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- PDB-9lu6: Structure of bacteriophage T4 protal-neck protein gp20-gp13-gp14-... -

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Basic information

Entry
Database: PDB / ID: 9lu6
TitleStructure of bacteriophage T4 protal-neck protein gp20-gp13-gp14-Hfq assembled in vitro in C6 symmetry
Components
  • Neck protein gp13
  • Neck protein gp14
  • Portal protein
  • RNA-binding protein Hfq
KeywordsVIRAL PROTEIN / Structural protein
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope, contractile tail mechanism / regulation of translation, ncRNA-mediated / viral genome packaging / regulation of RNA stability / viral release from host cell / virion component / viral capsid / regulation of DNA-templated transcription / RNA binding / cytosol
Similarity search - Function
Portal protein Gp20 / Bacteriophage T4, Gp14, neck protein / Bacteriophage T4-like portal protein (Gp20) / Virus neck protein / RNA-binding protein Hfq / Hfq protein / : / Sm domain profile. / LSM domain superfamily
Similarity search - Domain/homology
Portal protein / RNA-binding protein Hfq / Neck protein gp13 / Neck protein gp14
Similarity search - Component
Biological speciesEscherichia phage T4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsHan, L. / Mao, Q. / Sun, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of bacteriophage T4 protal-neck protein gp20-gp13-gp14-Hfq assembled in vitro in C6 symmetry
Authors: Han, L. / Mao, Q. / Sun, L.
History
DepositionFeb 7, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Neck protein gp13
l: Portal protein
X: RNA-binding protein Hfq
W: RNA-binding protein Hfq
V: RNA-binding protein Hfq
U: RNA-binding protein Hfq
T: RNA-binding protein Hfq
S: RNA-binding protein Hfq
N: Neck protein gp14
M: Neck protein gp14
O: Neck protein gp14
P: Neck protein gp14
Q: Neck protein gp14
R: Neck protein gp14
k: Portal protein
j: Portal protein
i: Portal protein
h: Portal protein
g: Portal protein
f: Portal protein
e: Portal protein
d: Portal protein
c: Portal protein
b: Portal protein
a: Portal protein
L: Neck protein gp13
A: Neck protein gp13
C: Neck protein gp13
D: Neck protein gp13
E: Neck protein gp13
F: Neck protein gp13
G: Neck protein gp13
H: Neck protein gp13
I: Neck protein gp13
J: Neck protein gp13
K: Neck protein gp13


Theoretical massNumber of molelcules
Total (without water)1,432,79036
Polymers1,432,79036
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
Neck protein gp13 / Gene product 13 / gp13


Mass: 35601.078 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: The sequence of organism Escherichia phage T4 is not available during the biocuration, replaced by P11110 temporarily.
Source: (gene. exp.) Escherichia phage T4 (virus) / Gene: 13 / Production host: Escherichia coli (E. coli) / References: UniProt: P11110
#2: Protein
Portal protein / gp20


Mass: 62177.188 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage T4 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7S9SW10
#3: Protein
RNA-binding protein Hfq


Mass: 12583.903 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: The sequence of organism Escherichia phage T4 is not available during the biocuration, replaced by A7ZV41 temporarily.
Source: (gene. exp.) Escherichia phage T4 (virus) / Gene: hfq, EcE24377A_4730 / Production host: Escherichia coli (E. coli) / References: UniProt: A7ZV41
#4: Protein
Neck protein gp14 / Gene product 14 / gp14


Mass: 30657.924 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: The sequence of organism Escherichia phage T4 is not available during the biocuration, replaced by P11111 temporarily.
Source: (gene. exp.) Escherichia phage T4 (virus) / Gene: 14 / Production host: Escherichia coli (E. coli) / References: UniProt: P11111
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: Complex of bacteriophage T4 protal-neck protein gp20-gp13-gp14-Hfq assembled in vitro
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia phage T4 (virus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
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: 2200 nm / Nominal defocus min: 1200 nm
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
1153GATAN K3 (6k x 4k)
2153FEI FALCON IV (4k x 4k)
3153FEI FALCON IV (4k x 4k)
4153FEI FALCON IV (4k x 4k)
5153FEI FALCON IV (4k x 4k)
6153FEI FALCON IV (4k x 4k)
7153FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1RELIONparticle selection
13RELION3D reconstruction
Image processing
IDImage recording-ID
11
22
33
44
55
66
77
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80622 / Symmetry type: POINT
RefinementHighest resolution: 2.91 Å

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