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- EMDB-18416: Cryo-EM structure of the monocin tail-tube, MttP. -

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Basic information

Entry
Database: EMDB / ID: EMD-18416
TitleCryo-EM structure of the monocin tail-tube, MttP.
Map dataMap at 2.3 Angstrom
Sample
  • Complex: Listeria monocytogenes 10403S monocin tail tube comprised of LMRG_02367 tail tube protein (MttP)
    • Protein or peptide: Antigen A
  • Ligand: water
KeywordsListeria / monocytogenes / tailocins / TOXIN
Function / homologyPhage major tail protein TP901-1 / Phage tail tube protein / Antigen A
Function and homology information
Biological speciesListera / Listeria monocytogenes 10403S
Methodhelical reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsNadejda S / Lichtenstein R / Schlussel S / Azulay G / Borovok I / Holdengraber V / Elad N / Wolf SG / Zalk R / Zarivach R ...Nadejda S / Lichtenstein R / Schlussel S / Azulay G / Borovok I / Holdengraber V / Elad N / Wolf SG / Zalk R / Zarivach R / Frank GA / Herskovits AA
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)817842European Union
CitationJournal: To Be Published
Title: Tailocin cell factories
Authors: Nadejda S / Lichtenstein R / Schlussel S / Azulay G / Borovok I / Holdengraber V / Elad N / Wolf SG / Zalk R / Zarivach R / Frank GA / Herskovits AA
History
DepositionSep 10, 2023-
Header (metadata) releaseJun 19, 2024-
Map releaseJun 19, 2024-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18416.png

Downloads & links

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Map

FileDownload / File: emd_18416.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap at 2.3 Angstrom
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 330.4 Å		0.83 Å/pix.
x 400 pix.
= 330.4 Å		0.83 Å/pix.
x 400 pix.
= 330.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-1.0359054 - 1.8021723
Average (Standard dev.)0.0008866526 (±0.055328216)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 330.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_18416_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_18416_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Listeria monocytogenes 10403S monocin tail tube comprised of LMRG...

EntireName: Listeria monocytogenes 10403S monocin tail tube comprised of LMRG_02367 tail tube protein (MttP)
Components
  • Complex: Listeria monocytogenes 10403S monocin tail tube comprised of LMRG_02367 tail tube protein (MttP)
    • Protein or peptide: Antigen A
  • Ligand: water

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Supramolecule #1: Listeria monocytogenes 10403S monocin tail tube comprised of LMRG...

SupramoleculeName: Listeria monocytogenes 10403S monocin tail tube comprised of LMRG_02367 tail tube protein (MttP)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Listera
Molecular weightTheoretical: 1 kDa/nm

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Macromolecule #1: Antigen A

MacromoleculeName: Antigen A / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes 10403S
Molecular weightTheoretical: 18.01026 KDa
Recombinant expressionOrganism: Listeria monocytogenes 10403S
SequenceString:
MAFEENLYCD YTPGAAKAVA GKDVILAVFN AAGDKLLAVA GQQGLTVNRS KDSIEITSKD TVGGWKSKIG GMKEWSIEND GLYVADAES HKELAKYFES DSPVCVKIIN QASKKGLFGG LAIVADYSFE APFDEAMTYS VKLDGMGALV DLTITEGGDQ M PGETPVAP AE

UniProtKB: Antigen A

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 337 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 30 % / Chamber temperature: 20 K / Details: Homemade pneumatic apparatus.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 15 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average exposure time: 2.0 sec. / Average electron dose: 49.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Segment selectionNumber selected: 503874 / Software - Name: cryoSPARC (ver. 4.1.2)
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 39.297 Å
Applied symmetry - Helical parameters - Δ&Phi: 25.078 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.2) / Software - details: Helical Refinement / Number images used: 490830
FSC plot (resolution estimation)

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