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- PDB-6m5s: The coordinates of the apo hexameric terminase complex -

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Basic information

Entry
Database: PDB / ID: 6m5s
TitleThe coordinates of the apo hexameric terminase complex
Components
  • Tripartite terminase subunit 1
  • Tripartite terminase subunit 2
  • Tripartite terminase subunit 3
KeywordsVIRAL PROTEIN / hexamer terminase complex / apo state
Function / homology
Function and homology information


viral DNA genome packaging / chromosome organization / Hydrolases; Acting on ester bonds / hydrolase activity / host cell nucleus / DNA binding / ATP binding / metal ion binding
Similarity search - Function
Tripartite terminase subunit 1 / Herpesvirus tripartite terminase subunit 2 / Herpesvirus processing and transport protein / Herpesvirus UL33-like protein / Probable DNA packing protein, C-terminal / Probable DNA packing protein, N-terminal / Tripartite terminase subunit 3 / Probable DNA packing protein, C-terminal domain superfamily / Probable DNA packing protein, C-terminus / Probable DNA packing protein, N-terminus / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA packaging protein UL33 / Tripartite terminase subunit 3 / Tripartite terminase subunit 1 / Tripartite terminase subunit 2
Similarity search - Component
Biological speciesHuman alphaherpesvirus 1 strain 17
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsYang, Y.X. / Yang, P. / Wang, N. / Chen, Z.H. / Zhou, Z.H. / Rao, Z.H. / Wang, X.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31800145 and 31570717 China
CitationJournal: 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
DepositionMar 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_point_symmetry / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: Tripartite terminase subunit 3
B: Tripartite terminase subunit 1
C: Tripartite terminase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,1815
Polymers174,0503
Non-polymers1312
Water00
1
A: Tripartite terminase subunit 3
B: Tripartite terminase subunit 1
C: Tripartite terminase subunit 2
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)1,045,08330
Polymers1,044,29818
Non-polymers78512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C6 (6 fold cyclic))

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Components

#1: Protein Tripartite terminase subunit 3 / Terminase large subunit


Mass: 76354.094 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
#2: Protein Tripartite terminase subunit 1


Mass: 84512.750 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 Tripartite terminase subunit 2


Mass: 13182.892 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
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: HSV-1 terminase complex / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Human alphaherpesvirus 1 strain 17
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 2 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25249 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039676
ELECTRON MICROSCOPYf_angle_d0.58113128
ELECTRON MICROSCOPYf_dihedral_angle_d31.3391352
ELECTRON MICROSCOPYf_chiral_restr0.0411491
ELECTRON MICROSCOPYf_plane_restr0.0041716

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