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- PDB-9lc0: tail complex of mature phage N4 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9lc0
Titletail complex of mature phage N4
Components
  • 30 kDa protein
  • 60 kDa protein
  • Gp54
  • Gp64
  • Non-contractile tail sheath
KeywordsVIRAL PROTEIN / Complex
Function / homology
Function and homology information


virus tail / adhesion receptor-mediated virion attachment to host cell / symbiont entry into host cell
Similarity search - Function
Leucine-rich repeat profile. / Leucine-rich repeat
Similarity search - Domain/homology
Gp64 / Non-contractile tail sheath / 60 kDa protein / 30 kDa protein / Gp54
Similarity search - Component
Biological speciesEnterobacteria phage N4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLiu, H. / Chen, W.
Funding support China, 7items
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)32200994 China
National Natural Science Foundation of China (NSFC)32401014 China
National Natural Science Foundation of China (NSFC)32271329 China
National Natural Science Foundation of China (NSFC)32071262 China
CitationJournal: To Be Published
Title: tail complex of mature phage N4
Authors: Liu, H. / Chen, W.
History
DepositionJan 3, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data 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
A: 60 kDa protein
B: 60 kDa protein
C: 60 kDa protein
D: 60 kDa protein
E: 60 kDa protein
F: 60 kDa protein
G: 60 kDa protein
L: 60 kDa protein
Q: 60 kDa protein
V: 60 kDa protein
a: 60 kDa protein
f: 60 kDa protein
M: Gp64
R: Gp64
I: Non-contractile tail sheath
N: Non-contractile tail sheath
J: 30 kDa protein
O: 30 kDa protein
S: 30 kDa protein
H: 30 kDa protein
K: Gp54
P: Gp54
T: Gp54
U: Gp54


Theoretical massNumber of molelcules
Total (without water)1,350,56224
Polymers1,350,56224
Non-polymers00
Water00
1
A: 60 kDa protein
B: 60 kDa protein
C: 60 kDa protein
D: 60 kDa protein
E: 60 kDa protein
F: 60 kDa protein
G: 60 kDa protein
L: 60 kDa protein
Q: 60 kDa protein
V: 60 kDa protein
a: 60 kDa protein
f: 60 kDa protein
M: Gp64
R: Gp64
I: Non-contractile tail sheath
N: Non-contractile tail sheath
J: 30 kDa protein
O: 30 kDa protein
S: 30 kDa protein
H: 30 kDa protein
K: Gp54
P: Gp54
T: Gp54
U: Gp54

A: 60 kDa protein
B: 60 kDa protein
C: 60 kDa protein
D: 60 kDa protein
E: 60 kDa protein
F: 60 kDa protein
G: 60 kDa protein
L: 60 kDa protein
Q: 60 kDa protein
V: 60 kDa protein
a: 60 kDa protein
f: 60 kDa protein
M: Gp64
R: Gp64
I: Non-contractile tail sheath
N: Non-contractile tail sheath
J: 30 kDa protein
O: 30 kDa protein
S: 30 kDa protein
H: 30 kDa protein
K: Gp54
P: Gp54
T: Gp54
U: Gp54

A: 60 kDa protein
B: 60 kDa protein
C: 60 kDa protein
D: 60 kDa protein
E: 60 kDa protein
F: 60 kDa protein
G: 60 kDa protein
L: 60 kDa protein
Q: 60 kDa protein
V: 60 kDa protein
a: 60 kDa protein
f: 60 kDa protein
M: Gp64
R: Gp64
I: Non-contractile tail sheath
N: Non-contractile tail sheath
J: 30 kDa protein
O: 30 kDa protein
S: 30 kDa protein
H: 30 kDa protein
K: Gp54
P: Gp54
T: Gp54
U: Gp54


Theoretical massNumber of molelcules
Total (without water)4,051,68672
Polymers4,051,68672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C3 (3 fold cyclic))

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Components

#1: Protein
60 kDa protein / gp66


Mass: 58943.914 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage N4 (virus) / References: UniProt: A0MZE8
#2: Protein Gp64


Mass: 48100.742 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage N4 (virus) / References: UniProt: A0MZE6
#3: Protein Non-contractile tail sheath / Gene product 65 / Gp65


Mass: 154255.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage N4 (virus) / References: UniProt: A0MZE7
#4: Protein
30 kDa protein / gp67


Mass: 27192.412 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage N4 (virus) / References: UniProt: A0MZE9
#5: Protein
Gp54


Mass: 32438.443 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage N4 (virus) / References: UniProt: Q859Q3
Has protein modificationY

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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 N4 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Escherichia phage N4 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
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: 4000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 32 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19.2_4158 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47179 / Symmetry type: POINT
RefinementHighest resolution: 3.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00452951
ELECTRON MICROSCOPYf_angle_d0.58472054
ELECTRON MICROSCOPYf_dihedral_angle_d4.9587059
ELECTRON MICROSCOPYf_chiral_restr0.0448003
ELECTRON MICROSCOPYf_plane_restr0.0069334

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