLLTGLSL ILCQLSLPSI LPNENEKVVQ LNSSFSLRCF GESEVSWQYP MSEEESSDVE IRNEENNSGL FVTVLEVSS ASAAHTGLYT CYYNHTQTEE NELEGRHIYI YVPDPDVAFV PLGMTDYLVI VEDDDSAIIP CRTTDPETPV T LHNSEGVV PASYDSRQGF NGTFTVGPYI CEATVKGKKF QTIPFNVYAL KATSELDLEM EALKTVYKSG ETIVVTCAVF NN EVVDLQW TYPGEVKGKG ITMLEEIKVP SIKLVYTLTV PEATVKDSGD YECAARQATR EVKEMKKVTI SVHEKGFIEI KPT FSQLEA VNLHEVKHFV VEVRAYPPPR ISWLKNNLTL IENLTEITTD VEKIQEIRYR SKLKLIRAKE EDSGHYTIVA QNED AVKSY TFELLTQVPS SILDLVDDHH GSTGGQTVRC TAEGTPLPDI EWMICKDIKK CNNETSWTIL ANNVSNIITE IHPRD RSTV EGRVTFAKVE ETIAVRCLAK NLLGAENREL KLVAPTLRSE ENLYFQ |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.6 mg/mL |
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Buffer | pH: 7.5 / Details: 300mM NaCl and 20mM HEPES7.5 |
Grid | Model: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 96 % / Chamber temperature: 293 K / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 75.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |