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Yorodumi- EMDB-29328: Structure of RdrA-RdrB complex from Escherichia coli RADAR defens... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29328 | |||||||||||||||
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Title | Structure of RdrA-RdrB complex from Escherichia coli RADAR defense system | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | anti-phage defense / adenosine deaminase / IMMUNE SYSTEM | |||||||||||||||
Function / homology | deaminase activity / Adenosine/adenine deaminase / Metal-dependent hydrolase / P-loop containing nucleoside triphosphate hydrolase / Adenosine deaminase / Archaeal ATPase Function and homology information | |||||||||||||||
Biological species | Escherichia coli (E. coli) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.73 Å | |||||||||||||||
Authors | Duncan-Lowey B / Johnson AG / Rawson S / Mayer ML / Kranzusch PJ | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29328.map.gz | 59.5 MB | EMDB map data format | |
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Header (meta data) | emd-29328-v30.xml emd-29328.xml | 17.4 KB 17.4 KB | Display Display | EMDB header |
Images | emd_29328.png | 45.5 KB | ||
Filedesc metadata | emd-29328.cif.gz | 6.6 KB | ||
Others | emd_29328_half_map_1.map.gz emd_29328_half_map_2.map.gz | 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29328 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29328 | HTTPS FTP |
-Validation report
Summary document | emd_29328_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_29328_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_29328_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | emd_29328_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29328 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29328 | HTTPS FTP |
-Related structure data
Related structure data | 8fnwMC 8fntC 8fnuC 8fnvC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_29328.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 2.57812 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_29328_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_29328_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Escherichia coli RdrA-RrdB complex
Entire | Name: Escherichia coli RdrA-RrdB complex |
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Components |
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-Supramolecule #1: Escherichia coli RdrA-RrdB complex
Supramolecule | Name: Escherichia coli RdrA-RrdB complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: Adenosine deaminase
Macromolecule | Name: Adenosine deaminase / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 92.216953 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 IYRFHDVS UniProtKB: Adenosine deaminase |
-Macromolecule #2: Archaeal ATPase
Macromolecule | Name: Archaeal ATPase / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 107.226594 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MTDSVQTETT KGKIIINLFA PNLSGSTKED DLIQKSLRDQ LVESIRNSIA YPDTDKFAGL TRFIDEPGRN VFFVDGTRGA GKTTFINSV VKSLNSDQDD VKVNIKCLPT IDPTKLPRHE PILVTVTARL NKMVSDKLKG YWASNDYRKQ KEQWQNHLAQ L QRGLHLLT ...String: MTDSVQTETT KGKIIINLFA PNLSGSTKED DLIQKSLRDQ LVESIRNSIA YPDTDKFAGL TRFIDEPGRN 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 EIKVKTEPSM QDIDAIDVRQ AIGDAVREGL NLREGSDADM YVNELLKQPV RLLMQVLQDF YTKKYHATSV KLDG KQSRN ERPDELSVPN LLRNALYGSM LSNIYRAGLN YEQHRFGMDS LCKDIFTYVK QDRDFNTGFY LRPQSESEAL RNCSI YLAS QVSENCQGSL SKFLQMLLVG CGSVSIFNQF VTELARAEND REKFEQLISE YVAYMSVGRI ESASHWANRC CAVVAN SPN DEKIGVFLGM VQLNRKSRQN MPEGYKKFNI 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 LHPFIFPIGG INCSVKALNK ETSFNKLIDE IVGDKLLSD EEWDYLTKNN DQKTNTRQQI FQNTITSLNS STIVGASYDK DTPARKTKSP SLGDSEEK UniProtKB: Archaeal ATPase |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 12 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 6.73 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9236 |
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |