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- PDB-9jz0: portal-tail complex of DNA-ejected T7 -

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Basic information

Entry
Database: PDB / ID: 9jz0
Titleportal-tail complex of DNA-ejected T7
Components
  • (Tail tubular protein ...) x 2
  • Internal virion protein gp14
  • Portal protein
  • Protein 6.7
  • Tail fiber protein
KeywordsVIRAL PROTEIN / Complex
Function / homology
Function and homology information


virus tail, tube / viral portal complex / virus tail, fiber / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / T=7 icosahedral viral capsid / adhesion receptor-mediated virion attachment to host cell / virion component / symbiont entry into host cell / virion attachment to host cell ...virus tail, tube / viral portal complex / virus tail, fiber / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / T=7 icosahedral viral capsid / 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
Bacteriophage T7-like, protein 6.7 / Bacteriophage T7-like, protein 6.7 / Internal virion protein Gp14 / T7 virus internal virion protein gp14 family / : / Tail fibre protein gp37 trimerization region / Bacteriophage T7, Gp17, C-terminal / Tail fibre protein gp37 C terminal domain / Tail tubular protein Gp11 / Tail tubular protein ...Bacteriophage T7-like, protein 6.7 / Bacteriophage T7-like, protein 6.7 / Internal virion protein Gp14 / T7 virus internal virion protein gp14 family / : / Tail fibre protein gp37 trimerization region / Bacteriophage T7, Gp17, C-terminal / Tail fibre protein gp37 C terminal domain / Tail tubular protein Gp11 / Tail tubular protein / Bacteriophage T7 tail fibre protein / Phage T7 tail fibre protein, N-terminal domain / Portal protein, Caudovirales / Head-to-tail connector protein, podovirus-type / Bacteriophage head to tail connecting protein
Similarity search - Domain/homology
Internal virion protein gp14 / Portal protein / Tail tubular protein gp11 / Tail tubular protein gp12 / Tail fiber protein / Protein 6.7
Similarity search - Component
Biological speciesEscherichia phage T7 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 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) China
CitationJournal: To Be Published
Title: portal-tail complex of DNA-ejected 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
0: Internal virion protein gp14
1: Internal virion protein gp14
2: Protein 6.7
3: Protein 6.7
4: Protein 6.7
5: Protein 6.7
6: Protein 6.7
7: Protein 6.7
8: Protein 6.7
9: Protein 6.7
A: Portal protein
AA: Protein 6.7
AB: Protein 6.7
AC: Protein 6.7
AD: Protein 6.7
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: Portal protein
L: Portal protein
M: Tail tubular protein gp11
N: Tail tubular protein gp11
O: Tail tubular protein gp11
P: Tail tubular protein gp11
Q: Tail tubular protein gp11
R: Tail tubular protein gp11
S: Tail tubular protein gp11
T: Tail tubular protein gp11
U: Tail tubular protein gp11
V: Tail tubular protein gp11
W: Tail tubular protein gp11
X: Tail tubular protein gp11
Y: Internal virion protein gp14
Z: Internal virion protein gp14
a: Tail fiber protein
b: Tail fiber protein
c: Tail fiber protein
d: Tail fiber protein
e: Tail fiber protein
f: Tail fiber protein
g: Tail fiber protein
h: Tail fiber protein
i: Tail fiber protein
j: Tail fiber protein
k: Tail fiber protein
l: Tail fiber protein
m: Tail fiber protein
n: Tail fiber protein
o: Tail fiber protein
p: Tail fiber protein
q: Tail fiber protein
r: Tail fiber protein
s: Tail tubular protein gp12
t: Tail tubular protein gp12
u: Tail tubular protein gp12
v: Tail tubular protein gp12
w: Tail tubular protein gp12
x: Tail tubular protein gp12
y: Internal virion protein gp14
z: Internal virion protein gp14


Theoretical massNumber of molelcules
Total (without water)2,862,41666
Polymers2,862,41666
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

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Protein , 4 types, 48 molecules 01YZyz23456789AAABACADABCDEFGHIJKL...

#1: Protein
Internal virion protein gp14 / Gene product 14 / Gp14


Mass: 20990.842 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T7 (virus) / References: UniProt: P03724
#2: Protein
Protein 6.7 / Gene product 6.7 / Gp6.7


Mass: 9354.512 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T7 (virus) / References: UniProt: P03801
#3: Protein
Portal protein / Gene product 8 / Gp8 / Head-to-tail connector


Mass: 59173.984 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T7 (virus) / References: UniProt: P03728
#5: Protein
Tail fiber protein / Gene product 17 / Gp17 / Tail fiber protein gp17


Mass: 61641.875 Da / Num. of mol.: 18 / 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, 18 molecules MNOPQRSTUVWXstuvwx

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


Mass: 22307.650 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T7 (virus) / References: UniProt: P03746
#6: Protein
Tail tubular protein gp12 / Gene product 12 / Gp12


Mass: 89480.594 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T7 (virus) / References: UniProt: P03747

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Details

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: YES / 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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23461 / Symmetry type: POINT

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