[English] 日本語
Yorodumi
- EMDB-29327: Structure of RdrB from Escherichia coli RADAR defense system -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-29327
TitleStructure of RdrB from Escherichia coli RADAR defense system
Map dataEscherichia coli RdrB map
Sample
  • Complex: Escherichia coli RdrB dodecamer
    • Protein or peptide: Adenosine deaminase
  • Ligand: ZINC ION
Keywordsadenosine deaminase / anti-phage defense / RADAR / IMMUNE SYSTEM
Function / homologydeaminase activity / Adenosine/adenine deaminase / Metal-dependent hydrolase / Adenosine deaminase
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.11 Å
AuthorsDuncan-Lowey B / Johnson AG / Rawson S / Mayer ML / Kranzusch PJ
Funding support United States, 4 items
OrganizationGrant numberCountry
The Pew Charitable Trusts United States
Burroughs Wellcome Fund United States
The G. Harold and Leila Y. Mathers Foundation United States
Parker Institute for Cancer Immunotherapy United States
CitationJournal: Cell / Year: 2023
Title: Cryo-EM structure of the RADAR supramolecular anti-phage defense complex.
Authors: Brianna Duncan-Lowey / Nitzan Tal / Alex G Johnson / Shaun Rawson / Megan L Mayer / Shany Doron / Adi Millman / Sarah Melamed / Taya Fedorenko / Assaf Kacen / Alexander Brandis / Tevie ...Authors: Brianna Duncan-Lowey / Nitzan Tal / Alex G Johnson / Shaun Rawson / Megan L Mayer / Shany Doron / Adi Millman / Sarah Melamed / Taya Fedorenko / Assaf Kacen / Alexander Brandis / Tevie Mehlman / Gil Amitai / Rotem Sorek / Philip J Kranzusch /
Abstract: RADAR is a two-protein bacterial defense system that was reported to defend against phage by "editing" messenger RNA. Here, we determine cryo-EM structures of the RADAR defense complex, revealing ...RADAR is a two-protein bacterial defense system that was reported to defend against phage by "editing" messenger RNA. Here, we determine cryo-EM structures of the RADAR defense complex, revealing RdrA as a heptameric, two-layered AAA+ ATPase and RdrB as a dodecameric, hollow complex with twelve surface-exposed deaminase active sites. RdrA and RdrB join to form a giant assembly up to 10 MDa, with RdrA docked as a funnel over the RdrB active site. Surprisingly, our structures reveal an RdrB active site that targets mononucleotides. We show that RdrB catalyzes ATP-to-ITP conversion in vitro and induces the massive accumulation of inosine mononucleotides during phage infection in vivo, limiting phage replication. Our results define ATP mononucleotide deamination as a determinant of RADAR immunity and reveal supramolecular assembly of a nucleotide-modifying machine as a mechanism of anti-phage defense.
History
DepositionDec 28, 2022-
Header (metadata) releaseFeb 1, 2023-
Map releaseFeb 1, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_29327.png

Downloads & links

-
Map

FileDownload / File: emd_29327.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEscherichia coli RdrB map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 480 pix.
= 396. Å		0.83 Å/pix.
x 480 pix.
= 396. Å		0.83 Å/pix.
x 480 pix.
= 396. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-2.5370476 - 5.050053
Average (Standard dev.)0.0025741556 (±0.14185682)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 396.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Escherichia coli RdrB half map A

Fileemd_29327_half_map_1.map
AnnotationEscherichia coli RdrB half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Escherichia coli RdrB half map B

Fileemd_29327_half_map_2.map
AnnotationEscherichia coli RdrB half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Escherichia coli RdrB dodecamer

EntireName: Escherichia coli RdrB dodecamer
Components
  • Complex: Escherichia coli RdrB dodecamer
    • Protein or peptide: Adenosine deaminase
  • Ligand: ZINC ION

-
Supramolecule #1: Escherichia coli RdrB dodecamer

SupramoleculeName: Escherichia coli RdrB dodecamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #1: Adenosine deaminase

MacromoleculeName: Adenosine deaminase / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 92.129875 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MERFLLNSTV LLYRLSTVSL DEVSLDERVE SSVFLAQYEQ ARSLPDHVAK SAWSYLVQQI KQRNMKLGPV AILRLIAEKF IKNEKGGPK IDLPMFSEWQ TLMSRVSCLP IIACHQVFNP GPASQEYSFR WPLYPYHPTV EDYITRECLH ETHQHLNGST S AEECWLDA ...String:
MERFLLNSTV LLYRLSTVSL DEVSLDERVE SSVFLAQYEQ ARSLPDHVAK SAWSYLVQQI KQRNMKLGPV AILRLIAEKF IKNEKGGPK IDLPMFSEWQ TLMSRVSCLP IIACHQVFNP GPASQEYSFR WPLYPYHPTV EDYITRECLH ETHQHLNGST S AEECWLDA LKHPEACLRD FEKGWASQEM KQLCAQIDPS LTPRIFKDRL QIACNIREIL CRVAQGVELP EWIASMQNPQ QL ANSTILH NGREYGFATV WPIDDKYSQE SEFCWLTGLL EKWRFNAPEG LERLLWIYLL IQNQYLTLLV QRDDFFGFEQ FQN YTMTEL REETEKSYLS RFKHAHGAGV YSQVRYLEGR FAPKSDPNKM QKLLFSVLRG YWEYLSAHMS MEWVHEKPLT ISQV LDNLE LVEPHGKCVE LALVPHFIKR KPKNGEAYPH ALLFKDLKNQ AAILMDMLKS EPRLTGWIRG VDAAANEMHA PPELF CPLF RVLAKSGIAH FTYHVGEDFP HLISGIRSID DALRFLPLRN GDRLGHCTAI GITPSIWKRS LPLSLSMTKE TRLLDL VFI WRELRSHPEL LRYASDAAIE AVRLAHKVFS LEEEVSITTL DQVFEMRGLL AESEGLLSEL NEPLKPKSLW LEEYERA RE LVKTTGMKRP LKLYKQWLTS DNVRKQRAEY VEVALEYLPD EAVVALQQAV MAKMADRNIA IECPPTSNTR ISQYRNVS E HHIFRWMGLP GEAIEGDVPM SICLGSDDPG IFAADLKSEF YHLFVVLTRK FGLSPADALR KVAEVNENGR IYRFHDV

UniProtKB: Adenosine deaminase

-
Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 12 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
100.0 mMKClpotassium chloride
50.0 mMHEPES
1.0 mMTCEP
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.11 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 233454
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

+
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