+Open data
-Basic information
Entry | Database: PDB / ID: 8hex | ||||||
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Title | C5 portal vertex in HCMV B-capsid | ||||||
Components |
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Keywords | VIRAL PROTEIN / B-capsid / C5 portal vertex / in-situ structure / VIRUS | ||||||
Function / homology | Function and homology information T=16 icosahedral viral capsid / viral genome packaging / viral capsid assembly / viral release from host cell / chromosome organization / viral process / viral capsid / host cell nucleus / structural molecule activity / DNA binding Similarity search - Function | ||||||
Biological species | Human betaherpesvirus 5 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | ||||||
Authors | Li, Z. / Yu, X. | ||||||
Funding support | China, 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hex.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8hex.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8hex.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/he/8hex ftp://data.pdbj.org/pub/pdb/validation_reports/he/8hex | HTTPS FTP |
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-Related structure data
Related structure data | 34696MC 8heuC 8hevC 8heyC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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3 |
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Symmetry | Point symmetry: (Schoenflies symbol: C5 (5 fold cyclic)) |
-Components
-Triplex capsid protein ... , 2 types, 6 molecules hInogm
#1: Protein | Mass: 34635.750 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Human betaherpesvirus 5 / References: UniProt: Q6RXF2 #2: Protein | Mass: 33071.270 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human betaherpesvirus 5 / References: UniProt: Q6RXH2 |
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-Capsid vertex component ... , 2 types, 3 molecules MNO
#3: Protein | Mass: 68567.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human betaherpesvirus 5 / References: UniProt: A0A6C0PJD3 |
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#4: Protein | Mass: 71269.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human betaherpesvirus 5 / References: UniProt: A0A3G6XKK5 |
-Protein , 2 types, 10 molecules RSijaBCDYZ
#5: Protein | Mass: 8495.924 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Human betaherpesvirus 5 / References: UniProt: A8T7C4 #6: Protein | Mass: 154048.906 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Human betaherpesvirus 5 / References: UniProt: A0A1U8QPG3 |
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-Protein/peptide , 3 types, 4 molecules AEFG
#7: Protein/peptide | Mass: 3592.419 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human betaherpesvirus 5 #8: Protein/peptide | | Mass: 1294.587 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human betaherpesvirus 5 #9: Protein/peptide | | Mass: 1124.378 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human betaherpesvirus 5 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Human betaherpesvirus 5 / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Human betaherpesvirus 5 |
Details of virus | Empty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2300 nm / Nominal defocus min: 900 nm |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26181 / Symmetry type: POINT |