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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-30182 | |||||||||
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Title | EcoR124I-DNA in the Restriction-Alleviation State | |||||||||
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![]() | Cryoelectron microscopy / Innate immune mechanism / Complex / IMMUNE SYSTEM | |||||||||
Function / homology | ![]() type I site-specific deoxyribonuclease / type I site-specific deoxyribonuclease activity / N-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / DNA restriction-modification system / methylation / DNA binding / ATP binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.54 Å | |||||||||
![]() | Gao Y / Gao P | |||||||||
![]() | ![]() Title: Structural insights into assembly, operation and inhibition of a type I restriction-modification system. Authors: Yina Gao / Duanfang Cao / Jingpeng Zhu / Han Feng / Xiu Luo / Songqing Liu / Xiao-Xue Yan / Xinzheng Zhang / Pu Gao / ![]() Abstract: Type I restriction-modification (R-M) systems are widespread in prokaryotic genomes and provide robust protection against foreign DNA. They are multisubunit enzymes with methyltransferase, ...Type I restriction-modification (R-M) systems are widespread in prokaryotic genomes and provide robust protection against foreign DNA. They are multisubunit enzymes with methyltransferase, endonuclease and translocase activities. Despite extensive studies over the past five decades, little is known about the molecular mechanisms of these sophisticated machines. Here, we report the cryo-electron microscopy structures of the representative EcoR124I R-M system in different assemblies (RMS, RMS and MS) bound to target DNA and the phage and mobile genetic element-encoded anti-restriction proteins Ocr and ArdA. EcoR124I can precisely regulate different enzymatic activities by adopting distinct conformations. The marked conformational transitions of EcoR124I are dependent on the intrinsic flexibility at both the individual-subunit and assembled-complex levels. Moreover, Ocr and ArdA use a DNA-mimicry strategy to inhibit multiple activities, but do not block the conformational transitions of the complexes. These structural findings, complemented by mutational studies of key intermolecular contacts, provide insights into assembly, operation and inhibition mechanisms of type I R-M systems. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 25.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.5 KB 14.5 KB | Display Display | ![]() |
Images | ![]() | 45.1 KB | ||
Filedesc metadata | ![]() | 6.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7btqMC ![]() 7bstC ![]() 7btoC ![]() 7btpC ![]() 7btrC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : EcoR124I-DNA
Entire | Name: EcoR124I-DNA |
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Components |
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-Supramolecule #1: EcoR124I-DNA
Supramolecule | Name: EcoR124I-DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Type I restriction enzyme EcoR124II M protein
Macromolecule | Name: Type I restriction enzyme EcoR124II M protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO EC number: site-specific DNA-methyltransferase (adenine-specific) |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 58.07709 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MKMTSIQQRA ELHRQIWQIA NDVRGSVDGW DFKQYVLGAL FYRFISENFS SYIEAGDDSI CYAKLDDSVI TDDIKDDAIK TKGYFIYPS QLFCNVAAKA NTNDRLNADL NSIFVAIESS AYGYPSEADI KGLFADFDTT SNRLGNTVKD KNARLAAVLK G VEGLKLGD ...String: MKMTSIQQRA ELHRQIWQIA NDVRGSVDGW DFKQYVLGAL FYRFISENFS SYIEAGDDSI CYAKLDDSVI TDDIKDDAIK TKGYFIYPS QLFCNVAAKA NTNDRLNADL NSIFVAIESS AYGYPSEADI KGLFADFDTT SNRLGNTVKD KNARLAAVLK G VEGLKLGD FNEHQIDLFG DAYEFLISNY AANAGKSGGE FFTPQHVSKL IAQLAMHGQT HVNKIYDPAA GSGSLLLQAK KQ FDNHIIE EGFFGQEINH TTYNLARMNM FLHNINYDKF DIKLGNTLTE PHFRDEKPFD AIVSNPPYSV KWIGSDDPTL IND ERFAPA GVLAPKSKAD FAFVLHALNY LSAKGRAAIV CFPGIFYRGG AEQKIRQYLV DNNYVETVIS LAPNLFFGTT IAVN ILVLS KHKTDTNVQF IDASELFKKE TNNNILTDAH IEQIMQVFAS KEDVAHLAKS VAFETVVAND YNLSVSSYVE AKDNR EIID IAELNAELKT TVSKIDQLRK DIDAIVAEIE GCEVQK UniProtKB: Type I restriction enzyme EcoR124I/EcoR124II methylase subunit |
-Macromolecule #4: Type-1 restriction enzyme EcoR124II specificity protein
Macromolecule | Name: Type-1 restriction enzyme EcoR124II specificity protein type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 46.235773 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSEMSYLEKL LDGVEVEWLP LGEITKYEQP TKYLVKAKDY HDTYTIPVLT AGKTFILGYT NETHGIYQAS KAPVIIFDDF TTANKWVDF DFKAKSSAMK MVTSCDDNKT LLKYVYYWLN TLPSEFAEGD HKRQWISNYS QKKIPIPCPD NPEKSLAIQS E IVRILDKF ...String: MSEMSYLEKL LDGVEVEWLP LGEITKYEQP TKYLVKAKDY HDTYTIPVLT AGKTFILGYT NETHGIYQAS KAPVIIFDDF TTANKWVDF DFKAKSSAMK MVTSCDDNKT LLKYVYYWLN TLPSEFAEGD HKRQWISNYS QKKIPIPCPD NPEKSLAIQS E IVRILDKF TALTAELTAE LNMRKKQYNY YRDQLLSFKE GEVEWKTLGE IGKWYGGGTP SKNKIEFWEN GSIPWISPKD MG RTLVDSS EDYITEEAVL HSSTKLIPAN SIAIVVRSSI LDKVLPSALI KVPATLNQDM KAVIPHENIL VKYIYHMIGS RGS DILRAA KKTGGSVASI DSKKLFSFKI PVPNINEQQR IVEILDKFDT LTNSITEGLP REIELRQKQY EYYRDLLFSF PKPE TVSN UniProtKB: Type I restriction enzyme EcoR124I/EcoR124II specificity subunit |
-Macromolecule #5: Type I restriction enzyme R Protein
Macromolecule | Name: Type I restriction enzyme R Protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: type I site-specific deoxyribonuclease |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 120.278859 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MTHQTHTIAE SNNFIVLDKY IKAEPTGDSY QSESDLEREL IQDLRNQGYE FISVKSQSAM LANVREQLQN LNGVVFNDSE WRRFTEQYL DNPSDGILDK TRKIHIDYIC DFIFDDERLE NIYLIDKKNL MRNKVQIIQQ FEQAGSHANR YDVTILVNGL P LVQIELKK ...String: MTHQTHTIAE SNNFIVLDKY IKAEPTGDSY QSESDLEREL IQDLRNQGYE FISVKSQSAM LANVREQLQN LNGVVFNDSE WRRFTEQYL DNPSDGILDK TRKIHIDYIC DFIFDDERLE NIYLIDKKNL MRNKVQIIQQ FEQAGSHANR YDVTILVNGL P LVQIELKK RGVAIREAFN QIHRYSKESF NSENSLFKYL QLFVISNGTD TRYFANTTKR DKNSFDFTMN WAKSDNTLIK DL KDFTATC FQKHTLLNVL VNYSVFDSSQ TLLVMRPYQI AATERILWKI KSSFTAKNWS KPESGGYIWH TTGSGKTLTS FKA ARLATE LDFIDKVFFV VDRKDLDYQT MKEYQRFSPD SVNGSENTAG LKRNLDKDDN KIIVTTIQKL NNLMKAESDL PVYN QQVVF IFDECHRSQF GEAQKNLKKK FKRYYQFGFT GTPIFPENAL GSETTASVFG RELHSYVITD AIRDEKVLKF KVDYN DVRP QFKSLETETD EKKLSAAENQ QAFLHPMRIQ EITQYILNNF RQKTHRTFPG SKGFNAMLAV SSVDAAKAYY ATFKRL QEE AANKSATYKP LRIATIFSFA ANEEQNAIGE ISDETFDTSA MDSSAKEFLD AAIREYNSHF KTNFSTDSNG FQNYYRD LA QRVKNQDIDL LIVVGMFLTG FDAPTLNTLF VDKNLRYHGL MQAFSRTNRI YDATKTFGNI VTFRDLERST IDAITLFG D KNTKNVVLEK SYTEYMEGFT DAATGEAKRG FMTVVSELEQ RFPDPTSIES EKEKKDFVKL FGEYLRAENI LQNYDEFAT LKALQQIDLS DPVAVEKFKA EHYVDDEKFA ELQTIRLPAD RKIQDYRSAY NDIRDWQRRE KEAEKKEKST TDWDDVVFEV DLLKSQEIN LDYILGLIFE HNRQNKGKGE MIEEVKRLIR SSLGNRAKEG LVVDFIQQTN LDDLPDKASI IDAFFTFAQR E QQREAEAL IKEENLNEDA AKRYIRTSLK REYATENGTE LNETLPKLSP LNPQYKTKKQ AVFQKIVSFI EKFKGVGGKI UniProtKB: Type I restriction enzyme EcoR124I/EcoR124II endonuclease subunit |
-Macromolecule #2: DNA (64-MER)
Macromolecule | Name: DNA (64-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 19.657736 KDa |
Sequence | String: (DC)(DC)(DA)(DG)(DA)(DA)(DA)(DC)(DC)(DC) (DC)(DC)(DA)(DA)(DA)(DA)(DA)(DT)(DC)(DT) (DA)(DA)(DA)(DA)(DT)(DC)(DG)(DA)(DA) (DT)(DT)(DC)(DG)(DA)(DG)(DG)(DT)(DC)(DG) (DA) (DA)(DA)(DA)(DA)(DG)(DA) ...String: (DC)(DC)(DA)(DG)(DA)(DA)(DA)(DC)(DC)(DC) (DC)(DC)(DA)(DA)(DA)(DA)(DA)(DT)(DC)(DT) (DA)(DA)(DA)(DA)(DT)(DC)(DG)(DA)(DA) (DT)(DT)(DC)(DG)(DA)(DG)(DG)(DT)(DC)(DG) (DA) (DA)(DA)(DA)(DA)(DG)(DA)(DG)(DA) (DA)(DA)(DA)(DA)(DC)(DC)(DG)(DC)(DC)(DA) (DA)(DA) (DC)(DA)(DC)(DC) |
-Macromolecule #3: DNA (64-MER)
Macromolecule | Name: DNA (64-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 19.792592 KDa |
Sequence | String: (DG)(DG)(DT)(DG)(DT)(DT)(DT)(DG)(DG)(DC) (DG)(DG)(DT)(DT)(DT)(DT)(DT)(DC)(DT)(DC) (DT)(DT)(DT)(DT)(DT)(DC)(DG)(DA)(DC) (DC)(DT)(DC)(DG)(DA)(DA)(DT)(DT)(DC)(DG) (DA) (DT)(DT)(DT)(DT)(DA)(DG) ...String: (DG)(DG)(DT)(DG)(DT)(DT)(DT)(DG)(DG)(DC) (DG)(DG)(DT)(DT)(DT)(DT)(DT)(DC)(DT)(DC) (DT)(DT)(DT)(DT)(DT)(DC)(DG)(DA)(DC) (DC)(DT)(DC)(DG)(DA)(DA)(DT)(DT)(DC)(DG) (DA) (DT)(DT)(DT)(DT)(DA)(DG)(DA)(DT) (DT)(DT)(DT)(DT)(DG)(DG)(DG)(DG)(DG)(DT) (DT)(DT) (DC)(DT)(DG)(DG) |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: EMDB MAP |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 83797 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |