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- EMDB-34966: Structure of tetradecameric RdrA ring in RNA-loading state -

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Basic information

Entry
Database: EMDB / ID: EMD-34966
TitleStructure of tetradecameric RdrA ring in RNA-loading state
Map data
Sample
  • Complex: RdrA-RNA complex
    • Protein or peptide: Archaeal ATPase
  • RNA: RNA (5'-R(*GP*UP*CP*CP*AP*GP*CP*GP*UP*CP*AP*UP*CP*GP*CP*UP*GP*GP*AP*C)-3')
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsCryoelectron microscopy / adenosine triphosphatase / IMMUNE SYSTEM
Function / homologyP-loop containing nucleoside triphosphate hydrolase / Archaeal ATPase
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.78 Å
AuthorsGao Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32100984 China
CitationJournal: Cell / Year: 2023
Title: Molecular basis of RADAR anti-phage supramolecular assemblies.
Authors: Yina Gao / Xiu Luo / Peipei Li / Zhaolong Li / Feng Ye / Songqing Liu / Pu Gao /
Abstract: Adenosine-to-inosine RNA editing has been proposed to be involved in a bacterial anti-phage defense system called RADAR. RADAR contains an adenosine triphosphatase (RdrA) and an adenosine deaminase ...Adenosine-to-inosine RNA editing has been proposed to be involved in a bacterial anti-phage defense system called RADAR. RADAR contains an adenosine triphosphatase (RdrA) and an adenosine deaminase (RdrB). Here, we report cryo-EM structures of RdrA, RdrB, and currently identified RdrA-RdrB complexes in the presence or absence of RNA and ATP. RdrB assembles into a dodecameric cage with catalytic pockets facing outward, while RdrA adopts both autoinhibited tetradecameric and activation-competent heptameric rings. Structural and functional data suggest a model in which RNA is loaded through the bottom section of the RdrA ring and translocated along its inner channel, a process likely coupled with ATP-binding status. Intriguingly, up to twelve RdrA rings can dock one RdrB cage with precise alignments between deaminase catalytic pockets and RNA-translocation channels, indicative of enzymatic coupling of RNA translocation and deamination. Our data uncover an interesting mechanism of enzymatic coupling and anti-phage defense through supramolecular assemblies.
History
DepositionDec 15, 2022-
Header (metadata) releaseFeb 1, 2023-
Map releaseFeb 1, 2023-
UpdateAug 16, 2023-
Current statusAug 16, 2023Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_34966.png

Downloads & links

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Map

FileDownload / File: emd_34966.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.045729212 - 0.08366355
Average (Standard dev.)0.00006384368 (±0.0035574941)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-200-200-200
Dimensions400400400
Spacing400400400
CellA=B=C: 423.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34966_half_map_1.map
Projections & Slices
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Slices (1/2)
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Half map: #1

Fileemd_34966_half_map_2.map
Projections & Slices
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Sample components

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Entire : RdrA-RNA complex

EntireName: RdrA-RNA complex
Components
  • Complex: RdrA-RNA complex
    • Protein or peptide: Archaeal ATPase
  • RNA: RNA (5'-R(*GP*UP*CP*CP*AP*GP*CP*GP*UP*CP*AP*UP*CP*GP*CP*UP*GP*GP*AP*C)-3')
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: RdrA-RNA complex

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

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Macromolecule #1: Archaeal ATPase

MacromoleculeName: Archaeal ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 107.132523 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTDSVQTETT EGKIIINLFA PNLPGSTKED DLIQKSLRDQ LVESIRNSIA YPDTDKFAGL TRFIDESGRN VFFVDGTRGA GKTTFINSV VKSLNSDQDD VKVNIKCLPT IDPTKLPRHE PILVTVTARL NKMVSDKLKG YWASNDYRKQ KEQWQNHLAQ L QRGLHLLT ...String:
MTDSVQTETT EGKIIINLFA PNLPGSTKED DLIQKSLRDQ LVESIRNSIA YPDTDKFAGL TRFIDESGRN VFFVDGTRGA GKTTFINSV VKSLNSDQDD VKVNIKCLPT IDPTKLPRHE PILVTVTARL NKMVSDKLKG YWASNDYRKQ KEQWQNHLAQ L QRGLHLLT DKEYKPEYFS DALKLDAQLD YSIGGQDLSE IFEELVKRAC EILDCKAILI TFDDIDTQFD AGWDVLESIR KF FNSRKLV VVATGDLRLY SQLIRGKQYE NYSKTLLEQE KESVRLAERG YMVEHLEQQY LLKLFPVQKR IQLKTMLQLV GEK GKAGKE EIKVKTEPGM QDIDAIDVRQ AIGDAVREGL NLREGSDADM YVNELLKQPV RLLMQVLQDF YTKKYHATSV KLDG KQSRN ERPNELSVPN LLRNALYGSM LSSIYRAGLN YEQHRFGMDS LCKDIFTYVK QDRDFNTGFY LRPQSESEAL RNCSI YLAS QVSENCQGSL SKFLQMLLVG CGSVSIFNQF VTELARAEND REKFEQLISE YVAYMSVGRI ESASHWANRC CAVVAN SPN DEKIGVFLGM VQLNRKSRQH MPGGYKKFNI DTENGLAKAA MASSLSTVAS NNLMDFCSVF NLIGAIADIS ACRCERS AI TNAFNKVIAQ TTCIVPPWSE AAVRAEMKGS SKSADNDAAV LDVDLDPKDD GVIDESQQDD ATEFSDAITK VEQWLKNV N EIEIGIRPSA LLIGKVWSRF YFNLNNVADQ HKTRLYRNAE HGRMASQSNA AKIMRFNVLA FLHAVLVEES LYHSVSDRE YIGEGLRLNP VTSVDEFEKK IKIIGEKLKA DNKTWKNTHP LFFLLISCPI LHPFIFPVGG INCSVKALNK ETSFNKLIDE IVGDKLLSD EEWDYLTKNN DQKTNTRQQI FQNTITSLNS STIVGASYDK DTPARKTKSP LLGDSEEK

UniProtKB: Archaeal ATPase

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Macromolecule #2: RNA (5'-R(*GP*UP*CP*CP*AP*GP*CP*GP*UP*CP*AP*UP*CP*GP*CP*UP*GP*GP*...

MacromoleculeName: RNA (5'-R(*GP*UP*CP*CP*AP*GP*CP*GP*UP*CP*AP*UP*CP*GP*CP*UP*GP*GP*AP*C)-3')
type: rna / ID: 2 / Number of copies: 6
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 6.374831 KDa
SequenceString:
GUCCAGCGUC AUCGCUGGAC

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 8 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 162577
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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