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- EMDB-61465: Architecture of a pentameric assembly of the tube tail protein -

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Basic information

Entry
Database: EMDB / ID: EMD-61465
TitleArchitecture of a pentameric assembly of the tube tail protein
Map datahalf_map_A
Sample
  • Complex: Architecture of a pentameric assembly of the tube tail protein
    • Protein or peptide: tail tube protein
KeywordsTail Tube Protein / Phages / ANTIVIRAL PROTEIN
Function / homologyUncharacterized protein
Function and homology information
Biological speciesBacillus subtilis (bacteria)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 3.5 Å
AuthorsLin W / Yuhang H / Hongtao Z
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: 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, 2024-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61465.png

Downloads & links

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Map

FileDownload / File: emd_61465.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhalf_map_A
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 332. Å		0.83 Å/pix.
x 400 pix.
= 332. Å		0.83 Å/pix.
x 400 pix.
= 332. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.019586876 - 2.085572
Average (Standard dev.)0.0021102154 (±0.031436324)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 332.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_61465_half_map_1.map
Annotationhalf_map_A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_61465_half_map_2.map
Annotationhalf_map_A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Architecture of a pentameric assembly of the tube tail protein

EntireName: Architecture of a pentameric assembly of the tube tail protein
Components
  • Complex: Architecture of a pentameric assembly of the tube tail protein
    • Protein or peptide: tail tube protein

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Supramolecule #1: Architecture of a pentameric assembly of the tube tail protein

SupramoleculeName: Architecture of a pentameric assembly of the tube tail protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus subtilis (bacteria)

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Macromolecule #1: tail tube protein

MacromoleculeName: tail tube protein / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 30.133572 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKTVIQDTAD VYFKRKSDGK LVFTAEAQTA SFSQAISEEK LRGGIGNKPL YILKSEKEIN LTVKNAFFDL EWLAMTQGET IQEETKVKV FDREHGLIVD DTNKVTLKGK PVSDVTFYNK KGLTYKIAVS TDGTYTIPTA FAAAKDKLTA VYQIEKVGRR L AIKASKFS ...String:
MKTVIQDTAD VYFKRKSDGK LVFTAEAQTA SFSQAISEEK LRGGIGNKPL YILKSEKEIN LTVKNAFFDL EWLAMTQGET IQEETKVKV FDREHGLIVD DTNKVTLKGK PVSDVTFYNK KGLTYKIAVS TDGTYTIPTA FAAAKDKLTA VYQIEKVGRR L AIKASKFS ERYEVEYRTI AYNPDTEEVY SDIYIQFPNV SPSGEFEMSL ENGNALAPEI KFEALADTDT DEMAVVIEAS RD ENTAAPV EDTTGSTQSS DLGGTTEHHH HHH

UniProtKB: Uncharacterized protein

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
Component:
ConcentrationName
40.0 mMTris HCL
150.0 mMNacl
10.0 mMimidazole
1.0 mMphenylmethylsulfonyl fluoride PMSF

Details: 40 mM Tris HCl, pH=8.0, 10 mM imidazole, 150 mM NaCl, and 1 mM phenylmethylsulfonyl fluoride PMSF
StainingType: NEGATIVE / Material: Uranyl Acetate
GridMaterial: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.5 µm / Calibrated defocus min: 1.5 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49339
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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