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- PDB-5lxk: NMR structure of the C-terminal domain of the Bacteriophage T5 de... -

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Basic information

Entry
Database: PDB / ID: 5lxk
TitleNMR structure of the C-terminal domain of the Bacteriophage T5 decoration protein pb10.
ComponentsDecoration protein
KeywordsVIRAL PROTEIN / Bacteriophage T5 Decoration Protein
Function / homologyviral capsid, decoration / Immunoglobulin domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Decoration protein
Function and homology information
Biological speciesEscherichia phage T5 (virus)
MethodSOLUTION NMR / simulated annealing
AuthorsVernhes, E. / Gilquin, B. / Cuniasse, P. / Boulanger, P. / Zinn-Justin, S.
Funding support France, 1items
OrganizationGrant numberCountry
FRISBIANR-10-INSB-05-01 France
CitationJournal: Sci Rep / Year: 2017
Title: High affinity anchoring of the decoration protein pb10 onto the bacteriophage T5 capsid.
Authors: Emeline Vernhes / Madalena Renouard / Bernard Gilquin / Philippe Cuniasse / Dominique Durand / Patrick England / Sylviane Hoos / Alexis Huet / James F Conway / Anatoly Glukhov / Vladimir ...Authors: Emeline Vernhes / Madalena Renouard / Bernard Gilquin / Philippe Cuniasse / Dominique Durand / Patrick England / Sylviane Hoos / Alexis Huet / James F Conway / Anatoly Glukhov / Vladimir Ksenzenko / Eric Jacquet / Naïma Nhiri / Sophie Zinn-Justin / Pascale Boulanger /
Abstract: Bacteriophage capsids constitute icosahedral shells of exceptional stability that protect the viral genome. Many capsids display on their surface decoration proteins whose structure and function ...Bacteriophage capsids constitute icosahedral shells of exceptional stability that protect the viral genome. Many capsids display on their surface decoration proteins whose structure and function remain largely unknown. The decoration protein pb10 of phage T5 binds at the centre of the 120 hexamers formed by the major capsid protein. Here we determined the 3D structure of pb10 and investigated its capsid-binding properties using NMR, SAXS, cryoEM and SPR. Pb10 consists of an α-helical capsid-binding domain and an Ig-like domain exposed to the solvent. It binds to the T5 capsid with a remarkably high affinity and its binding kinetics is characterized by a very slow dissociation rate. We propose that the conformational exchange events observed in the capsid-binding domain enable rearrangements upon binding that contribute to the quasi-irreversibility of the pb10-capsid interaction. Moreover we show that pb10 binding is a highly cooperative process, which favours immediate rebinding of newly dissociated pb10 to the 120 hexamers of the capsid protein. In extreme conditions, pb10 protects the phage from releasing its genome. We conclude that pb10 may function to reinforce the capsid thus favouring phage survival in harsh environments.
History
DepositionSep 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Decoration protein


Theoretical massNumber of molelcules
Total (without water)10,3391
Polymers10,3391
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5570 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Decoration protein / Capsid protein pb10


Mass: 10339.291 Da / Num. of mol.: 1 / Fragment: C-terminal domain, UNP residues 73-164
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage T5 (virus) / Gene: N5, T5.151, T5p147 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6QGD6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic23D TOCSY-NOESY
131isotropic23D HNHA
141isotropic23D CBCA(CO)NH
151isotropic23D HN(CA)CB
161isotropic23D HNCO
171isotropic23D HN(CA)CO
181isotropic23D HBHA(CO)NH
191isotropic23D HN(CO)CA
1101isotropic23D HN(CA)NNH

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Sample preparation

DetailsType: solution
Contents: 200 uM [U-99% 13C; U-99% 15N] c72, 90% H2O/10% D2O
Label: 15N_C13_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 200 uM / Component: c72 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 25 mM / Label: condition_1 / pH: 7.2 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX7002

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Processing

NMR software
NameDeveloperClassification
CcpNmr AnalysisCCPNdata analysis
INCASavarin P., Zinn-Justin S., Gilquin B., 19,2001, J. Biomol NMR, pp. 49-62structure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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