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- PDB-6pxe: Crystal structure of the complex between periplasmic domains of a... -

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Basic information

Entry
Database: PDB / ID: 6pxe
TitleCrystal structure of the complex between periplasmic domains of antiholin RI and holin T from T4 phage, in P21
Components
  • Antiholin
  • Holin
KeywordsVIRAL PROTEIN / phage / lysis inhibition
Function / homology
Function and homology information


host cell periplasmic space / pore-forming activity / molecular function inhibitor activity / viral release from host cell by cytolysis / killing of cells of another organism / host cell plasma membrane / DNA binding / membrane
Similarity search - Function
Bacteriophage T4, GpT, holin / Bacteriophage T holin / Antiholin T4 type / T4-like virus antiholin family
Similarity search - Domain/homology
Holin / Holin / Antiholin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Escherichia phage vB_EcoM_NBG2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKrieger, I.V. / Sacchettini, J.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Welch FoundationA-0015 United States
CitationJournal: J Mol Biol / Year: 2020
Title: The Structural Basis of T4 Phage Lysis Control: DNA as the Signal for Lysis Inhibition.
Authors: Inna V Krieger / Vladimir Kuznetsov / Jeng-Yih Chang / Junjie Zhang / Samir H Moussa / Ryland F Young / James C Sacchettini /
Abstract: Optimal phage propagation depends on the regulation of the lysis of the infected host cell. In T4 phage infection, lysis occurs when the holin protein (T) forms lesions in the host membrane. However, ...Optimal phage propagation depends on the regulation of the lysis of the infected host cell. In T4 phage infection, lysis occurs when the holin protein (T) forms lesions in the host membrane. However, the lethal function of T can be blocked by an antiholin (RI) during lysis inhibition (LIN). LIN sets if the infected cell undergoes superinfection, then the lysis is delayed until host/phage ratio becomes more favorable for the release of progeny. It has been thought that a signal derived from the superinfection is required to activate RI. Here we report structures that suggest a radically different model in which RI binds to T irrespective of superinfection, causing it to accumulate in a membrane as heterotetrameric 2RI-2T complex. Moreover, we show the complex binds non-specifically to DNA, suggesting that the gDNA from the superinfecting phage serves as the LIN signal and that stabilization of the complex by DNA binding is what defines LIN. Finally, we show that soluble domain of free RI crystallizes in a domain-swapped homotetramer, which likely works as a sink for RI molecules released from the RI-T complex to ensure efficient lysis. These results constitute the first structural basis and a new model not only for the historic LIN phenomenon but also for the temporal regulation of phage lysis in general.
History
DepositionJul 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: Antiholin
T: Holin
A: Antiholin
B: Holin
C: Antiholin
D: Holin
E: Antiholin
F: Holin


Theoretical massNumber of molelcules
Total (without water)112,0548
Polymers112,0548
Non-polymers00
Water55831
1
R: Antiholin
T: Holin
A: Antiholin
B: Holin


Theoretical massNumber of molelcules
Total (without water)56,0274
Polymers56,0274
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-24 kcal/mol
Surface area19700 Å2
MethodPISA
2
C: Antiholin
D: Holin
E: Antiholin
F: Holin


Theoretical massNumber of molelcules
Total (without water)56,0274
Polymers56,0274
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
ΔGint-24 kcal/mol
Surface area21170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.590, 82.560, 81.433
Angle α, β, γ (deg.)90.000, 102.160, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Antiholin / Protein rI


Mass: 8801.884 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: rI, 58.6, rIA, tk.-2 / Production host: Escherichia coli (E. coli) / References: UniProt: P13304
#2: Protein
Holin


Mass: 19211.615 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage vB_EcoM_NBG2 (virus) / Gene: vBEcoMNBG2_239 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2U8QQK7, UniProt: P06808*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.63 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 25% PEG 3,350 with 0.1M citric acid pH 3.5

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.987 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.3→45.8 Å / Num. obs: 44230 / % possible obs: 97.4 % / Redundancy: 5.07 % / Biso Wilson estimate: 35.29 Å2 / Rmerge(I) obs: 0.1506 / Net I/σ(I): 7.57
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.7874 / Num. unique obs: 2168

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Processing

Software
NameVersionClassification
SAINTdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
PROTEUM PLUSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PSK

6psk


Resolution: 2.3→39.803 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 33.14
RfactorNum. reflection% reflection
Rfree0.2928 2152 4.87 %
Rwork0.2318 --
obs0.2347 44144 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.32 Å2 / Biso mean: 37.7695 Å2 / Biso min: 14.41 Å2
Refinement stepCycle: final / Resolution: 2.3→39.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7297 0 0 31 7328
Biso mean---30.52 -
Num. residues----889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017492
X-RAY DIFFRACTIONf_angle_d1.03310114
X-RAY DIFFRACTIONf_chiral_restr0.0511048
X-RAY DIFFRACTIONf_plane_restr0.0071304
X-RAY DIFFRACTIONf_dihedral_angle_d5.9044500
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.35350.37161250.3027273695
2.3535-2.41240.41261280.3128275095
2.4124-2.47760.41711280.3153275896
2.4776-2.55050.36381310.3068277496
2.5505-2.63280.37071590.2989276597
2.6328-2.72690.36951640.2836279198
2.7269-2.8360.30541570.2755280298
2.836-2.96510.34911310.2789282299
2.9651-3.12130.32851320.2513286799
3.1213-3.31680.29891510.2433280498
3.3168-3.57280.31171500.2354281698
3.5728-3.9320.32691290.2187276795
3.932-4.50030.21311420.1812281698
4.5003-5.66730.22371500.1764286699
5.6673-39.80.20861750.1807285897

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