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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
Keywordsviral entry glycoprotein in complex with receptor / VIRAL PROTEIN
Function / homology
Function and homology information


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 / platelet-derived growth factor receptor-ligand complex / platelet-derived growth factor alpha-receptor activity / metanephric glomerular capillary formation / regulation of mesenchymal stem cell differentiation ...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 / platelet-derived growth factor receptor-ligand complex / platelet-derived growth factor alpha-receptor activity / 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 / vascular endothelial growth factor binding / embryonic skeletal system morphogenesis / retina vasculature development in camera-type eye / vascular endothelial growth factor receptor activity / embryonic digestive tract morphogenesis / cardiac myofibril assembly / Leydig cell differentiation / Signaling by PDGF / cell activation / male genitalia development / positive regulation of chemotaxis / embryonic cranial skeleton morphogenesis / phospholipase C activator activity / platelet-derived growth factor receptor binding / estrogen metabolic process / face morphogenesis / signal transduction involved in regulation of gene expression / adrenal gland development / microvillus / platelet-derived growth factor receptor signaling pathway / odontogenesis of dentin-containing tooth / roof of mouth development / 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 / extracellular matrix organization / Downstream signal transduction / positive regulation of calcium-mediated signaling / lung development / cell surface receptor protein tyrosine kinase signaling pathway / host cell endosome membrane / peptidyl-tyrosine phosphorylation / cell chemotaxis / cellular response to reactive oxygen species / regulation of actin cytoskeleton organization / cellular response to amino acid stimulus / wound healing / receptor protein-tyrosine kinase / platelet aggregation / positive regulation of fibroblast proliferation / Constitutive Signaling by Aberrant PI3K in Cancer / cell junction / cell migration / PIP3 activates AKT signaling / protein autophosphorylation / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / host cell Golgi apparatus / in utero embryonic development / entry receptor-mediated virion attachment to host cell / positive regulation of ERK1 and ERK2 cascade / receptor complex / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein kinase activity / nuclear body / cilium / positive regulation of cell migration / fusion of virus membrane with host plasma membrane / external side of plasma membrane / positive regulation of cell population proliferation / viral envelope / endoplasmic reticulum membrane / symbiont entry into host cell / protein-containing complex binding / host cell plasma membrane / virion membrane / Golgi apparatus / protein homodimerization activity / protein-containing complex / nucleoplasm / ATP binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Herpesvirus UL74, glycoprotein / Herpes UL74 glycoproteins / Platelet-derived growth factor receptor alpha / Cytomegalovirus glycoprotein L / Cytomegalovirus glycoprotein L / Betaherpesvirus glycoprotein L (gL) domain profile. / Herpesvirus glycoprotein H main domain / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H, C-terminal / Herpesvirus glycoprotein H, C-terminal domain superfamily ...Herpesvirus UL74, glycoprotein / Herpes UL74 glycoproteins / Platelet-derived growth factor receptor alpha / Cytomegalovirus glycoprotein L / Cytomegalovirus glycoprotein L / Betaherpesvirus glycoprotein L (gL) domain profile. / Herpesvirus glycoprotein H main domain / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H, C-terminal / Herpesvirus glycoprotein H, C-terminal domain superfamily / Herpesvirus glycoprotein H C-terminal domain / Platelet-derived growth factor receptor Ig-like domain 4 / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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 / 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
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: Liu J / Vanarsdall A / Chen DH / Chin A / Johnson D / Jardetzky TS
History
DepositionJul 2, 2021-
Header (metadata) releaseJun 8, 2022-
Map releaseJun 8, 2022-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24369.png

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)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 360 pix.
= 381.6 Å		1.06 Å/pix.
x 360 pix.
= 381.6 Å		1.06 Å/pix.
x 360 pix.
= 381.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
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
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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 / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human herpesvirus 5 strain AD169

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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)

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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

UniProtKB: Envelope glycoprotein H

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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

UniProtKB: Envelope glycoprotein L

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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

UniProtKB: Glycoprotein O

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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

UniProtKB: Platelet-derived growth factor receptor alpha

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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 / Pretreatment - Time: 2 sec.
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

Startup modelType of model: OTHER
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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