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- PDB-6z6e: Crystal structure of the HK97 bacteriophage small terminase -

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Basic information

Entry
Database: PDB / ID: 6z6e
TitleCrystal structure of the HK97 bacteriophage small terminase
ComponentsTerminase small subunit
KeywordsVIRAL PROTEIN / genome packaging / bacteriophage / DNA binding
Function / homologyIODIDE ION / Terminase small subunit
Function and homology information
Biological speciesEnterobacteria phage HK97 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Terminase small subunit
B: Terminase small subunit
C: Terminase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,24112
Polymers55,0993
Non-polymers1,1429
Water6,089338
1
A: Terminase small subunit
B: Terminase small subunit
C: Terminase small subunit
hetero molecules

A: Terminase small subunit
B: Terminase small subunit
C: Terminase small subunit
hetero molecules

A: Terminase small subunit
B: Terminase small subunit
C: Terminase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,72436
Polymers165,2989
Non-polymers3,42627
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area27010 Å2
ΔGint-44 kcal/mol
Surface area37340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.281, 123.281, 78.991
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALAA23 - 12322 - 122
21VALVALBB23 - 12322 - 122
12ASPASPAA24 - 12323 - 122
22ASPASPCC24 - 12323 - 122
13ASPASPBB24 - 12323 - 122
23ASPASPCC24 - 12323 - 122

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Terminase small subunit


Mass: 18366.453 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage HK97 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9MBW4
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.1 Å3/Da / Density % sol: 41.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 9% (w/v) PEG 3350, 0.1 M succinic acid, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.4→44.23 Å / Num. obs: 86871 / % possible obs: 98.8 % / Redundancy: 2.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.049 / Net I/σ(I): 10.3
Reflection shellResolution: 1.4→1.43 Å / Rmerge(I) obs: 0.707 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3870 / CC1/2: 0.525

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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: SAD / Resolution: 1.4→44.23 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.981 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.045 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1704 4469 5.1 %RANDOM
Rwork0.1591 ---
obs0.1596 82402 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.35 Å2 / Biso mean: 22.026 Å2 / Biso min: 12.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å2-0.3 Å20 Å2
2---0.6 Å20 Å2
3---1.95 Å2
Refinement stepCycle: final / Resolution: 1.4→44.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2465 0 9 338 2812
Biso mean--30.52 33 -
Num. residues----307
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192516
X-RAY DIFFRACTIONr_bond_other_d0.0020.022400
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.963408
X-RAY DIFFRACTIONr_angle_other_deg0.98535546
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7675310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.30323.543127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.81115466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6351529
X-RAY DIFFRACTIONr_chiral_restr0.0870.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212779
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02498
X-RAY DIFFRACTIONr_sphericity_free19.9557
X-RAY DIFFRACTIONr_sphericity_bonded19.46952
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.04 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A6580
12B6580
21A6518
22C6518
31B6604
32C6604
LS refinement shellResolution: 1.401→1.437 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 327 -
Rwork0.323 5644 -
all-5971 -
obs--91.78 %

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