[English] 日本語
Yorodumi
- EMDB-52464: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52464
TitleBacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 (oligomerization mutant R551E)
Map datasharpened map (phenix.auto_sharpen b_iso_to_d_cut, 3.55)
Sample
  • Complex: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 (oligomerization mutant R551E)
    • Protein or peptide: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 (oligomerization mutant R551E)
KeywordsApeA / HEPN domain / bacterial antiviral defence / RNA BINDING PROTEIN
Biological speciesEscherichia coli 2-156-04_S4_C1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.55 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_52464.png

Downloads & links

-
Map

FileReleased
Annotationsharpened map (phenix.auto_sharpen b_iso_to_d_cut, 3.55)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.1 Å/pix.
x 200 pix.
= 220. Å		1.1 Å/pix.
x 200 pix.
= 220. Å		1.1 Å/pix.
x 200 pix.
= 220. 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: 4.0
Minimum - Maximum-33.204543999999999 - 46.971670000000003
Average (Standard dev.)0.000000000000191 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 220.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_52464_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_52464_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_52464_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_52464_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Bacterial antiviral defense protein Ec2ApeA from Escherichia coli...

EntireName: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 (oligomerization mutant R551E)
Components
  • Complex: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 (oligomerization mutant R551E)
    • Protein or peptide: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 (oligomerization mutant R551E)

-
Supramolecule #1: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli...

SupramoleculeName: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 (oligomerization mutant R551E)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli 2-156-04_S4_C1 (bacteria)

-
Macromolecule #1: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli...

MacromoleculeName: Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 (oligomerization mutant R551E)
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli 2-156-04_S4_C1 (bacteria)
Molecular weightTheoretical: 69.245969 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKFRRLHNWN HIEQCTALIY FTELMEELLF DYTHSTYKPS IMNTPSLCIE AISTIDDIEK GNISPAHISH VIDELTKNIK NDDIAISLL KNPLGSFLDQ LQNNQLGNKN LKITLELLRV QLNVGNYESK LISELCSTIT SEYNPNKIRK FTRLLITHLI S KGLSQEYL ...String:
MKFRRLHNWN HIEQCTALIY FTELMEELLF DYTHSTYKPS IMNTPSLCIE AISTIDDIEK GNISPAHISH VIDELTKNIK NDDIAISLL KNPLGSFLDQ LQNNQLGNKN LKITLELLRV QLNVGNYESK LISELCSTIT SEYNPNKIRK FTRLLITHLI S KGLSQEYL MESLKKHFFQ REREISSNEE IITFLENIPS ETQEYSVYFN AEKSFSYITP CLSQLEIEVV LETPENINET DF FDNHEQR TILVKHVKAL DPFTARRVAE RNLKLASTLL SLYHHKQEAS WSAENIVVSE NGEKINIRSS INPMHRCKDL VQE HASRRL EQFMNNFRMR KDSFNKFIRS VQLHSMALQT NAVENQLLNL WIAIESLIPD ESKKEEQSTI EHIVNSLTPF LNLN YIEDL VRNLIKDLQR WNHPRTMSLL RLIGDSDAAK SFVILVASQE HAPSINQFKI ELSQFPLLKE RFEYISNLIS STDTM YQAL KNHAERINWQ IRRIYRTRNL IVHTGKTPSK TNVLVEHAHI YLDAVINSLI KLSSHPVEIL SVAQGFENVE MKYKMY IQK LNKKNIELTP ENIISFIFNQ LESGHHHHHH

-
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: 990 / 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: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 252998
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-9hxd:
Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 (oligomerization mutant R551E)

+
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