+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-44640 | |||||||||||||||||||||
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Title | HCMV B-capsid vertex | |||||||||||||||||||||
Map data | map | |||||||||||||||||||||
Sample |
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Keywords | B-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 | |||||||||||||||||||||
Biological species | Human herpesvirus 5 strain AD169 | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||||||||||||||
Authors | Zhou H / Stevens A | |||||||||||||||||||||
Funding support | United States, 6 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_44640.map.gz | 483.3 MB | EMDB map data format | |
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Header (meta data) | emd-44640-v30.xml emd-44640.xml | 22.7 KB 22.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_44640_fsc.xml | 16.9 KB | Display | FSC data file |
Images | emd_44640.png | 215.2 KB | ||
Filedesc metadata | emd-44640.cif.gz | 6.8 KB | ||
Others | emd_44640_half_map_1.map.gz emd_44640_half_map_2.map.gz | 475.5 MB 475.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-44640 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-44640 | HTTPS FTP |
-Validation report
Summary document | emd_44640_validation.pdf.gz | 1.5 MB | Display | EMDB validaton report |
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Full document | emd_44640_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | emd_44640_validation.xml.gz | 26.8 KB | Display | |
Data in CIF | emd_44640_validation.cif.gz | 35.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44640 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44640 | HTTPS FTP |
-Related structure data
Related structure data | 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_44640.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.064 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half b
File | emd_44640_half_map_1.map | ||||||||||||
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Annotation | half b | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half b
File | emd_44640_half_map_2.map | ||||||||||||
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Annotation | half b | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human herpesvirus 5 strain AD169
Entire | Name: Human herpesvirus 5 strain AD169 |
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Components |
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-Supramolecule #1: Human herpesvirus 5 strain AD169
Supramolecule | Name: 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 |
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Host (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 216 MDa |
Virus shell | Shell ID: 1 / Name: capsid / Diameter: 1320.0 Å / T number (triangulation number): 16 |
-Macromolecule #1: Small capsomere-interacting protein
Macromolecule | Name: Small capsomere-interacting protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Human herpesvirus 5 strain AD169 |
Sequence | String: MSWTKQRVPF LDDDDGEEEN DVQDDVDSPV PTRPLVIDED AEPAAGTSGG LEGGGGDDED GEDGHALPDL DDDLLLQFEP MLPRVYDLLL PSLDARLNFV NAGQKYAAFL KYVHGDCATC SHGEILREKT QLLTAIVSKL MDINGILEGK DEPAPGK UniProtKB: DNA packaging protein UL33 |
-Macromolecule #2: Major Capsid Protein
Macromolecule | Name: Major Capsid Protein / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Human herpesvirus 5 strain AD169 |
Sequence | String: 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 |
-Macromolecule #3: Triplex protein 1
Macromolecule | Name: Triplex protein 1 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Human herpesvirus 5 strain AD169 |
Sequence | String: 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 |
-Macromolecule #4: Triplex Protein 2
Macromolecule | Name: Triplex Protein 2 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Human herpesvirus 5 strain AD169 |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||||||||
Details | HCMV B-capsids isolated from ARPE-19 cells |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated 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 stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |