+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34693 | |||||||||
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Title | C12 portal in HCMV B-capsid | |||||||||
Map data | ||||||||||
Sample |
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Keywords | B-capsid / portal / in-situ structure / VIRUS / VIRAL PROTEIN | |||||||||
Function / homology | Herpesvirus portal protein / Herpesvirus UL6 like / chromosome organization / Capsid portal protein Function and homology information | |||||||||
Biological species | Human betaherpesvirus 5 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Li Z / Yu X | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Cryo-electron microscopy structures of capsids and in situ portals of DNA-devoid capsids of human cytomegalovirus. Authors: Zhihai Li / Jingjing Pang / Rongchao Gao / Qingxia Wang / Maoyan Zhang / Xuekui Yu / Abstract: The portal-scaffold complex is believed to nucleate the assembly of herpesvirus procapsids. During capsid maturation, two events occur: scaffold expulsion and DNA incorporation. The portal-scaffold ...The portal-scaffold complex is believed to nucleate the assembly of herpesvirus procapsids. During capsid maturation, two events occur: scaffold expulsion and DNA incorporation. The portal-scaffold interaction and the conformational changes that occur to the portal during the different stages of capsid formation have yet to be elucidated structurally. Here we present high-resolution structures of the A- and B-capsids and in-situ portals of human cytomegalovirus. We show that scaffolds bind to the hydrophobic cavities formed by the dimerization and Johnson-fold domains of the major capsid proteins. We further show that 12 loop-helix-loop fragments-presumably from the scaffold domain-insert into the hydrophobic pocket of the portal crown domain. The portal also undergoes significant changes both positionally and conformationally as it accompanies DNA packaging. These findings unravel the mechanism by which the portal interacts with the scaffold to nucleate capsid assembly and further our understanding of scaffold expulsion and DNA incorporation. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34693.map.gz | 7.2 MB | EMDB map data format | |
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Header (meta data) | emd-34693-v30.xml emd-34693.xml | 14.1 KB 14.1 KB | Display Display | EMDB header |
Images | emd_34693.png | 35.9 KB | ||
Filedesc metadata | emd-34693.cif.gz | 5.3 KB | ||
Others | emd_34693_half_map_1.map.gz emd_34693_half_map_2.map.gz | 4.5 MB 4.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34693 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34693 | HTTPS FTP |
-Validation report
Summary document | emd_34693_validation.pdf.gz | 933.3 KB | Display | EMDB validaton report |
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Full document | emd_34693_full_validation.pdf.gz | 932.8 KB | Display | |
Data in XML | emd_34693_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | emd_34693_validation.cif.gz | 9.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34693 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34693 | HTTPS FTP |
-Related structure data
Related structure data | 8hevMC 8heuC 8hexC 8heyC 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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-Map
File | Download / File: emd_34693.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.625 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_34693_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34693_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human betaherpesvirus 5
Entire | Name: Human betaherpesvirus 5 |
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Components |
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-Supramolecule #1: Human betaherpesvirus 5
Supramolecule | Name: Human betaherpesvirus 5 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10359 / Sci species name: Human betaherpesvirus 5 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes |
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-Macromolecule #1: Portal protein
Macromolecule | Name: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Human betaherpesvirus 5 |
Molecular weight | Theoretical: 78.634805 KDa |
Sequence | String: MERNHWNEKS SGAKRSRERD LTLSTIRSIL AADERLRIKA SSYLGVGRGV DDEAVIDIFP TGQTMSFLRL LHGFLGTCRG QSMHQVLRD PCVLRKQLLY GVCKTLFDTI TVRRVAEEWK LHAALFPYRA LDEEDLEQYL LVWSASLRQS VQTGVLGALR D ILYQYADN ...String: MERNHWNEKS SGAKRSRERD LTLSTIRSIL AADERLRIKA SSYLGVGRGV DDEAVIDIFP TGQTMSFLRL LHGFLGTCRG QSMHQVLRD PCVLRKQLLY GVCKTLFDTI TVRRVAEEWK LHAALFPYRA LDEEDLEQYL LVWSASLRQS VQTGVLGALR D ILYQYADN DDYGLYVDWC VTVGLVPLLD VKTKPSEAAE RAQFVRAAVQ RATETHPLAQ DLLQANLALL LQVAERLGAV RV ANAPEVR VFKKVRSERL EAQLRGKHIR LYVAAEPLAY ERDKLLFTTP VAHLHEEILR YDGLCRHQKI CQLLNTFPVK VVT ASRHEL NCKKLVEMME QHDRGSDAKK SIMKFLLNVS DSKSRIGIED SVESFLQDLT PSLVDQNRLL PARGPGGPGV VGPG GAVVG GPAGHVGLLP PPPGPAAPER DIRDLFKKQV IKCLEEQIQS QVDEIQDLRT LNQTWENRVR ELRDLLTRYA SRRED SMSL GARDAELYHL PVLEAVRKAR DAAPFRPLAV EDNRLVANSF FSQFVPGTES LERFLTQLWE NEYFRTFRLR RLVTHQ GAE EAIVYSNYTV ERVTLPYLCH ILALGTLDPV PEAYLQLSFG EIVAAAYDDS KFCRYVELIC SREKARRRQM SREAAGG VP ERGTASSGGP GTLERSAPRR LITADEERRG PERVGRFRNG GPDDPRRAGG PYGFH UniProtKB: Capsid portal protein |
-Macromolecule #2: Unknown peptide
Macromolecule | Name: Unknown peptide / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Human betaherpesvirus 5 |
Molecular weight | Theoretical: 1.294587 KDa |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.9 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 18426 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |