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- PDB-9jyy: core proteins of mature T7 -

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Basic information

Entry
Database: PDB / ID: 9jyy
Titlecore proteins of mature T7
Components
  • Internal virion protein gp14
  • Internal virion protein gp15
  • Peptidoglycan transglycosylase gp16
  • Protein 6.7
KeywordsVIRAL PROTEIN / Complex
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope / : / symbiont entry into host cell via disruption of host cell wall peptidoglycan / peptidoglycan lytic transglycosylase activity / symbiont genome ejection through host cell envelope, short tail mechanism / symbiont entry into host cell via disruption of host cell envelope / peptidoglycan metabolic process / symbiont entry into host / T=7 icosahedral viral capsid / virion component ...symbiont genome ejection through host cell envelope / : / symbiont entry into host cell via disruption of host cell wall peptidoglycan / peptidoglycan lytic transglycosylase activity / symbiont genome ejection through host cell envelope, short tail mechanism / symbiont entry into host cell via disruption of host cell envelope / peptidoglycan metabolic process / symbiont entry into host / T=7 icosahedral viral capsid / virion component / killing of cells of another organism / hydrolase activity / defense response to bacterium / host cell plasma membrane / membrane
Similarity search - Function
Bacteriophage T7-like, protein 6.7 / Bacteriophage T7-like, protein 6.7 / Internal virion protein Gp16 / Internal virion protein Gp14 / T7 virus internal virion protein gp14 family / Prokaryotic transglycosylase, active site / Prokaryotic transglycosylases signature. / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Internal virion protein gp14 / Peptidoglycan transglycosylase gp16 / Protein 6.7
Similarity search - Component
Biological speciesEscherichia phage T7 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsLiu, H.R. / Chen, W.Y.
Funding support China, 6items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32430020 China
National Natural Science Foundation of China (NSFC)32071209 China
National Natural Science Foundation of China (NSFC)32371263 China
National Natural Science Foundation of China (NSFC)32200994 China
National Natural Science Foundation of China (NSFC)32401014 China
CitationJournal: To Be Published
Title: core proteins of mature T7
Authors: Liu, H.R. / Chen, W.Y.
History
DepositionOct 13, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
a: Protein 6.7
b: Protein 6.7
A: Protein 6.7
D: Protein 6.7
B: Protein 6.7
E: Protein 6.7
C: Protein 6.7
F: Protein 6.7
S: Internal virion protein gp14
T: Internal virion protein gp14
c: Internal virion protein gp14
d: Internal virion protein gp14
e: Internal virion protein gp14
f: Internal virion protein gp14
g: Internal virion protein gp14
h: Internal virion protein gp14
M: Internal virion protein gp15
N: Internal virion protein gp15
O: Internal virion protein gp15
P: Internal virion protein gp15
Q: Internal virion protein gp15
R: Internal virion protein gp15
G: Internal virion protein gp15
H: Internal virion protein gp15
I: Peptidoglycan transglycosylase gp16
J: Peptidoglycan transglycosylase gp16
K: Peptidoglycan transglycosylase gp16
L: Peptidoglycan transglycosylase gp16


Theoretical massNumber of molelcules
Total (without water)1,494,50828
Polymers1,494,50828
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Protein 6.7 / Gene product 6.7 / Gp6.7


Mass: 9354.512 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T7 (virus) / References: UniProt: P03801
#2: Protein
Internal virion protein gp14 / Gene product 14 / Gp14


Mass: 20990.842 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T7 (virus) / References: UniProt: P03724
#3: Protein
Internal virion protein gp15


Mass: 84454.008 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T7 (virus)
#4: Protein
Peptidoglycan transglycosylase gp16 / Internal core protein gp16


Mass: 144028.219 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T7 (virus)
References: UniProt: P03726, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
Has protein modificationN

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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: SPECIES / Type: VIRION
Buffer solutionpH: 7.4
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 35 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 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45731 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00689024
ELECTRON MICROSCOPYf_angle_d0.72119880
ELECTRON MICROSCOPYf_dihedral_angle_d5.75612232
ELECTRON MICROSCOPYf_chiral_restr0.04413132
ELECTRON MICROSCOPYf_plane_restr0.00615936

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