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Yorodumi- PDB-6q1f: Atomic structure of the Human Herpesvirus 6B Capsid and Capsid-As... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q1f | |||||||||||||||
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Title | Atomic structure of the Human Herpesvirus 6B Capsid and Capsid-Associated Tegument Complexes | |||||||||||||||
Components |
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Keywords | VIRUS / beta-herpesvirus / HHV-6B / murine cytomegalovirus / human cytomegalovirus / pp150 / pU11 / pUL32 / pM32 / pU14 | |||||||||||||||
Function / homology | Function and homology information T=16 icosahedral viral capsid / viral tegument / viral capsid assembly / viral process / viral capsid / host cell nucleus / structural molecule activity / DNA binding Similarity search - Function | |||||||||||||||
Biological species | Human herpesvirus 6B | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9 Å | |||||||||||||||
Authors | Zhang, Y.B. / Liu, W. / Li, Z.H. / Kumar, V. / Alvarez-Cabrera, A.L. / Leibovitch, E. / Cui, Y.X. / Mei, Y. / Bi, G.Q. / Jacobson, S. / Zhou, Z.H. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Nat Commun / Year: 2019 Title: Atomic structure of the human herpesvirus 6B capsid and capsid-associated tegument complexes. Authors: Yibo Zhang / Wei Liu / Zihang Li / Vinay Kumar / Ana L Alvarez-Cabrera / Emily C Leibovitch / Yanxiang Cui / Ye Mei / Guo-Qiang Bi / Steve Jacobson / Z Hong Zhou / Abstract: Human herpesvirus 6B (HHV-6B) belongs to the β-herpesvirus subfamily of the Herpesviridae. To understand capsid assembly and capsid-tegument interactions, here we report atomic structures of HHV-6B ...Human herpesvirus 6B (HHV-6B) belongs to the β-herpesvirus subfamily of the Herpesviridae. To understand capsid assembly and capsid-tegument interactions, here we report atomic structures of HHV-6B capsid and capsid-associated tegument complex (CATC) obtained by cryoEM and sub-particle reconstruction. Compared to other β-herpesviruses, HHV-6B exhibits high similarity in capsid structure but organizational differences in its CATC (pU11 tetramer). 180 "VΛ"-shaped CATCs are observed in HHV-6B, distinguishing from the 255 "Λ"-shaped dimeric CATCs observed in murine cytomegalovirus and the 310 "Δ"-shaped CATCs in human cytomegalovirus. This trend in CATC quantity correlates with the increasing genomes sizes of these β-herpesviruses. Incompatible distances revealed by the atomic structures rationalize the lack of CATC's binding to triplexes Ta, Tc, and Tf in HHV-6B. Our results offer insights into HHV-6B capsid assembly and the roles of its tegument proteins, including not only the β-herpesvirus-specific pU11 and pU14, but also those conserved across all subfamilies of Herpesviridae. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6q1f.cif.gz | 5.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6q1f.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6q1f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6q1f_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 6q1f_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 6q1f_validation.xml.gz | 622.4 KB | Display | |
Data in CIF | 6q1f_validation.cif.gz | 1004.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/6q1f ftp://data.pdbj.org/pub/pdb/validation_reports/q1/6q1f | HTTPS FTP |
-Related structure data
Related structure data | 20557MC 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
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 152260.047 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 6B (strain Z29) / Strain: Z29 / References: UniProt: Q9QJ26 #2: Protein | Mass: 95738.125 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 6B (strain Z29) / Strain: Z29 / References: UniProt: Q69535 #3: Protein | Mass: 9827.329 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 6B (strain Z29) / Strain: Z29 / References: UniProt: Q9WT32 #4: Protein | Mass: 34162.508 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 6B (strain Z29) / Strain: Z29 / References: UniProt: Q9WT35 #5: Protein | Mass: 33514.332 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 6B (strain Z29) / Strain: Z29 / References: UniProt: Q9QJ27 |
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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 herpesvirus 6 strain Z29 / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Human herpesvirus 6 strain Z29 / Strain: Z29 |
Details of virus | Empty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION |
Buffer solution | pH: 7.4 / Details: PBS buffer, pH 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: The grids were manually plunged into the 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 magnification: 64000 X / Calibrated magnification: 64000 X / Nominal defocus max: 3200 nm / Nominal defocus min: 2200 nm / Calibrated defocus min: 2200 nm / Calibrated defocus max: 3200 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 23 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 4828 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
Particle selection | Num. of particles selected: 7430 | ||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||
3D reconstruction | Resolution: 9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6443 / Details: bin4 reconstrction / Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: OTHER |