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- PDB-5hx2: In vitro assembled star-shaped hubless T4 baseplate -

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Basic information

Entry
Database: PDB / ID: 5hx2
TitleIn vitro assembled star-shaped hubless T4 baseplate
Components
  • Baseplate wedge protein gp10
  • Baseplate wedge protein gp53
  • Baseplate wedge protein gp6
  • Baseplate wedge protein gp7
  • Baseplate wedge protein gp8
KeywordsVIRAL PROTEIN / T4 / baseplate / complex
Function / homology
Function and homology information


virus tail, baseplate / viral tail assembly / viral release from host cell / identical protein binding
Similarity search - Function
GMP Synthetase; Chain A, domain 3 - #200 / baseplate structural protein gp8, domain 2 / baseplate structural protein gp8, domain 2 / baseplate structural protein gp8, domain 1 / baseplate structural protein gp8, domain 1 / Baseplate wedge protein gp53, bacteriophage T4 / Baseplate wedge protein gp7 / : / : / : ...GMP Synthetase; Chain A, domain 3 - #200 / baseplate structural protein gp8, domain 2 / baseplate structural protein gp8, domain 2 / baseplate structural protein gp8, domain 1 / baseplate structural protein gp8, domain 1 / Baseplate wedge protein gp53, bacteriophage T4 / Baseplate wedge protein gp7 / : / : / : / Base plate wedge protein 53 / Baseplate wedge protein gp7, domain V / Baseplate wedge protein gp7, helical domain / Baseplate wedge protein gp7, domain VI / Baseplate wedge protein gp10 / 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 / Bacteriophage T4, Gp8 / Bacteriophage T4, Gp8 superfamily / Bacteriophage T4, Gp8 / Baseplate structural protein Gp9/Gp10 / Baseplate structural protein Gp9/Gp10 middle domain superfamily / Gp9-like superfamily / Bacteriophage T4 gp9/10-like protein / GMP Synthetase; Chain A, domain 3 / Beta Complex / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Baseplate wedge protein gp10 / Baseplate wedge protein gp53 / Baseplate wedge protein gp6 / Baseplate wedge protein gp7 / Baseplate wedge protein gp8
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsYap, M.L. / Klose, T. / Fokine, A. / Rossmann, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI081726 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2016
Title: Role of bacteriophage T4 baseplate in regulating assembly and infection.
Authors: Moh Lan Yap / Thomas Klose / Fumio Arisaka / Jeffrey A Speir / David Veesler / Andrei Fokine / Michael G Rossmann /
Abstract: Bacteriophage T4 consists of a head for protecting its genome and a sheathed tail for inserting its genome into a host. The tail terminates with a multiprotein baseplate that changes its conformation ...Bacteriophage T4 consists of a head for protecting its genome and a sheathed tail for inserting its genome into a host. The tail terminates with a multiprotein baseplate that changes its conformation from a "high-energy" dome-shaped to a "low-energy" star-shaped structure during infection. Although these two structures represent different minima in the total energy landscape of the baseplate assembly, as the dome-shaped structure readily changes to the star-shaped structure when the virus infects a host bacterium, the dome-shaped structure must have more energy than the star-shaped structure. Here we describe the electron microscopy structure of a 3.3-MDa in vitro-assembled star-shaped baseplate with a resolution of 3.8 Å. This structure, together with other genetic and structural data, shows why the high-energy baseplate is formed in the presence of the central hub and how the baseplate changes to the low-energy structure, via two steps during infection. Thus, the presence of the central hub is required to initiate the assembly of metastable, high-energy structures. If the high-energy structure is formed and stabilized faster than the low-energy structure, there will be insufficient components to assemble the low-energy structure.
History
DepositionJan 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Mar 23, 2016Group: Database references
Revision 1.3Jul 26, 2017Group: Author supporting evidence / Data collection / Category: em_software / pdbx_audit_support
Item: _em_software.details / _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.4Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.name
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Dec 18, 2019Group: Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 1.7Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_oper_list
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 / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • Biological unit as complete point assembly
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  • Deposited structure unit
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  • Superimposition on EM map
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  • Imaged by UCSF Chimera
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  • EMDB-8064
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Baseplate wedge protein gp7
B: Baseplate wedge protein gp8
C: Baseplate wedge protein gp8
D: Baseplate wedge protein gp6
E: Baseplate wedge protein gp6
F: Baseplate wedge protein gp53
G: Baseplate wedge protein gp10
H: Baseplate wedge protein gp10
I: Baseplate wedge protein gp10


Theoretical massNumber of molelcules
Total (without water)566,2419
Polymers566,2419
Non-polymers00
Water0
1
A: Baseplate wedge protein gp7
B: Baseplate wedge protein gp8
C: Baseplate wedge protein gp8
D: Baseplate wedge protein gp6
E: Baseplate wedge protein gp6
F: Baseplate wedge protein gp53
G: Baseplate wedge protein gp10
H: Baseplate wedge protein gp10
I: Baseplate wedge protein gp10
x 6


Theoretical massNumber of molelcules
Total (without water)3,397,44654
Polymers3,397,44654
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C6 (6 fold cyclic))

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Components

#1: Protein Baseplate wedge protein gp7 / Gene product 7 / gp7


Mass: 119336.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 7 / Plasmid: pET29 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19061
#2: Protein Baseplate wedge protein gp8 / Gene product 8 / gp8


Mass: 38041.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 8 / Plasmid: pET29 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19062
#3: Protein Baseplate wedge protein gp6 / Gene product 6 / gp6


Mass: 74492.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 6 / Plasmid: pET29 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19060
#4: Protein Baseplate wedge protein gp53 / Gene product 53 / gp53


Mass: 22990.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 53 / Plasmid: pET29 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P16011
#5: Protein Baseplate wedge protein gp10 / Gene product 10 / gp10


Mass: 66281.680 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 10 / Plasmid: pET29 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P10928

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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: In vitro assembled hubless T4 baseplate / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 3.3 MDa / Experimental value: NO
Source (natural)Organism: Enterobacteria phage T4 (virus)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pET29
Buffer solutionpH: 8
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 400-mesh copper CF-1.2/1.3-4C / Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: CF-1.2/1.3-4C
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 80 % / Details: Plunged into liquid ethane (GATAN CRYOPLUNGE 3).

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 22500 X / Calibrated magnification: 38168 X / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm / Calibrated defocus min: 400 nm / Calibrated defocus max: 3740 nm / Cs: 2.7 mm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 7.6 sec. / Electron dose: 35 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 1725
Image scansWidth: 7676 / Height: 7420 / Movie frames/image: 38 / Used frames/image: 3-38

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Processing

EM software
IDNameVersionCategoryDetails
1EMAN2.1particle selection
2Leginon3.1image acquisition
4CTFFIND3CTF correction
7Coot0.8.1model fitting
9RELION1.3initial Euler assignment
10jsprfinal Euler assignment
11RELION1.3classification
12jspr3D reconstruction
19PHENIX1.10.1model refinementPHENIX.real_space_refine
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 69920
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45607 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
13H2T

3h2t

13H2T1PDBexperimental model
21N80

1n80

11N802PDBexperimental model
32FKK

2fkk

12FKK3PDBexperimental model

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