[English] 日本語
Yorodumi
- EMDB-49576: Cryo-EM structure of Retron-displaced free PtuAB complex, PtuA:Pt... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-49576
TitleCryo-EM structure of Retron-displaced free PtuAB complex, PtuA:PtuB (4:2)
Map data
Sample
  • Complex: Retron-displaced free PtuAB complex
    • Protein or peptide: Retreon I-A effector PtuA
    • Protein or peptide: Retron I-A effector PtuB
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsRetron effector / ATPase / HNH nuclease / TOXIN
Function / homology
Function and homology information


DNA synthesis involved in DNA repair / double-strand break repair / endonuclease activity / defense response to virus / ATP hydrolysis activity / ATP binding
Similarity search - Function
: / : / Retron Ec78 putative HNH endonuclease-like / AAA domain, putative AbiEii toxin, Type IV TA system / ATPase, AAA-type, core / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Retron Ec78 probable ATPase / Retron Ec78 putative HNH endonuclease
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsWang B / Li H
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 United States
CitationJournal: To Be Published
Title: Structure Basis for Retron Co-option of Anti-phage ATPase-nuclease
Authors: Wang B / Hou YM / Li H
History
DepositionMar 5, 2025-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_49576.png

Downloads & links

-
Map

FileDownload / File: emd_49576.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 352 pix.
= 291.456 Å		0.83 Å/pix.
x 352 pix.
= 291.456 Å		0.83 Å/pix.
x 352 pix.
= 291.456 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.117
Minimum - Maximum-1.354989 - 1.8150676
Average (Standard dev.)0.00047612877 (±0.033340774)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 291.456 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_49576_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_49576_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Retron-displaced free PtuAB complex

EntireName: Retron-displaced free PtuAB complex
Components
  • Complex: Retron-displaced free PtuAB complex
    • Protein or peptide: Retreon I-A effector PtuA
    • Protein or peptide: Retron I-A effector PtuB
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

-
Supramolecule #1: Retron-displaced free PtuAB complex

SupramoleculeName: Retron-displaced free PtuAB complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #1: Retreon I-A effector PtuA

MacromoleculeName: Retreon I-A effector PtuA / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 62.451805 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTKQYERKAK GGNLLSAFEL YQRNSDKAPG LGEMLVGEWF EMCRDYIQDG HVDESGIFRP DNAFYLRRLT LKDFRRFSLL EIKLEEDLT VIIGNNGKGK TSILYAIAKT LSWFVANILK EGGSGQRLSE MTDIKNDAED RYSDVSSTFF FGKGLKSVPI R LSRSALGT ...String:
MTKQYERKAK GGNLLSAFEL YQRNSDKAPG LGEMLVGEWF EMCRDYIQDG HVDESGIFRP DNAFYLRRLT LKDFRRFSLL EIKLEEDLT VIIGNNGKGK TSILYAIAKT LSWFVANILK EGGSGQRLSE MTDIKNDAED RYSDVSSTFF FGKGLKSVPI R LSRSALGT AERRDSEVKP AKDLADIWRV INEVNTINLP TFALYNVERS QPFNRNIKDN TGRREERFDA YSQTLGGAGR FD HFVEWYI YLHKRTVSDI SSSIKELEQQ VNDLQRTVDG GMVSVKSLLE QMKFKLSEAI ERNDAAVSSR VLTESVQKSI VEK AICSVV PSISNIWVEM ITGSDLVKVT NDGHDVTIDQ LSDGLRVFLS LVADLARRMV MLNPLLENPL EGRGIVLIDQ IELH LHPKW QQEVILNLRS AFPNIQFIIT THSPIVLSTI EKRCIREFEP NDDGDQSFLD SPDMQTKGSE NAQILEQVMN VHSTP PGIA ESHWLGNFEL LLLDNSGELD NHSQVLYDQI KAHFGIDSIE LKKADSLIRI NKMKNKLNKI RAEKGK

UniProtKB: Retron Ec78 probable ATPase

-
Macromolecule #2: Retron I-A effector PtuB

MacromoleculeName: Retron I-A effector PtuB / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 24.966066 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRELARLERP EILDQYIAGQ NDWMEIDQSA VWPKLTEMQG GFCAYCECRL NRCHIEHFRP RGKFPALTFI WNNLFGSCGD SRKSGGWSR CGIYKDNGAG AYNADDLIKP DEENPDDYLL FLTTGEVVPA IGLTGRALKK AQETIRVFNL NGDIKLFGSR R TAVQAIMP ...String:
MRELARLERP EILDQYIAGQ NDWMEIDQSA VWPKLTEMQG GFCAYCECRL NRCHIEHFRP RGKFPALTFI WNNLFGSCGD SRKSGGWSR CGIYKDNGAG AYNADDLIKP DEENPDDYLL FLTTGEVVPA IGLTGRALKK AQETIRVFNL NGDIKLFGSR R TAVQAIMP NVEYLYTLLE EFDEDDWNEM LRDELEKIES DEYKTALKHA WTFNQEFA

UniProtKB: Retron Ec78 putative HNH endonuclease

-
Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 1.7 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 281151
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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