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- PDB-6z6d: Crystal structure of the HK97 bacteriophage large terminase -

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Basic information

Entry
Database: PDB / ID: 6z6d
TitleCrystal structure of the HK97 bacteriophage large terminase
ComponentsTerminase large subunit
KeywordsVIRAL PROTEIN / genome packaging / bacteriophage / ATPase / nuclease
Function / homologyTerminase large subunit-like / Terminase large subunit-like, ATPase domain / Terminase large subunit-like, endonuclease domain / Terminase large subunit, ATPase domain / Terminase large subunit, endonuclease domain / endonuclease activity / P-loop containing nucleoside triphosphate hydrolase / BROMIDE ION / Terminase large subunit
Function and homology information
Biological speciesEnterobacteria phage HK97 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsFung, H.K.H. / Chechik, M. / Baumann, C.G. / Antson, A.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust098230 United Kingdom
Wellcome Trust095024MA United Kingdom
CitationJournal: Nucleic Acids Res / Year: 2022
Title: Structural basis of DNA packaging by a ring-type ATPase from an archetypal viral system.
Authors: Herman K H Fung / Shelley Grimes / Alexis Huet / Robert L Duda / Maria Chechik / Joseph Gault / Carol V Robinson / Roger W Hendrix / Paul J Jardine / James F Conway / Christoph G Baumann / Alfred A Antson /
Abstract: Many essential cellular processes rely on substrate rotation or translocation by a multi-subunit, ring-type NTPase. A large number of double-stranded DNA viruses, including tailed bacteriophages and ...Many essential cellular processes rely on substrate rotation or translocation by a multi-subunit, ring-type NTPase. A large number of double-stranded DNA viruses, including tailed bacteriophages and herpes viruses, use a homomeric ring ATPase to processively translocate viral genomic DNA into procapsids during assembly. Our current understanding of viral DNA packaging comes from three archetypal bacteriophage systems: cos, pac and phi29. Detailed mechanistic understanding exists for pac and phi29, but not for cos. Here, we reconstituted in vitro a cos packaging system based on bacteriophage HK97 and provided a detailed biochemical and structural description. We used a photobleaching-based, single-molecule assay to determine the stoichiometry of the DNA-translocating ATPase large terminase. Crystal structures of the large terminase and DNA-recruiting small terminase, a first for a biochemically defined cos system, reveal mechanistic similarities between cos and pac systems. At the same time, mutational and biochemical analyses indicate a new regulatory mechanism for ATPase multimerization and coordination in the HK97 system. This work therefore establishes a framework for studying the evolutionary relationships between ATP-dependent DNA translocation machineries in double-stranded DNA viruses.
History
DepositionMay 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Terminase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,80918
Polymers56,4501
Non-polymers1,35817
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-3 kcal/mol
Surface area20910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)211.787, 39.146, 65.450
Angle α, β, γ (deg.)90.000, 103.390, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Terminase large subunit


Mass: 56450.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage HK97 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9MCT1
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.6 M ammonium sulfate, pH 7.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9198 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9198 Å / Relative weight: 1
ReflectionResolution: 2.2→103.23 Å / Num. obs: 26796 / % possible obs: 99.6 % / Redundancy: 3.3 % / CC1/2: 0.991 / Rmerge(I) obs: 0.136 / Net I/σ(I): 7.1
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 0.842 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2242 / CC1/2: 0.595 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSOct 15, 2015data reduction
XDSOct 15, 2015data scaling
SHELXD2013/2phasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→103.23 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.913 / SU B: 8.595 / SU ML: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.264 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2542 1244 4.6 %RANDOM
Rwork0.2051 ---
obs0.2072 25551 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 106.49 Å2 / Biso mean: 36.887 Å2 / Biso min: 16.64 Å2
Baniso -1Baniso -2Baniso -3
1--1.69 Å20 Å2-1.69 Å2
2---1.01 Å20 Å2
3---3.14 Å2
Refinement stepCycle: final / Resolution: 2.2→103.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3522 0 18 93 3633
Biso mean--66.24 33.34 -
Num. residues----479
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193591
X-RAY DIFFRACTIONr_bond_other_d0.0010.023316
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.964894
X-RAY DIFFRACTIONr_angle_other_deg0.90537647
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8015.042479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.6524.526137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.08615549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9131518
X-RAY DIFFRACTIONr_chiral_restr0.0640.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214064
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02698
LS refinement shellResolution: 2.204→2.261 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 88 -
Rwork0.33 1820 -
all-1908 -
obs--97.85 %

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