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- PDB-9jyz: portal-tail complex of mature T7 -

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Basic information

Entry
Database: PDB / ID: 9jyz
Titleportal-tail complex of mature T7
Components
  • (Tail tubular protein ...) x 2
  • Portal protein
  • Protein 6.7
  • Protein 7.3
  • Tail fiber protein
KeywordsVIRAL PROTEIN / Complex
Function / homology
Function and homology information


virus tail, tube / viral portal complex / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / viral tail assembly / virus tail, fiber / virus tail / T=7 icosahedral viral capsid / adhesion receptor-mediated virion attachment to host cell / symbiont entry into host cell ...virus tail, tube / viral portal complex / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / viral tail assembly / virus tail, fiber / virus tail / T=7 icosahedral viral capsid / adhesion receptor-mediated virion attachment to host cell / symbiont entry into host cell / virion attachment to host cell / identical protein binding
Similarity search - Function
Bacteriophage T7-like virion assembly protein / Bacteriophage T7 virion assembly protein / Bacteriophage T7-like, protein 6.7 / Bacteriophage T7-like, protein 6.7 / : / 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 virion assembly protein / Bacteriophage T7 virion assembly protein / Bacteriophage T7-like, protein 6.7 / Bacteriophage T7-like, protein 6.7 / : / 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
Portal protein / Tail tubular protein gp11 / Tail tubular protein gp12 / Tail fiber protein / Protein 7.3 / Protein 6.7
Similarity search - Component
Biological speciesEscherichia phage T7 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 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: J Virol / Year: 2025
Title: Conformational changes in and translocation of small proteins: insights into the ejection mechanism of podophages.
Authors: Jing Zheng / Hao Xiao / Hao Pang / Li Wang / Jingdong Song / Wenyuan Chen / Lingpeng Cheng / Hongrong Liu /
Abstract: Podophage tails are too short to span the cell envelope during infection. Consequently, podophages initially eject the core proteins within the head for the formation of an elongated trans-envelope ...Podophage tails are too short to span the cell envelope during infection. Consequently, podophages initially eject the core proteins within the head for the formation of an elongated trans-envelope channel for DNA ejection. Although the core proteins of bacteriophage T7 have been resolved at near-atomic resolution, the mechanisms of core proteins and DNA ejection remain to be fully elucidated. In this study, we provided improved structures of core proteins in mature T7 and the portal-tail complex in lipopolysaccharide-induced DNA-ejected T7 to resolutions of approximately 3 Å. Using these structures, we identified three small proteins, namely gp14, gp6.7, and gp7.3, and illustrated the conformational changes in and translocation of these proteins from the mature to DNA-ejected states. Our structures indicate that gp6.7, which participates in the assembly of the core and trans-envelope channel, is a core protein, and that gp7.3 serves as a structural scaffold to assist the assembly of the nozzle into the adaptor.
IMPORTANCE: Podophage T7 core proteins form an elongated trans-envelope channel for genomic DNA delivery into the host cell. The structures of the core proteins within the mature T7 and assembled in ...IMPORTANCE: Podophage T7 core proteins form an elongated trans-envelope channel for genomic DNA delivery into the host cell. The structures of the core proteins within the mature T7 and assembled in the periplasmic tunnel form in the DNA-ejected T7 have been resolved previously. Here, we resolved the structures of two new structural proteins (gp6.7 and gp7.3) within mature T7 and receptor-induced DNA-ejected T7. The gp6.7 protein participates in the assembly of the core complex within mature T7 and the trans-envelope channel during T7 infection; therefore, gp6.7 is a core protein. Before T7 infection, gp7.3 plays a role in promoting the assembly of the nozzle into the adaptor.
History
DepositionOct 13, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: Protein 6.7
1: Protein 7.3
2: Protein 7.3
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: Tail fiber protein
AA: Protein 6.7
AB: Protein 6.7
AC: Protein 6.7
AD: Protein 6.7
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 tubular protein gp12
Q: Tail tubular protein gp12
R: Tail tubular protein gp12
S: Tail tubular protein gp12
T: Tail tubular protein gp12
U: Tail tubular protein gp11
V: Tail tubular protein gp11
W: Tail tubular protein gp11
X: Tail tubular protein gp11
Y: Tail tubular protein gp11
Z: Tail tubular protein gp11
a: Tail fiber protein
b: Tail fiber protein
c: Tail fiber protein
d: Tail tubular protein gp11
e: Tail tubular protein gp11
f: Tail tubular protein gp11
g: Tail tubular protein gp11
h: Tail tubular protein gp11
i: Tail tubular protein gp11
j: Portal protein
k: Portal protein
l: Portal protein
m: Portal protein
n: Portal protein
o: Portal protein
p: Portal protein
q: Portal protein
r: Portal protein
s: Portal protein
t: Portal protein
u: Portal protein
v: Protein 7.3
w: Protein 7.3
x: Tail tubular protein gp12
y: Protein 7.3
z: Protein 7.3


Theoretical massNumber of molelcules
Total (without water)2,797,00366
Polymers2,797,00366
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 03456789AAABACAD12vwyzABCDEFGHIJKL...

#1: 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
#2: Protein
Protein 7.3 / Gene product 7.3 / Gp7.3


Mass: 10088.708 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T7 (virus) / References: UniProt: P03751
#3: 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
#6: 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

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Tail tubular protein ... , 2 types, 18 molecules PQRSTxUVWXYZdefghi

#4: 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
#5: 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

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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: 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: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65620 / Symmetry type: POINT

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