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- 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
TitleCryo-EM Structure of the HCMV gHgLgO Trimer Derived from AD169 and TR strains in complex with PDGFRalpha
Map data
Sample
  • Complex: HCMV trimer in complex with receptor PDGFRalpha
    • Complex: human platelet-derived growth factor receptor alpha extracellular domain
      • Protein or peptide: Platelet-derived growth factor receptor alpha
    • Protein or peptide: Envelope glycoprotein H
    • Protein or peptide: Envelope glycoprotein L
    • Protein or peptide: Envelope glycoprotein O
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 / 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 / : / 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 / Downstream signal transduction / extracellular matrix organization / host cell endosome membrane / cell chemotaxis / regulation of actin cytoskeleton organization / cellular response to amino acid stimulus / lung development / wound healing / receptor protein-tyrosine kinase / cilium / platelet aggregation / cellular response to reactive oxygen species / peptidyl-tyrosine phosphorylation / Constitutive Signaling by Aberrant PI3K in Cancer / 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 / in utero embryonic development / entry receptor-mediated virion attachment to host cell / protein autophosphorylation / membrane => GO:0016020 / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / 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
Herpesvirus UL74, glycoprotein / Herpes UL74 glycoproteins / Platelet-derived growth factor receptor alpha / Cytomegalovirus glycoprotein L / Cytomegalovirus glycoprotein L / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H, C-terminal / Herpesvirus glycoprotein H, C-terminal domain superfamily / Herpesvirus glycoprotein H C-terminal domain / Tyrosine-protein kinase, receptor class III, conserved site ...Herpesvirus UL74, glycoprotein / Herpes UL74 glycoproteins / Platelet-derived growth factor receptor alpha / Cytomegalovirus glycoprotein L / Cytomegalovirus glycoprotein L / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H, C-terminal / Herpesvirus glycoprotein H, C-terminal domain superfamily / Herpesvirus glycoprotein H C-terminal domain / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Envelope glycoprotein H / Platelet-derived growth factor receptor alpha / Envelope glycoprotein L / Envelope glycoprotein O
Similarity search - Component
Biological speciesHuman herpesvirus 5 strain AD169 / Homo sapiens (human) / Human betaherpesvirus 5
Methodsingle particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsLiu J / Vanarsdall AL / Chen D / Johnson DC / Jardetzky TS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI150659 United States
CitationJournal: 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
DepositionJul 2, 2021-
Header (metadata) releaseJun 8, 2022-
Map releaseJun 8, 2022-
UpdateJun 8, 2022-
Current statusJun 8, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_24369.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.34
Minimum - Maximum-1.5162776 - 2.4831285
Average (Standard dev.)0.00057504117 (±0.034504823)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 381.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #3

Fileemd_24369_additional_1.map
Projections & Slices
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Additional map: #2

Fileemd_24369_additional_2.map
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Additional map: #1

Fileemd_24369_additional_3.map
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Half map: #2

Fileemd_24369_half_map_1.map
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Half map: #1

Fileemd_24369_half_map_2.map
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Sample components

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Entire : HCMV trimer in complex with receptor PDGFRalpha

EntireName: HCMV trimer in complex with receptor PDGFRalpha
Components
  • Complex: HCMV trimer in complex with receptor PDGFRalpha
    • Complex: human platelet-derived growth factor receptor alpha extracellular domain
      • Protein or peptide: Platelet-derived growth factor receptor alpha
    • Protein or peptide: Envelope glycoprotein H
    • Protein or peptide: Envelope glycoprotein L
    • Protein or peptide: Envelope glycoprotein O

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Supramolecule #1: HCMV trimer in complex with receptor PDGFRalpha

SupramoleculeName: HCMV trimer in complex with receptor PDGFRalpha / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human herpesvirus 5 strain AD169
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #2: human platelet-derived growth factor receptor alpha extracellular...

SupramoleculeName: human platelet-derived growth factor receptor alpha extracellular domain
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Envelope glycoprotein H

MacromoleculeName: Envelope glycoprotein H / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 5 strain AD169 / Strain: AD169
Molecular weightTheoretical: 80.43543 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #2: Envelope glycoprotein L

MacromoleculeName: Envelope glycoprotein L / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 5 strain AD169 / Strain: AD169
Molecular weightTheoretical: 27.138018 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #3: Envelope glycoprotein O

MacromoleculeName: Envelope glycoprotein O / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human betaherpesvirus 5
Molecular weightTheoretical: 53.937715 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #4: Platelet-derived growth factor receptor alpha

MacromoleculeName: Platelet-derived growth factor receptor alpha / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: receptor protein-tyrosine kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.370016 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.6 mg/mL
BufferpH: 7.5 / Details: 300mM NaCl and 20mM HEPES7.5
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 96 % / Chamber temperature: 293 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 75.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 345997
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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