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- PDB-5tjt: T5 bacteriophage major capsid protein - one PB8 hexon -

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Basic information

Entry
Database: PDB / ID: 5tjt
TitleT5 bacteriophage major capsid protein - one PB8 hexon
ComponentsMajor capsid protein
KeywordsVIRAL PROTEIN / capsid / HK97 fold / hexon
Function / homologyviral scaffold / T=13 icosahedral viral capsid / Phage capsid / Phage capsid family / evasion of host immune response / viral capsid / Major capsid protein
Function and homology information
Biological speciesEscherichia phage T5 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9 Å
AuthorsConway, J. / Huet, A.
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
DepositionOct 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Database references / Category: database_2 / em_software / Item: _em_software.name
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.name
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)197,5886
Polymers197,5886
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Major capsid protein / Capsid protein pb8 / Major head protein


Mass: 32931.359 Da / Num. of mol.: 6 / Fragment: UNP residues 160-458 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T5 (virus) / References: UniProt: Q6QGD8
Has protein modificationY

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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: T5 bacteriophage major capsid protein / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Escherichia phage T5 (virus)
Details of virusEmpty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: E.Coli
Virus shellName: capsid / Diameter: 900 nm / Triangulation number (T number): 13
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 2 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) / Num. of real images: 1939
Image scansMovie frames/image: 10

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Processing

EM software
IDNameCategory
1X3Dparticle selection
4CTFFIND3CTF correction
7UCSF Chimeramodel fitting
9Auto3DEMinitial Euler assignment
10Auto3DEMfinal Euler assignment
11Auto3DEMclassification
12Auto3DEM3D reconstruction
13MDFFmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 9 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 1856 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

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