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- EMDB-24939: Structure of DrmAB:ADP:DNA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-24939
TitleStructure of DrmAB:ADP:DNA complex
Map data
Sample
  • Complex: DrmAB:ADP:DNA
    • Complex: DrmAB
      • Protein or peptide: DrmA
      • Protein or peptide: DrmB
    • Complex: DNA
      • DNA: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*T)-3')
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Biological speciesSerratia (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsBravo JPK / Taylor DW / Brounds SJJ / Aparicio-Maldonado C
Funding support United States, 1 items
OrganizationGrant numberCountry
Welch FoundationF-1938 United States
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for broad anti-phage immunity by DISARM.
Authors: Jack P K Bravo / Cristian Aparicio-Maldonado / Franklin L Nobrega / Stan J J Brouns / David W Taylor /
Abstract: In the evolutionary arms race against phage, bacteria have assembled a diverse arsenal of antiviral immune strategies. While the recently discovered DISARM (Defense Island System Associated with ...In the evolutionary arms race against phage, bacteria have assembled a diverse arsenal of antiviral immune strategies. While the recently discovered DISARM (Defense Island System Associated with Restriction-Modification) systems can provide protection against a wide range of phage, the molecular mechanisms that underpin broad antiviral targeting but avoiding autoimmunity remain enigmatic. Here, we report cryo-EM structures of the core DISARM complex, DrmAB, both alone and in complex with an unmethylated phage DNA mimetic. These structures reveal that DrmAB core complex is autoinhibited by a trigger loop (TL) within DrmA and binding to DNA substrates containing a 5' overhang dislodges the TL, initiating a long-range structural rearrangement for DrmAB activation. Together with structure-guided in vivo studies, our work provides insights into the mechanism of phage DNA recognition and specific activation of this widespread antiviral defense system.
History
DepositionSep 21, 2021-
Header (metadata) releaseJun 15, 2022-
Map releaseJun 15, 2022-
UpdateJun 15, 2022-
Current statusJun 15, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24939.png

Downloads & links

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Map

FileDownload / File: emd_24939.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy EMDB: 0.35
Minimum - Maximum-3.0754225 - 4.1776166
Average (Standard dev.)2.93193e-13 (±0.045290057)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : DrmAB:ADP:DNA

EntireName: DrmAB:ADP:DNA
Components
  • Complex: DrmAB:ADP:DNA
    • Complex: DrmAB
      • Protein or peptide: DrmA
      • Protein or peptide: DrmB
    • Complex: DNA
      • DNA: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*T)-3')
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: DrmAB:ADP:DNA

SupramoleculeName: DrmAB:ADP:DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: DrmAB

SupramoleculeName: DrmAB / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Serratia (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: DrmA

MacromoleculeName: DrmA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Serratia (bacteria)
Molecular weightTheoretical: 147.980766 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTDNNKSSKT PNAWIAIDHN FSRAQVLTYY TLQLKGEHSL HQAISDNDWI LVLDTTGNIT RVGRILRIRS DLETTTIFFD RMLQVKSVV SIGITPFKFP PNDRAGRIQW TDFIETLPKE LHITIADIPK IEDQTYIREL LQLAVMDDLL GPAGGPNELI V DMGVRDRY ...String:
MTDNNKSSKT PNAWIAIDHN FSRAQVLTYY TLQLKGEHSL HQAISDNDWI LVLDTTGNIT RVGRILRIRS DLETTTIFFD RMLQVKSVV SIGITPFKFP PNDRAGRIQW TDFIETLPKE LHITIADIPK IEDQTYIREL LQLAVMDDLL GPAGGPNELI V DMGVRDRY LVGKLAPREA AERGQEFPID AEDIEDEEPD LIVKAKTAKV NSPSVLGSGE TDTAEEIDAA SNQSLVPSSL GM TFCVDGD VDRVEIEARW GRYERVPNDE HQFFKSNGQK AKVWKRIPCG GKIVLPLIEG SISHNAPDST SPEVRVQGSI RAK NDNGDR LITLFLVNAQ EEPDTNRDTA WVFQPELIVR AAKDAAKPAI FRRRPVLDAD GMDPEREALE MIYRDRVEFA VGHG VAVHA EIADDVTLAT EVRTTVMPQY EVQATETPGL ELSDRPAMRE MVSSGLLDMQ RLATLDIDPL VDALSVLTND YATWI DEQN LNVSSKAKGF DTQAQTAINR CQEIHTRLQE GINTLKSNEN ALAAFRFANQ AMATQRIRSL YALAMRRGED VTLDKF DVL KNRSWRPFQL AFLLLSIPSL ADPCHPDRVK PIEAYADLLW FPTGGGKTEA YLGVAAFTMA IRRMQGNLGG YDSSRGL TV IMRYTLRLLT LQQFQRATAL ICAMEVLRRE ALNKGDKSLG TEPFTIGLWV GNKVTPGTTE DSHNAIEKTR NPGSYNAG T ASPVQLTSCP WCGTEIVPGQ DVEVKKDKAG GRTFVYCGDK KGRCEFSKGK SSTQPHPGIP VLVVDEEIYH RPPTMMIAT VDKFAMMAWR GQVRTLFGRV EKECERHGLL WPGANCTGNH QAFKGQPSAK VKAIPPIRPP DLIIQDEFHL ISGPLGTMVG LYETAVDEL CSWTLNGKTV KPKIIASTAT VRKAKEQVNN VFMRQVSVFP PHGLDVEDNF FSVQRHIKDK FGRRYLGVCS P GSSRPAML IRVYTAFLTA AQELFDHFGE PADPYMTMVG YFNSLRELGG MKRLAEDDVQ TRSYRVQMSM VERPALAQRS VN NIRELTS RVSSQDIPKY LDNLEVKFKA EFDSSAGKYV TKWQEGDTRA IDVVLATNML SVGVDVNRLG LMAVNGQPKG TAE YIQATS RVGRSFPGLV CTVLTWARPR DLSHYETFEH YHATFYKHVE AQSVTPFSPR AMDRGLTGSL LSLMRLKNNE FSPN EGAGK LDMSNQSELA HAIEVLATRA GNVAEDNARK LLAENELKER ADEWAKEASK GGRILGYEKR GPDKDKTVAL IKSPG LQAW DNWTVPMSMR EVESGVRLIM DTKFIKDDHD WKPRPATKDE D

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Macromolecule #2: DrmB

MacromoleculeName: DrmB / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Serratia (bacteria)
Molecular weightTheoretical: 68.667039 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIINNKTPVG EVRPSQLLWT YGPGALIDLP SLSVVTLGID RWERERCQPI QEARLLAAVR KVLGPQVENL RMPPFQKSEL VDPWSAEAN IGVPVRPFPR WMRCVKCGLL SPFDDGLLEI KEDRFRAERT RFVHKGCTGS KGNLPAKDAD AVPARFLLAC R DGHLDDFP ...String:
MIINNKTPVG EVRPSQLLWT YGPGALIDLP SLSVVTLGID RWERERCQPI QEARLLAAVR KVLGPQVENL RMPPFQKSEL VDPWSAEAN IGVPVRPFPR WMRCVKCGLL SPFDDGLLEI KEDRFRAERT RFVHKGCTGS KGNLPAKDAD AVPARFLLAC R DGHLDDFP WHYFVHGGNS TCKGTLRFFE SGASLQTENL WVRCDSCEAS RSMAHAFGKA GKENLPACRG RHPHLDQFDI DC GEEPRAV LLGATNSWFP ITLSALAIPQ SKNPLSQLIQ DGWPLFEAIT AEVMVPIVVQ TLKLTGGLPG IDKYSVSDIW SAI EMHRSG GDSEFVGEAD IKGPEWEVLT EANPPTDYPH FMSKKIGTPA QFIPYISRVL LLERLREVNA LLGFTRVEAP EGSG EINER PQMASLARNK PEWVPANQVH GEGIFIQFNE KTLVAWESLD AVKQVDEMLR GGHTGWRNSR NLDPNEDYPG IRYAM LHTL SHLLIRELAL ECGYNAASIR ERIYADTSNG SPQAGILIYT AAADSDGTLG GLVDLGKPEN LGRLLVQALN RSKICS SDP LCSEHNPEKD RSLHAAACHA CTLVAETSCE QGNRYLDRSL LIPTLERIHA AFFKGF

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Macromolecule #3: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*T)-3')

MacromoleculeName: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*T)-3') / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 2.084392 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

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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 / Details: 150 mM NaCl, 25 mM HEPES pH 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 80.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 121764

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