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- PDB-5gai: Probabilistic Structural Models of Mature P22 Bacteriophage Porta... -

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Basic information

Entry
Database: PDB / ID: 5gai
TitleProbabilistic Structural Models of Mature P22 Bacteriophage Portal, Hub, and Tailspike proteins
Components
  • Peptidoglycan hydrolase gp4
  • Portal protein
  • Tail fiber protein
KeywordsVIRAL PROTEIN / virion / portal / tailspike / adhesin
Function / homology
Function and homology information


viral DNA genome packaging, headful / endo-1,3-alpha-L-rhamnosidase activity / symbiont entry into host cell via disruption of host cell envelope lipopolysaccharide / symbiont entry into host cell via disruption of host cell wall peptidoglycan / viral portal complex / virus tail, fiber / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / symbiont entry into host cell via disruption of host cell envelope / symbiont entry into host ...viral DNA genome packaging, headful / endo-1,3-alpha-L-rhamnosidase activity / symbiont entry into host cell via disruption of host cell envelope lipopolysaccharide / symbiont entry into host cell via disruption of host cell wall peptidoglycan / viral portal complex / virus tail, fiber / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / symbiont entry into host cell via disruption of host cell envelope / symbiont entry into host / virus tail / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / adhesion receptor-mediated virion attachment to host cell / virion assembly / hydrolase activity / virion attachment to host cell
Similarity search - Function
Tail accessory factor GP4 / Phage P22-like portal protein / Peptidoglycan hydrolase Gp4 superfamily / P22 tail accessory factor / Phage P22-like portal protein / P22 tailspike C-terminal domain / Salmonella phage P22 tail-spike / Bacteriophage P22 tailspike, N-terminal / Phage P22 tailspike-like, N-terminal domain superfamily / Head binding ...Tail accessory factor GP4 / Phage P22-like portal protein / Peptidoglycan hydrolase Gp4 superfamily / P22 tail accessory factor / Phage P22-like portal protein / P22 tailspike C-terminal domain / Salmonella phage P22 tail-spike / Bacteriophage P22 tailspike, N-terminal / Phage P22 tailspike-like, N-terminal domain superfamily / Head binding / Autotransporter, pectate lyase C-like domain superfamily / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
Tail spike protein / Portal protein / Peptidoglycan hydrolase gp4
Similarity search - Component
Biological speciesEnterobacteria phage P22 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10.5 Å
AuthorsPintilie, G. / Chen, D.H. / Haase-Pettingell, C.A. / King, J.A. / Chiu, W.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103832 United States
National Institutes of Health/National Eye Institute (NIH/NEI)PN2EY016525 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM079429 United States
CitationJournal: Biophys J / Year: 2016
Title: Resolution and Probabilistic Models of Components in CryoEM Maps of Mature P22 Bacteriophage.
Authors: Grigore Pintilie / Dong-Hua Chen / Cameron A Haase-Pettingell / Jonathan A King / Wah Chiu /
Abstract: CryoEM continues to produce density maps of larger and more complex assemblies with multiple protein components of mixed symmetries. Resolution is not always uniform throughout a cryoEM map, and it ...CryoEM continues to produce density maps of larger and more complex assemblies with multiple protein components of mixed symmetries. Resolution is not always uniform throughout a cryoEM map, and it can be useful to estimate the resolution in specific molecular components of a large assembly. In this study, we present procedures to 1) estimate the resolution in subcomponents by gold-standard Fourier shell correlation (FSC); 2) validate modeling procedures, particularly at medium resolutions, which can include loop modeling and flexible fitting; and 3) build probabilistic models that combine high-accuracy priors (such as crystallographic structures) with medium-resolution cryoEM densities. As an example, we apply these methods to new cryoEM maps of the mature bacteriophage P22, reconstructed without imposing icosahedral symmetry. Resolution estimates based on gold-standard FSC show the highest resolution in the coat region (7.6 Å), whereas other components are at slightly lower resolutions: portal (9.2 Å), hub (8.5 Å), tailspike (10.9 Å), and needle (10.5 Å). These differences are indicative of inherent structural heterogeneity and/or reconstruction accuracy in different subcomponents of the map. Probabilistic models for these subcomponents provide new insights, to our knowledge, and structural information when taking into account uncertainty given the limitations of the observed density.
History
DepositionDec 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2May 25, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Data collection / Category: em_software / pdbx_audit_support
Item: _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.4Jul 18, 2018Group: Data collection / Category: em_imaging_optics / Item: _em_imaging_optics.energyfilter_name
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Dec 25, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.7Mar 6, 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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Assembly

Deposited unit
A: Portal protein
B: Portal protein
C: Portal protein
D: Portal protein
E: Portal protein
F: Portal protein
G: Portal protein
H: Portal protein
I: Portal protein
J: Portal protein
K: Peptidoglycan hydrolase gp4
L: Peptidoglycan hydrolase gp4
M: Peptidoglycan hydrolase gp4
N: Peptidoglycan hydrolase gp4
O: Peptidoglycan hydrolase gp4
P: Peptidoglycan hydrolase gp4
Q: Peptidoglycan hydrolase gp4
R: Peptidoglycan hydrolase gp4
S: Peptidoglycan hydrolase gp4
T: Peptidoglycan hydrolase gp4
U: Peptidoglycan hydrolase gp4
V: Peptidoglycan hydrolase gp4
W: Portal protein
X: Portal protein
Y: Tail fiber protein
Z: Tail fiber protein
0: Tail fiber protein


Theoretical massNumber of molelcules
Total (without water)1,394,35427
Polymers1,394,35427
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area365240 Å2
ΔGint-1351 kcal/mol
Surface area365230 Å2

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Components

#1: Protein
Portal protein / Gene product 1 / Gp1 / Head-to-tail connector


Mass: 82397.906 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P22 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: P26744
#2: Protein
Peptidoglycan hydrolase gp4 / Gene product 4 / Gp4 / Internal virion protein gp4


Mass: 15957.813 Da / Num. of mol.: 12 / Mutation: P150A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P22 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: P26746
#3: Protein Tail fiber protein / Endo-1 / 3-alpha-L-rhamnosidase / Endorhamnosidase / Gene product 9 / gp9 / Tail spike protein / TSP


Mass: 71361.875 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P22 (virus) / Production host: Escherichia coli (E. coli)
References: UniProt: P12528, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds

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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: Enterobacteria phage P22 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightValue: 50.7 MDa / Experimental value: YES
Source (natural)Organism: Enterobacteria phage P22 (virus) / Strain: 13-am H101/C17
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Salmonella enterica subsp. enterica serovar Typhimurium
Strain: LT2
Virus shellName: gp5 / Diameter: 710 nm / Triangulation number (T number): 7
Buffer solutionpH: 7.6
Buffer componentName: 25 mM MgCl2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 120 K / Details: Blot for 2 seconds before plunging.

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Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 40000 X / Calibrated magnification: 70600 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 4000 nm / Cs: 4.1 mm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL 3200FSC CRYOHOLDER / Temperature (max): 102 K / Temperature (min): 100 K
Image recordingElectron dose: 25 e/Å2 / Film or detector model: GATAN ULTRASCAN 10000 (10k x 10k) / Num. of real images: 1130
Details: Every image was 2x hardware binned from Gatan 10kx10k CCD.
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV
Image scansSampling size: 9 µm / Width: 5000 / Height: 5000

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Processing

EM software
IDNameVersionCategoryDetails
1ETHAN1particle selectionParticle images were automatically boxed out using the program ethan.
4EMAN1CTF correction
10MPSAinitial Euler assignment
11MPSAfinal Euler assignment
12MPSAclassification
13MPSA3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 79731
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 10.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 79731 / Algorithm: FOURIER SPACE / Symmetry type: POINT

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