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- PDB-8e4g: Remodeling of the bacteriophage T7 during initial infection -

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Basic information

Entry
Database: PDB / ID: 8e4g
TitleRemodeling of the bacteriophage T7 during initial infection
Components
  • (Internal virion protein ...) x 2
  • (Tail tubular protein ...) x 2
  • Portal protein
  • Tail fiber protein
KeywordsVIRUS / T7 / tail machine / adsorption / genome ejection
Function / homology
Function and homology information


host cell periplasmic space / virus tail, tube / viral portal complex / virus tail, fiber / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / adhesion receptor-mediated virion attachment to host cell / virion component / symbiont entry into host cell / virion attachment to host cell ...host cell periplasmic space / virus tail, tube / viral portal complex / virus tail, fiber / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / adhesion receptor-mediated virion attachment to host cell / virion component / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / identical protein binding / membrane
Similarity search - Function
Internal virion protein Gp14 / : / Tail fibre protein gp37 trimerization region / Bacteriophage T7, Gp17, C-terminal / Internal virion protein Gp15 / Tail fibre protein gp37 C terminal domain / Tail tubular protein Gp11 / Tail tubular protein / Bacteriophage T7 tail fibre protein / Phage T7 tail fibre protein ...Internal virion protein Gp14 / : / Tail fibre protein gp37 trimerization region / Bacteriophage T7, Gp17, C-terminal / Internal virion protein Gp15 / Tail fibre protein gp37 C terminal domain / Tail tubular protein Gp11 / Tail tubular protein / Bacteriophage T7 tail fibre protein / Phage T7 tail fibre protein / Portal protein, Caudovirales / Head-to-tail connector protein, podovirus-type / Bacteriophage head to tail connecting protein
Similarity search - Domain/homology
Internal virion protein gp14 / Internal virion protein gp15 / Portal protein / Tail tubular protein gp11 / Tail tubular protein gp12 / Tail fiber protein
Similarity search - Component
Biological speciesEscherichia phage T7 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWang, C. / Liu, J. / Molineux, I.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Virion remodeling of bacteriophage T7 during infection initiation
Authors: Wang, C. / Park, T. / Liu, J. / Molineux, I.J.
History
DepositionAug 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
r: Portal protein
0: Tail tubular protein gp11
5: Tail tubular protein gp11
O: Tail fiber protein
P: Tail tubular protein gp12
Y: Tail fiber protein
a: Internal virion protein gp14
x: Internal virion protein gp15
g: Tail fiber protein
u: Portal protein


Theoretical massNumber of molelcules
Total (without water)320,49910
Polymers320,49910
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 5 molecules ruOYg

#1: Protein Portal protein / Gene product 8 / Gp8 / Head-to-tail connector


Mass: 55414.727 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T7 (virus) / References: UniProt: P03728
#3: Protein Tail fiber protein


Mass: 18604.920 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T7 (virus) / References: UniProt: P03748

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Tail tubular protein ... , 2 types, 3 molecules 05P

#2: Protein Tail tubular protein gp11 / Gene product 11 / Gp11


Mass: 22307.650 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T7 (virus) / References: UniProt: P03746
#4: Protein Tail tubular protein gp12


Mass: 89563.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T7 (virus) / References: UniProt: P03747

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Internal virion protein ... , 2 types, 2 molecules ax

#5: Protein Internal virion protein gp14


Mass: 14016.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T7 (virus) / References: UniProt: P03724
#6: Protein Internal virion protein gp15


Mass: 5659.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T7 (virus) / References: UniProt: P03725

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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: Escherichia phage T7 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Escherichia phage T7 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1200 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29784 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00322574
ELECTRON MICROSCOPYf_angle_d0.49830595
ELECTRON MICROSCOPYf_dihedral_angle_d3.9783110
ELECTRON MICROSCOPYf_chiral_restr0.0413407
ELECTRON MICROSCOPYf_plane_restr0.0044023

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