[English] 日本語
Yorodumi
- EMDB-52482: Putative bacterial antiviral defense protein Ec4ApeA from Escheri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52482
TitlePutative bacterial antiviral defense protein Ec4ApeA from Escherichia coli strain 10434wH10
Map datasharpened map (phenix.auto_sharpen b_iso_to_d_cut, 2.65)
Sample
  • Complex: Putative bacterial antiviral defense protein Ec4ApeA from Escherichia coli strain 10434wH10
    • Protein or peptide: Putative bacterial antiviral defense protein Ec4ApeA from Escherichia coli strain 10434wH10
KeywordsApeA / HEPN domain / bacterial antiviral defence / RNA BINDING PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsSasnauskas G / Juozapaitis J / Puteikiene R / Tamulaitiene G
Funding supportLithuania, 1 items
OrganizationGrant numberCountry
Research Council of LithuaniaS-MIP-22-13Lithuania
CitationJournal: To Be Published
Title: ApeA is a deoxyribodinucleotide binding antiviral defense system targeting tRNA
Authors: Juozapaitis J / Silanskas A / Ruksenaite A / Puteikiene R / Truncaite L / Songailiene I / Tamulaitiene G / Siksnys V / Sasnauskas G
History
DepositionJan 7, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_52482.png

Downloads & links

-
Map

FileReleased
Annotationsharpened map (phenix.auto_sharpen b_iso_to_d_cut, 2.65)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.0
Minimum - Maximum-15.336760999999999 - 30.693403
Average (Standard dev.)-0.000000000001524 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_52482_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: unsharpened map, input to phenix.auto sharpen

Fileemd_52482_additional_1.map
Annotationunsharpened map, input to phenix.auto_sharpen
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 1

Fileemd_52482_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 2

Fileemd_52482_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Putative bacterial antiviral defense protein Ec4ApeA from Escheri...

EntireName: Putative bacterial antiviral defense protein Ec4ApeA from Escherichia coli strain 10434wH10
Components
  • Complex: Putative bacterial antiviral defense protein Ec4ApeA from Escherichia coli strain 10434wH10
    • Protein or peptide: Putative bacterial antiviral defense protein Ec4ApeA from Escherichia coli strain 10434wH10

-
Supramolecule #1: Putative bacterial antiviral defense protein Ec4ApeA from Escheri...

SupramoleculeName: Putative bacterial antiviral defense protein Ec4ApeA from Escherichia coli strain 10434wH10
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli) / Strain: 10434wH10

-
Macromolecule #1: Putative bacterial antiviral defense protein Ec4ApeA from Escheri...

MacromoleculeName: Putative bacterial antiviral defense protein Ec4ApeA from Escherichia coli strain 10434wH10
type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: 10434wH10
Molecular weightTheoretical: 71.1805 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MRIDRRLSRD VLTERQLYFI ECWSNFCHKN SPDTDRVGYS NPLSTIRELL FLYEMEDRFS ADKKRLRVAT ELLELLETDQ VLKREAFED IPAQLVTLLD RDLLVDPTRS PVEKRPRLIC SLCVQLADIT EASYITEALE MLEQELFAGP PLDEHHARDI Y SLTNGVMS ...String:
MRIDRRLSRD VLTERQLYFI ECWSNFCHKN SPDTDRVGYS NPLSTIRELL FLYEMEDRFS ADKKRLRVAT ELLELLETDQ VLKREAFED IPAQLVTLLD RDLLVDPTRS PVEKRPRLIC SLCVQLADIT EASYITEALE MLEQELFAGP PLDEHHARDI Y SLTNGVMS VLLTRGMTLT ECYLLYINIF RNVSTDPNAF RAAFHSFRQK LVTPTRDVTV RMFITSEKLH TLLNTQGPTL QF NGCVFMP LDEARQRFSL SVDIPVCSMS DTSARNMAGQ MLRESLDVIA YMVGKGDITV QKQFMIIRDE DETEVPRFDN EIE ANADRL TDEEFARFMV AMNRLFTDTP DVSRKKISSA FRFFRNGIES QVQESRFTAY WSALESLTLG VAPGTPSHEQ HVIS VVAPC MVLDYVVKQL FSLRKVLRFI LREPGHPLRT PEIASLPLGQ LYALLKDADR VRELQTDLQH FPYVMYRVRK LAGIC ASPE KMADKLGQHA EKVTRHLHRL YLLRNTIVHN AGTSPHIDLL TVNLEHYLRA TISALFNIVV IHPTVSTAEE AFTRCQ FTS ESVFRELNPL HGITEKKVYT AIDNQLKNGT LSRSDARLIA WLNAHHLESG HHHHHH

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1092 / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 92000
Sample stageCooling holder cryogen: NITROGEN

+
Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: cryoSPARC ab-initio model
Final reconstructionApplied symmetry - Point group: D5 (2x5 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.0) / Number images used: 76888
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-9hxm:
Putative bacterial antiviral defense protein Ec4ApeA from Escherichia coli strain 10434wH10

+
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