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- PDB-6m5t: The coordinate of the nuclease domain of the apo terminase complex -

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Basic information

Entry
Database: PDB / ID: 6m5t
TitleThe coordinate of the nuclease domain of the apo terminase complex
ComponentsTripartite terminase subunit 3
KeywordsVIRAL PROTEIN / HSV-1 / nuclease domain / apo terminase complex
Function / homology
Function and homology information


chromosome organization / Hydrolases; Acting on ester bonds / hydrolase activity / host cell nucleus / DNA binding
Similarity search - Function
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
Tripartite terminase subunit 3
Similarity search - Component
Biological speciesHuman alphaherpesvirus 1 strain 17
MethodELECTRON MICROSCOPY / single particle reconstruction / MOLECULAR REPLACEMENT / cryo EM / Resolution: 3.6 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 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.ls_d_res_high / _refine.ls_d_res_low

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Structure visualization

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Assembly

Deposited unit
A: Tripartite terminase subunit 3


Theoretical massNumber of molelcules
Total (without water)30,9191
Polymers30,9191
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12650 Å2

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Components

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


Mass: 30918.906 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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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 nuclease domain of terminase complex / Type: COMPLEX / Entity ID: all / 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: 1.8.1_1168 / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42053 / Symmetry type: POINT
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3N4P

3n4p


Resolution: 3.6→3.6 Å / SU ML: 0.29 / σ(F): 1.36 / Phase error: 26.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.247 1718 5.01 %
Rwork0.203 --
obs0.205 34293 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.77 Å2
Refinement stepCycle: LAST / Resolution: 2.46→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1715 0 0 0 1715
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.015243
ELECTRON MICROSCOPYf_angle_d1.357126
ELECTRON MICROSCOPYf_dihedral_angle_d16.9121853
ELECTRON MICROSCOPYf_chiral_restr0.092826
ELECTRON MICROSCOPYf_plane_restr0.008913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.458-2.52980.30661350.25762560ELECTRON MICROSCOPY95
2.5298-2.61130.31361400.23062660ELECTRON MICROSCOPY99
2.6113-2.70440.2551410.21792670ELECTRON MICROSCOPY100
2.7044-2.81240.26981410.22272677ELECTRON MICROSCOPY100
2.8124-2.940.27511430.22982706ELECTRON MICROSCOPY100
2.94-3.09440.31511410.23482675ELECTRON MICROSCOPY100
3.0944-3.28750.30091410.23642703ELECTRON MICROSCOPY100
3.2875-3.540.27061440.2052703ELECTRON MICROSCOPY100
3.54-3.89380.25261450.18872751ELECTRON MICROSCOPY100
3.8938-4.45170.20261430.16752737ELECTRON MICROSCOPY100
4.4517-5.58760.23141480.182795ELECTRON MICROSCOPY100
5.5876-19.79920.21711560.21472938ELECTRON MICROSCOPY100
Refinement TLS params.Method: refined / Origin x: 56.6268 Å / Origin y: 36.7358 Å / Origin z: 11.8879 Å
111213212223313233
T0.3639 Å2-0.0166 Å2-0.0491 Å2-0.297 Å20.0416 Å2--0.4978 Å2
L0.5702 °2-0.1437 °2-0.056 °2-0.4471 °20.253 °2--0.5053 °2
S0.0107 Å °-0.0214 Å °-0.1035 Å °0.1706 Å °0.0011 Å °-0.0697 Å °0.1718 Å °0.0138 Å °-0.0079 Å °
Refinement TLS groupSelection details: all

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