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- PDB-9ld7: The capsid of mature phage N4 -

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Basic information

Entry
Database: PDB / ID: 9ld7
TitleThe capsid of mature phage N4
Components
  • 32 kDa protein
  • Major capsid protein
KeywordsVIRUS / Complex
Function / homologyviral capsid / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / 32 kDa protein / Major capsid protein
Function and homology information
Biological speciesEnterobacteria phage N4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 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: The capsid of mature phage N4
Authors: Liu, H. / Chen, W.
History
DepositionJan 5, 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

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Assembly

Deposited unit
A: Major capsid protein
E: 32 kDa protein
G: 32 kDa protein
H: Major capsid protein
B: Major capsid protein
J: Major capsid protein
C: Major capsid protein
D: Major capsid protein
I: Major capsid protein
F: Major capsid protein
K: Major capsid protein
L: 32 kDa protein


Theoretical massNumber of molelcules
Total (without water)484,29112
Polymers484,29112
Non-polymers00
Water00
1
A: Major capsid protein
E: 32 kDa protein
G: 32 kDa protein
H: Major capsid protein
B: Major capsid protein
J: Major capsid protein
C: Major capsid protein
D: Major capsid protein
I: Major capsid protein
F: Major capsid protein
K: Major capsid protein
L: 32 kDa protein
x 60


Theoretical massNumber of molelcules
Total (without water)29,057,463720
Polymers29,057,463720
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Major capsid protein
E: 32 kDa protein
G: 32 kDa protein
H: Major capsid protein
B: Major capsid protein
J: Major capsid protein
C: Major capsid protein
D: Major capsid protein
I: Major capsid protein
F: Major capsid protein
K: Major capsid protein
L: 32 kDa protein
x 5


  • icosahedral pentamer
  • 2.42 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)2,421,45560
Polymers2,421,45560
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Major capsid protein
E: 32 kDa protein
G: 32 kDa protein
H: Major capsid protein
B: Major capsid protein
J: Major capsid protein
C: Major capsid protein
D: Major capsid protein
I: Major capsid protein
F: Major capsid protein
K: Major capsid protein
L: 32 kDa protein
x 6


  • icosahedral 23 hexamer
  • 2.91 MDa, 72 polymers
Theoretical massNumber of molelcules
Total (without water)2,905,74672
Polymers2,905,74672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


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

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Components

#1: Protein
Major capsid protein / Gene product 56 / gp56 / Major head protein


Mass: 44074.816 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage N4 (virus) / References: UniProt: Q859Q5
#2: Protein 32 kDa protein / gp17


Mass: 29205.900 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage N4 (virus) / References: UniProt: A0MZA7
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 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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18940 / Symmetry type: POINT
RefinementHighest resolution: 3.4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00334611
ELECTRON MICROSCOPYf_angle_d0.53946926
ELECTRON MICROSCOPYf_dihedral_angle_d4.4254761
ELECTRON MICROSCOPYf_chiral_restr0.0445391
ELECTRON MICROSCOPYf_plane_restr0.0066042

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