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- PDB-6m5u: The coordinates of the monomeric terminase complex in the presenc... -

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Basic information

Entry
Database: PDB / ID: 6m5u
TitleThe coordinates of the monomeric terminase complex in the presence of the ADP-BeF3
Components(Tripartite terminase subunit ...) x 3
KeywordsVIRAL PROTEIN / HSV-1 / terminase complex / ADP-BeF3 / monomer
Function / homology
Function and homology information


viral DNA genome packaging / chromosome organization / Hydrolases; Acting on ester bonds / hydrolase activity / host cell nucleus / DNA binding / zinc ion binding / ATP 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
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA packaging protein UL33 / Tripartite terminase subunit 3 / Tripartite terminase subunit 1 / Tripartite terminase subunit 2
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
Human alphaherpesvirus 1 strain 17
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsYang, Y.X. / Yang, P. / Wang, N. / Zhu, L. / 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 1.0Oct 28, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 28, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 28, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Oct 28, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 28, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 18, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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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)174,8458
Polymers174,1973
Non-polymers6485
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area27530 Å2
ΔGint-215 kcal/mol
Surface area61110 Å2

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Components

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Tripartite terminase subunit ... , 3 types, 3 molecules ABC

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


Mass: 76501.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 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 herpesvirus 1 (strain 17) / Strain: 17 / Gene: UL33, TRM2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: B9VQG1, UniProt: P10217*PLUS

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Non-polymers , 4 types, 5 molecules

#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-ZN / ZINC ION


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

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Details

Has ligand of interestN
Has protein modificationN

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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 in presence of ADP-BeF3 / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Human herpesvirus 1 (Herpes simplex virus type 1)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding 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
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 106572 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039104
ELECTRON MICROSCOPYf_angle_d0.6312362
ELECTRON MICROSCOPYf_dihedral_angle_d30.0551269
ELECTRON MICROSCOPYf_chiral_restr0.041414
ELECTRON MICROSCOPYf_plane_restr0.0051599

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