[English] 日本語
Yorodumi
- EMDB-18416: Cryo-EM structure of the monocin tail-tube, MttP. -

+
Open data


ID or keywords:

Loading...

-
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 (plant) / Listeria monocytogenes 10403S (bacteria)
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

-
Structure visualization

Supplemental images

emd_18416.png

Downloads & links

-
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 °

-
Supplemental data

-
Half map: #1

Fileemd_18416_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_18416_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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 (plant)
Molecular weightTheoretical: 1 kDa/nm

-
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 (bacteria)
Molecular weightTheoretical: 18.01026 KDa
Recombinant expressionOrganism: Listeria monocytogenes 10403S (bacteria)
SequenceString:
MAFEENLYCD YTPGAAKAVA GKDVILAVFN AAGDKLLAVA GQQGLTVNRS KDSIEITSKD TVGGWKSKIG GMKEWSIEND GLYVADAES HKELAKYFES DSPVCVKIIN QASKKGLFGG LAIVADYSFE APFDEAMTYS VKLDGMGALV DLTITEGGDQ M PGETPVAP AE

UniProtKB: Antigen A

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

-
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.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 15 eV
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

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
Segment selectionNumber selected: 503874 / Software - Name: cryoSPARC (ver. 4.1.2)
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more