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- PDB-9jgh: cryo-EM structure of the TTP polymer at the tube's end -

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Basic information

Entry
Database: PDB / ID: 9jgh
Titlecryo-EM structure of the TTP polymer at the tube's end
Componentstube tail protein
KeywordsANTIVIRAL PROTEIN / Tail Tube Protein / Phages
Function / homologyUncharacterized protein
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / negative staining / cryo EM / Resolution: 3.7 Å
AuthorsLin, W. / Yuhang, H. / Hongtao, Z.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
Citation
Journal: Chin Phys Lett / Year: 2024
Title: Pentameric Assembly Architecture of the Tail Tube Protein in SPR Phages
Authors: Wang, L. / He, Y. / Zhu, K. / Cui, S. / Gao, X. / Shang, K. / Zhu, H.
#1: Journal: Protein Sci / Year: 2018
Title: UCSF ChimeraX: Meeting modern challenges in visualization and analysis.
Authors: Thomas D Goddard / Conrad C Huang / Elaine C Meng / Eric F Pettersen / Gregory S Couch / John H Morris / Thomas E Ferrin /
Abstract: UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and ...UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility. ChimeraX is free for noncommercial use and is available from http://www.rbvi.ucsf.edu/chimerax/ for Windows, Mac, and Linux.
History
DepositionSep 7, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tube tail protein
B: tube tail protein
C: tube tail protein
D: tube tail protein
E: tube tail protein
F: tube tail protein
G: tube tail protein
H: tube tail protein
I: tube tail protein
J: tube tail protein
K: tube tail protein
L: tube tail protein
M: tube tail protein
N: tube tail protein
O: tube tail protein


Theoretical massNumber of molelcules
Total (without water)452,00415
Polymers452,00415
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
tube tail protein


Mass: 30133.572 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4122_1986, J5227_09585 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A162TY69
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: cryo-EM structure of the TTP polymer at the tube's end
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Bacillus subtilis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
Details: 40 mM Tris HCl, pH=8.0, 10 mM imidazole, 150 mM NaCl, and 1 mM phenylmethylsulfonyl fluoride PMSF
Buffer component
IDConc.NameBuffer-ID
140 mMTris HCL1
2150 mMNacl1
310 mMimidazole1
41 mMphenylmethylsulfonyl fluoride PMSF1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES
EM stainingType: NEGATIVE / Material: Uranyl Acetate
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 4 K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI SPIRIT
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 1500 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 96299 / Symmetry type: POINT
RefinementHighest resolution: 3.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00226144
ELECTRON MICROSCOPYf_angle_d0.63635286
ELECTRON MICROSCOPYf_dihedral_angle_d4.2963469
ELECTRON MICROSCOPYf_chiral_restr0.0444025
ELECTRON MICROSCOPYf_plane_restr0.0034530

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