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- PDB-8es4: Focused reconstruction of HRP29 tail -

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Basic information

Entry
Database: PDB / ID: 8es4
TitleFocused reconstruction of HRP29 tail
Components
  • Gp35
  • Gp39CD154
  • Gp40
  • Gp44
KeywordsVIRUS / HRP29
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope, short tail mechanism / outer membrane / virion component
Similarity search - Function
Tail tubular protein Gp11 / Tail tubular protein / Bacteriophage T7 tail fibre protein / Phage T7 tail fibre protein / Head-to-tail connector protein, podovirus-type / Bacteriophage head to tail connecting protein / Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter adhesin
Similarity search - Domain/homology
Head-tail connector protein / Putative tail protein / Putative tail protein / Putative tail protein
Similarity search - Component
Biological speciesShigella phage Buco (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSubramanian, S. / Bergland Drarvik, S.M. / Parent, K.N.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110185 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116789 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140803 United States
National Science Foundation (NSF, United States)1750125 United States
CitationJournal: To Be Published
Title: Structure of Shigella bacteriophage HRP29
Authors: Subramanian, S. / Bergland Drarvik, S.M. / Parent, K.N.
History
DepositionOct 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gp35
C: Gp39
E: Gp40
G: Gp44
H: Gp44
F: Gp44
B: Gp35
D: Gp39


Theoretical massNumber of molelcules
Total (without water)326,1698
Polymers326,1698
Non-polymers00
Water0
1
A: Gp35
C: Gp39
E: Gp40
G: Gp44
H: Gp44
F: Gp44
B: Gp35
D: Gp39
x 6


Theoretical massNumber of molelcules
Total (without water)1,957,01448
Polymers1,957,01448
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
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: C6 (6 fold cyclic))

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Components

#1: Protein Gp35 / Head-tail connector protein


Mass: 56983.391 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Shigella phage Buco (virus) / References: UniProt: A0A482JG67
#2: Protein Gp39 / CD154 / Putative tail protein


Mass: 20815.510 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Shigella phage Buco (virus) / References: UniProt: A0A482JKT9
#3: Protein Gp40 / Putative tail protein


Mass: 84783.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Shigella phage Buco (virus) / References: UniProt: A0A482JLU9
#4: Protein Gp44 / Putative tail protein


Mass: 28595.883 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Shigella phage Buco (virus) / References: UniProt: A0A482JMG8

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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: Shigella phage Buco / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Shigella phage Buco (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 7.5
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 33 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24391 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00218808
ELECTRON MICROSCOPYf_angle_d0.44225640
ELECTRON MICROSCOPYf_dihedral_angle_d3.3232682
ELECTRON MICROSCOPYf_chiral_restr0.042991
ELECTRON MICROSCOPYf_plane_restr0.0043322

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