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- PDB-3h3w: Fitting of the gp6 crystal structure into 3D cryo-EM reconstructi... -

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Basic information

Entry
Database: PDB / ID: 3h3w
TitleFitting of the gp6 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 dome-shaped baseplate
ComponentsBaseplate structural protein Gp6
KeywordsVIRAL PROTEIN / viral structural protein / Virion
Function / homology
Function and homology information


virus tail, baseplate / viral tail assembly / identical protein binding
Similarity search - Function
Baseplate wedge protein gp6 / : / : / : / : / : / Baseplate wedge protein gp6-like, helical domain / Baseplate structural protein gp6, C-terminal domain I / Baseplate structural protein gp6, C-terminal domain II / Baseplate wedge protein gp6, domain II / Baseplate structural protein gp6, C-terminal domain III
Similarity search - Domain/homology
Baseplate wedge protein gp6
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12 Å
AuthorsAksyuk, A.A. / Leiman, P.G. / Shneider, M.M. / Mesyanzhinov, V.V. / Rossmann, M.G.
CitationJournal: Structure / Year: 2009
Title: The structure of gene product 6 of bacteriophage T4, the hinge-pin of the baseplate.
Authors: Anastasia A Aksyuk / Petr G Leiman / Mikhail M Shneider / Vadim V Mesyanzhinov / Michael G Rossmann /
Abstract: The baseplate of bacteriophage T4 is a multicomponent protein complex, which controls phage attachment to the host. It assembles from six wedges and a central hub. During infection the baseplate ...The baseplate of bacteriophage T4 is a multicomponent protein complex, which controls phage attachment to the host. It assembles from six wedges and a central hub. During infection the baseplate undergoes a large conformational change from a dome-shaped to a flat, star-shaped structure. We report the crystal structure of the C-terminal half of gene product (gp) 6 and investigate its motion with respect to the other proteins during the baseplate rearrangement. Six gp6 dimers interdigitate, forming a ring that maintains the integrity of the baseplate in both conformations. One baseplate wedge contains an N-terminal dimer of gp6, whereas neighboring wedges are tied together through the C-terminal dimer of gp6. The dimeric interactions are preserved throughout the rearrangement of the baseplate. However, the hinge angle between the N- and C-terminal parts of gp6 changes by approximately 15 degrees , accounting for a 10 A radial increase in the diameter of the gp6 ring.
History
DepositionApr 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _struct_ref_seq_dif.details

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Baseplate structural protein Gp6
B: Baseplate structural protein Gp6
C: Baseplate structural protein Gp6
D: Baseplate structural protein Gp6
E: Baseplate structural protein Gp6
F: Baseplate structural protein Gp6
G: Baseplate structural protein Gp6
H: Baseplate structural protein Gp6
I: Baseplate structural protein Gp6
J: Baseplate structural protein Gp6
K: Baseplate structural protein Gp6
L: Baseplate structural protein Gp6


Theoretical massNumber of molelcules
Total (without water)459,65312
Polymers459,65312
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
SymmetryPoint symmetry: (Schoenflies symbol: C6 (6 fold cyclic))

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Components

#1: Protein
Baseplate structural protein Gp6 / Baseplate wedge protein 6


Mass: 38304.449 Da / Num. of mol.: 12 / Fragment: gene product 6 deletion fragment / Mutation: residues 334-660
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19060

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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

Component
IDNameTypeParent-IDDetails
1bacteriophage T4 dome-shaped baseplateVIRUS0
2ring of 12 molecules of gene product 61assembly of gp6 in the dome-shaped baseplate of bacteriophage T4
Buffer solutionpH: 7
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM300FEG/T / Date: Jan 30, 2001
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 45000 X / Calibrated magnification: 47000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: 626 Single Tilt Cryotransfer System
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 12 Å

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Processing

EM software
IDNameCategoryDetails
1SITUS COLORESmodel fittingCOLORES from the SITUS program package was used for the fitting
2SPIDER3D reconstruction
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 12 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 945 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 3H2T

3h2t


Accession code: 3H2T / Source name: PDB / Type: experimental model
RefinementHighest resolution: 12 Å
Refinement stepCycle: LAST / Highest resolution: 12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31380 0 0 0 31380

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