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Yorodumi- PDB-6m5v: The coordinate of the hexameric terminase complex in the presence... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6m5v | ||||||
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Title | The coordinate of the hexameric terminase complex in the presence of the ADP-BeF3 | ||||||
Components | (Tripartite terminase subunit ...) x 3 | ||||||
Keywords | VIRAL PROTEIN | ||||||
Function / homology | Function and homology information viral DNA genome packaging / nuclease activity / viral capsid assembly / chromosome organization / viral release from host cell / protein processing / Hydrolases; Acting on ester bonds / host cell nucleus / DNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Human alphaherpesvirus 1 strain 17 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å | ||||||
Authors | Yang, Y.X. / Yang, P. / Wang, N. / Chen, Z.H. / Zhou, Z.H. / Rao, Z.H. / Wang, X.X. | ||||||
Funding support | China, 1items
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Citation | Journal: Protein Cell / Year: 2020 Title: Architecture of the herpesvirus genome-packaging complex and implications for DNA translocation. Authors: Yunxiang Yang / Pan Yang / Nan Wang / Zhonghao Chen / Dan Su / Z Hong Zhou / Zihe Rao / Xiangxi Wang / Abstract: Genome packaging is a fundamental process in a viral life cycle and a prime target of antiviral drugs. Herpesviruses use an ATP-driven packaging motor/terminase complex to translocate and cleave ...Genome packaging is a fundamental process in a viral life cycle and a prime target of antiviral drugs. Herpesviruses use an ATP-driven packaging motor/terminase complex to translocate and cleave concatemeric dsDNA into procapsids but its molecular architecture and mechanism are unknown. We report atomic structures of a herpesvirus hexameric terminase complex in both the apo and ADP•BeF3-bound states. Each subunit of the hexameric ring comprises three components-the ATPase/terminase pUL15 and two regulator/fixer proteins, pUL28 and pUL33-unlike bacteriophage terminases. Distal to the nuclease domains, six ATPase domains form a central channel with conserved basic-patches conducive to DNA binding and trans-acting arginine fingers are essential to ATP hydrolysis and sequential DNA translocation. Rearrangement of the nuclease domains mediated by regulatory domains converts DNA translocation mode to cleavage mode. Our structures favor a sequential revolution model for DNA translocation and suggest mechanisms for concerted domain rearrangements leading to DNA cleavage. | ||||||
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 | 6m5v.cif.gz | 256 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m5v.ent.gz | 198.4 KB | Display | PDB format |
PDBx/mmJSON format | 6m5v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/6m5v ftp://data.pdbj.org/pub/pdb/validation_reports/m5/6m5v | HTTPS FTP |
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-Related structure data
Related structure data | 30094MC 6m5rC 6m5sC 6m5tC 6m5uC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Tripartite terminase subunit ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 76064.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human alphaherpesvirus 1 strain 17 / Strain: 17 / Gene: TRM3, UL15 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P04295, Hydrolases; Acting on ester bonds |
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#2: Protein | Mass: 84187.359 Da / Num. of mol.: 1 / Mutation: R216S, R312Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human alphaherpesvirus 1 strain 17 / Strain: 17 / Gene: TRM1, UL28 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P10212 |
#3: Protein | Mass: 13081.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human alphaherpesvirus 1 strain 17 / Strain: 17 / Gene: UL33, TRM2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: B9VQG1, UniProt: P10217*PLUS |
-Non-polymers , 4 types, 5 molecules
#4: Chemical | ChemComp-ADP / |
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#5: Chemical | ChemComp-BEF / |
#6: Chemical | ChemComp-MG / |
#7: Chemical |
-Details
Has ligand of interest | N |
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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: HSV-1 terminase complex in presence of ADP-BeF3 / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Source (natural) | Organism: Human alphaherpesvirus 1 strain 17 |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.5 |
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 FIELDBright-field microscopy |
Image recording | Electron dose: 2 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7841 / Symmetry type: POINT |