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- EMDB-44640: HCMV B-capsid vertex -

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Basic information

Entry
Database: EMDB / ID: EMD-44640
TitleHCMV B-capsid vertex
Map datamap
Sample
  • Virus: Human herpesvirus 5 strain AD169
    • Protein or peptide: Small capsomere-interacting protein
    • Protein or peptide: Major Capsid Protein
    • Protein or peptide: Triplex protein 1
    • Protein or peptide: Triplex Protein 2
KeywordsB-capsid / HCMV / capsid / DNA-free / VIRUS
Function / homology
Function and homology information


T=16 icosahedral viral capsid / viral DNA genome packaging / viral capsid assembly / viral capsid / host cell nucleus / structural molecule activity / DNA binding
Similarity search - Function
Herpesvirus tripartite terminase subunit 2 / Herpesvirus UL33-like protein / Herpesvirus capsid shell protein 1 / Herpesvirus capsid shell protein VP19C / Herpesvirus capsid protein 2 / Herpesvirus VP23 like capsid protein / Herpesvirus major capsid protein / Herpesvirus major capsid protein, upper domain superfamily / Herpes virus major capsid protein
Similarity search - Domain/homology
DNA packaging protein UL33 / Triplex capsid protein 2 / Major capsid protein / Triplex capsid protein 1
Similarity search - Component
Biological speciesHuman herpesvirus 5 strain AD169
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZhou H / Stevens A
Funding support United States, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE028583 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI007323 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116792 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)RR23057 United States
CitationJournal: Virology / Year: 2024
Title: Structure-guided mutagenesis targeting interactions between pp150 tegument protein and small capsid protein identify five lethal and two live-attenuated HCMV mutants.
Authors: Alexander Stevens / Ruth Cruz-Cosme / Najealicka Armstrong / Qiyi Tang / Z Hong Zhou /
Abstract: Human cytomegalovirus (HCMV) replication relies on a nucleocapsid coat of the 150 kDa, subfamily-specific tegument phosphoprotein (pp150) to regulate cytoplasmic virion maturation. While recent ...Human cytomegalovirus (HCMV) replication relies on a nucleocapsid coat of the 150 kDa, subfamily-specific tegument phosphoprotein (pp150) to regulate cytoplasmic virion maturation. While recent structural studies revealed pp150-capsid interactions, the role of specific amino-acids involved in these interactions have not been established experimentally. In this study, pp150 and the small capsid protein (SCP), one of pp150's binding partners found atop the major capsid protein (MCP), were subjected to mutational and structural analyses. Mutations to clusters of polar or hydrophobic residues along the pp150-SCP interface abolished viral replication, with no replication detected in mutant virus-infected cells. Notably, a single amino acid mutation (pp150 K255E) at the pp150-MCP interface significantly attenuated viral replication, unlike in pp150-deletion mutants where capsids degraded outside host nuclei. These functionally significant mutations targeting pp150-capsid interactions, particularly the pp150 K255E replication-attenuated mutant, can be explored to overcome the historical challenges of developing effective antivirals and vaccines against HCMV infection.
History
DepositionApr 26, 2024-
Header (metadata) releaseJun 12, 2024-
Map releaseJun 12, 2024-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44640.png

Downloads & links

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Map

FileDownload / File: emd_44640.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
Voxel sizeX=Y=Z: 1.064 Å
Density
Contour LevelBy AUTHOR: 0.117
Minimum - Maximum-0.4232996 - 0.77993846
Average (Standard dev.)0.0007313447 (±0.04734646)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 544.768 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half b

Fileemd_44640_half_map_1.map
Annotationhalf b
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half b

Fileemd_44640_half_map_2.map
Annotationhalf b
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human herpesvirus 5 strain AD169

EntireName: Human herpesvirus 5 strain AD169
Components
  • Virus: Human herpesvirus 5 strain AD169
    • Protein or peptide: Small capsomere-interacting protein
    • Protein or peptide: Major Capsid Protein
    • Protein or peptide: Triplex protein 1
    • Protein or peptide: Triplex Protein 2

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Supramolecule #1: Human herpesvirus 5 strain AD169

SupramoleculeName: Human herpesvirus 5 strain AD169 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Cultured in ARPE-19 cells. / NCBI-ID: 10360 / Sci species name: Human herpesvirus 5 strain AD169 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 216 MDa
Virus shellShell ID: 1 / Name: capsid / Diameter: 1320.0 Å / T number (triangulation number): 16

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Macromolecule #1: Small capsomere-interacting protein

MacromoleculeName: Small capsomere-interacting protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 5 strain AD169
SequenceString:
MSWTKQRVPF LDDDDGEEEN DVQDDVDSPV PTRPLVIDED AEPAAGTSGG LEGGGGDDED GEDGHALPDL DDDLLLQFEP MLPRVYDLLL PSLDARLNFV NAGQKYAAFL KYVHGDCATC SHGEILREKT QLLTAIVSKL MDINGILEGK DEPAPGK

UniProtKB: DNA packaging protein UL33

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Macromolecule #2: Major Capsid Protein

MacromoleculeName: Major Capsid Protein / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 5 strain AD169
SequenceString: MENWSALELL PKVGIPTDFL THVKTSAGEE MFEALRIYYG DDPERYNIHF EAIFGTFCNR LEWVYFLTSG LAAAAHAIKF HDLNKLTTGK MLFHVQVPRV ASGAGLPTSR QTTIMVTKYS EKSPITIPFE LSAACLTYLR ETFEGTILDK ILNVEAMHTV LRALKNTADA ...String:
MENWSALELL PKVGIPTDFL THVKTSAGEE MFEALRIYYG DDPERYNIHF EAIFGTFCNR LEWVYFLTSG LAAAAHAIKF HDLNKLTTGK MLFHVQVPRV ASGAGLPTSR QTTIMVTKYS EKSPITIPFE LSAACLTYLR ETFEGTILDK ILNVEAMHTV LRALKNTADA MERGLIHSFL QTLLRKAPPY FVVQTLVENA TLARQALNRI QRSNILQSFK AKMLATLFLL NRTRDRDYVL KFLTRLAEAA TDSILDNPTT YTTSSGAKIS GVMVSTANVM QIIMSLLSSH ITKETVSAPA TYGNFVLSPE NAVTAISYHS ILADFNSYKA HLTSGQPHLP NDSLSQAGAH SLTPLSMDVI RLGEKTVIME NLRRVYKNTD TKDPLERNVD LTFFFPVGLY LPEDRGYTTV ESKVKLNDTV RNALPTTAYL LNRDRAVQKI DFVDALKTLC HPVLHEPAPC LQTFTERGPP SEPAMQRLLE CRFQQEPMGG AARRIPHFYR VRREVPRTVN EMKQDFVVTD FYKVGNITLY TELHPFFDFT HCQENSETVA LCTPRIVIGN LPDGLAPGPF HELRTWEIME HMRLRPPPDY EETLRLFKTT VTSPNYPELC YLVDVLVHGN VDAFLLIRTF VARCIVNMFH TRQLLVFAHS YALVTLIAEH LADGALPPQL LFHYRNLVAV LRLVTRISAL PGLNNGQLAE EPLSAYVNAL HDHRLWPPFV THLPRNMEGV QVVADRQPLN PANIEARHHG VSDVPRLGAM DADEPLFVDD YRATDDEWTL QKVFYLCLMP AMTNNRACGL GLNLKTLLVD LFYRPAFLLM PAATAVSTSG TTSKESTSGV TPEDSIAAQR QAVGEMLTEL VEDVATDAHT PLLQACRELF LAVQFVGEHV KVLEVRAPLD HAQRQGLPDF ISRQHVLYNG CCVVTAPKTL IEYSLPVPFH RFYSNPTICA ALSDDIKRYV TEFPHYHRHD GGFPLPTAFA HEYHNWLRSP FSRYSATCPN VLHSVMTLAA MLYKISPVSL VLQTKAHIHP GFALTAVRTD TFEVDMLLYS GKSCTSVIIN NPIVTKEERD ISTTYHVTQN INTVDMGLGY TSNTCVAYVN RVRTDMGVRV QDLFRVFPMN VYRHDEVDRW IRHAAGVERP QLLDTETISM LTFGSMSERN AAATVHGQKA ACELILTPVT MDVNYFKIPN NPRGRASCML AVDPYDTEAA TKAIYDHREA DAQTFAATHN PWASQAGCLS DVLYNTRHRE RLGYNSKFYS PCAQYFNTEE IIAANKTLFK TIDEYLLRAK DCIRGDTDTQ YVCVEGTEQL IENPCRLTQE ALPILSTTTL ALMETKLKGG AGAFATSETH FGNYVVGEII PLQQSMLFNS

UniProtKB: Major capsid protein

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Macromolecule #3: Triplex protein 1

MacromoleculeName: Triplex protein 1 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 5 strain AD169
SequenceString: MDARAVAKRP RDPADEDNEL VTALKAKREV NTISVRYLYH ADHQALTARF FVPEGLVEFE AQPGALLIRM ETGCDSPRHL YISLYLLGIR ASNVSASTRC LLESVYTASA ARAALQWLDL GPHLLHRRLE TLGCVKTVSL GITSLLTCVM RGYLYNTLKT EVFALMIPKD ...String:
MDARAVAKRP RDPADEDNEL VTALKAKREV NTISVRYLYH ADHQALTARF FVPEGLVEFE AQPGALLIRM ETGCDSPRHL YISLYLLGIR ASNVSASTRC LLESVYTASA ARAALQWLDL GPHLLHRRLE TLGCVKTVSL GITSLLTCVM RGYLYNTLKT EVFALMIPKD MYLTWEETRG RLQYVYLIIV YDYDGPETRP GIYVLTSSIA HWQTLVDVAR GKFARERCSF VNRRITRPRQ IPLCTGVIQK LGWCLADDIH TSFLVHKELK LSVVRLDNFS VELGDFREFV

UniProtKB: Triplex capsid protein 1

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Macromolecule #4: Triplex Protein 2

MacromoleculeName: Triplex Protein 2 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 5 strain AD169
SequenceString: MAAMEANIFC TFDHKLSIAD VGKLTKLVAA VVPIPQRLHL IKHYQLGLHQ FVDHTRGYVR LRGLLRNMTL TLMRRVEGNQ ILLHVPTHGL LYTVLNTGPV TWEKGDALCV LPPLFHGPLA RENLLTLGQW ELVLPWIVPM PLALEINQRL LIMGLFSLDR SYEEVKAAVQ ...String:
MAAMEANIFC TFDHKLSIAD VGKLTKLVAA VVPIPQRLHL IKHYQLGLHQ FVDHTRGYVR LRGLLRNMTL TLMRRVEGNQ ILLHVPTHGL LYTVLNTGPV TWEKGDALCV LPPLFHGPLA RENLLTLGQW ELVLPWIVPM PLALEINQRL LIMGLFSLDR SYEEVKAAVQ QLQTITFRDA TFTIPDPVID QHLLIDMKTA CLSMSMVANL ASELTMTYVR KLALEDSSML LVKCQELLMR LDRERSVGEP RTPARPQHVS PDDEIARLSA LFVMLRQLDD LIREQVVFTV CDVSPDNKSA TCIFKG

UniProtKB: Triplex capsid protein 2

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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

BufferpH: 7.4
Component:
ConcentrationFormulaName
387.0 mMNaClsodium chloride
2.7 mMKClPotassium Chloride
10.0 mMNa2HPO4sodium phosphate dibasic
1.8 mMKH2PO4Potassium phosphate mono basic
1.0 mMC10H16N2O8Ethylenediaminetetraacetic acid
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
DetailsHCMV B-capsids isolated from ARPE-19 cells

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.0 µm / Calibrated defocus min: 1.2 µm / Calibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 81000
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

Particle selectionNumber selected: 16242
Details: 1527 whole capsid particles selected preceding symmetry expansion and relaxation to identify positions of sub particles at each 5-fold symmetrical vertex
Startup modelType of model: OTHER / Details: gaussian ball used as whole capsid initial model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4)
Details: Sub-particle reconstruction of full capsid vertex. up to 12 sub particles per capsid
Number images used: 16242
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4) / Details: sub-particles refined using Cryosparc
FSC plot (resolution estimation)

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