6M5R

The coordinates of the apo monomeric terminase complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Architecture of the herpesvirus genome-packaging complex and implications for DNA translocation.

Yang, Y.Yang, P.Wang, N.Chen, Z.Su, D.Zhou, Z.H.Rao, Z.Wang, X.

(2020) Protein Cell 11: 339-351

  • DOI: 10.1007/s13238-020-00710-0
  • Primary Citation of Related Structures:  
    6M5R, 6M5S, 6M5T, 6M5U, 6M5V

  • PubMed 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 concatemeric dsDNA into procapsids but its molecular architecture and mechanism are unknown ...

    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.


    Organizational Affiliation

    CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. xiangxi@ibp.ac.cn.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tripartite terminase subunit 3A694Human alphaherpesvirus 1 strain 17Mutation(s): 0 
Gene Names: TRM3UL15
EC: 3.1
UniProt
Find proteins for P04295 (Human herpesvirus 1 (strain 17))
Explore P04295 
Go to UniProtKB:  P04295
Entity Groups  
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UniProt GroupP04295
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tripartite terminase subunit 1B774Human alphaherpesvirus 1 strain 17Mutation(s): 2 
Gene Names: TRM1UL28
UniProt
Find proteins for P10212 (Human herpesvirus 1 (strain 17))
Explore P10212 
Go to UniProtKB:  P10212
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UniProt GroupP10212
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Tripartite terminase subunit 2C118Human alphaherpesvirus 1 strain 17Mutation(s): 0 
Gene Names: UL33TRM2
UniProt
Find proteins for P10217 (Human herpesvirus 1 (strain 17))
Explore P10217 
Go to UniProtKB:  P10217
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10217
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth B],
E [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31800145 and 31570717

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-28
    Type: Initial release