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- EMDB-14403: Endonuclease state of the E. coli Mre11-Rad50 (SbcCD) head comple... -
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Open data
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Basic information
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Title | Endonuclease state of the E. coli Mre11-Rad50 (SbcCD) head complex bound to ADP and extended dsDNA | |||||||||
![]() | LAFTER-filtered endonuclease state map with extended DNA | |||||||||
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![]() | ABC-type ATPase / Nuclease / DNA repair / DNA BINDING PROTEIN | |||||||||
Function / homology | ![]() double-stranded DNA endonuclease activity / DNA exonuclease activity / single-stranded DNA endodeoxyribonuclease activity / DNA repair complex / 3'-5'-DNA exonuclease activity / 3'-5' exonuclease activity / double-strand break repair / DNA recombination / DNA replication / DNA repair ...double-stranded DNA endonuclease activity / DNA exonuclease activity / single-stranded DNA endodeoxyribonuclease activity / DNA repair complex / 3'-5'-DNA exonuclease activity / 3'-5' exonuclease activity / double-strand break repair / DNA recombination / DNA replication / DNA repair / ATP hydrolysis activity / DNA binding / ATP binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
![]() | Gut F / Kaeshammer L | |||||||||
Funding support | European Union, ![]()
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![]() | ![]() Title: Structural mechanism of endonucleolytic processing of blocked DNA ends and hairpins by Mre11-Rad50. Authors: Fabian Gut / Lisa Käshammer / Katja Lammens / Joseph D Bartho / Anna-Maria Boggusch / Erik van de Logt / Brigitte Kessler / Karl-Peter Hopfner / ![]() Abstract: DNA double-strand breaks (DSBs) threaten genome stability and are linked to tumorigenesis in humans. Repair of DSBs requires the removal of attached proteins and hairpins through a poorly understood ...DNA double-strand breaks (DSBs) threaten genome stability and are linked to tumorigenesis in humans. Repair of DSBs requires the removal of attached proteins and hairpins through a poorly understood but physiologically critical endonuclease activity by the Mre11-Rad50 complex. Here, we report cryoelectron microscopy (cryo-EM) structures of the bacterial Mre11-Rad50 homolog SbcCD bound to a protein-blocked DNA end and a DNA hairpin. The structures reveal that Mre11-Rad50 bends internal DNA for endonucleolytic cleavage and show how internal DNA, DNA ends, and hairpins are processed through a similar ATP-regulated conformational state. Furthermore, Mre11-Rad50 is loaded onto blocked DNA ends with Mre11 pointing away from the block, explaining the distinct biochemistries of 3' → 5' exonucleolytic and endonucleolytic incision through the way Mre11-Rad50 interacts with diverse DNA ends. In summary, our results unify Mre11-Rad50's enigmatic nuclease diversity within a single structural framework and reveal how blocked DNA ends and hairpins are processed. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 108 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.8 KB 21.8 KB | Display Display | ![]() |
Images | ![]() | 59.9 KB | ||
Filedesc metadata | ![]() | 6.7 KB | ||
Others | ![]() ![]() ![]() | 62.7 MB 116.2 MB 116.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7z03MC ![]() 7yzoC ![]() 7yzpC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | LAFTER-filtered endonuclease state map with extended DNA | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.059 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_14403_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_14403_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_14403_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Complex of Mre11 dimer, Rad50 dimer and double-stranded DNA
Entire | Name: Complex of Mre11 dimer, Rad50 dimer and double-stranded DNA |
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Components |
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-Supramolecule #1: Complex of Mre11 dimer, Rad50 dimer and double-stranded DNA
Supramolecule | Name: Complex of Mre11 dimer, Rad50 dimer and double-stranded DNA type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Nuclease SbcCD subunit C
Macromolecule | Name: Nuclease SbcCD subunit C / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 118.851508 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MKILSLRLKN LNSLKGEWKI DFTREPFASN GLFAITGPTG AGKTTLLDAI CLALYHETPR LSNVSQSQND LMTRDTAECL AEVEFEVKG EAYRAFWSQN RARNQPDGNL QVPRVELARC ADGKILADKV KDKLELTATL TGLDYGRFTR SMLLSQGQFA A FLNAKPKE ...String: MKILSLRLKN LNSLKGEWKI DFTREPFASN GLFAITGPTG AGKTTLLDAI CLALYHETPR LSNVSQSQND LMTRDTAECL AEVEFEVKG EAYRAFWSQN RARNQPDGNL QVPRVELARC ADGKILADKV KDKLELTATL TGLDYGRFTR SMLLSQGQFA A FLNAKPKE RAELLEELTG TEIYGQISAM VFEQHKSART ELEKLQAQAS GVTLLTPEQV QSLTASLQVL TDEEKQLITA QQ QEQQSLN WLTRQDELQQ EASRRQQALQ QALAEEEKAQ PQLAALSLAQ PARNLRPHWE RIAEHSAALA HIRQQIEEVN TRL QSTMAL RASIRHHAAK QSAELQQQQQ SLNTWLQEHD RFRQWNNEPA GWRAQFSQQT SDREHLRQWQ QQLTHAEQKL NALA AITLT LTADEVATAL AQHAEQRPLR QHLVALHGQI VPQQKRLAQL QVAIQNVTQE QTQRNAALNE MRQRYKEKTQ QLADV KTIC EQEARIKTLE AQRAQLQAGQ PCPLCGSTSH PAVEAYQALE PGVNQSRLLA LENEVKKLGE EGATLRGQLD AITKQL QRD ENEAQSLRQD EQALTQQWQA VTASLNITLQ PLDDIQPWLD AQDEHERQLR LLSQRHELQG QIAAHNQQII QYQQQIE QR QQLLLTTLTG YALTLPQEDE EESWLATRQQ EAQSWQQRQN ELTALQNRIQ QLTPILETLP QSDELPHCEE TVVLENWR Q VHEQCLALHS QQQTLQQQDV LAAQSLQKAQ AQFDTALQAS VFDDQQAFLA ALMDEQTLTQ LEQLKQNLEN QRRQAQTLV TQTAETLAQH QQHRPDDGLA LTVTVEQIQQ ELAQTHQKLR ENTTSQGEIR QQLKQDADNR QQQQTLMQQI AQMTQQVEDW GYLNSLIGS KEGDKFRKFA QGLTLDNLVH LANQQLTRLH GRYLLQRKAS EALEVEVVDT WQADAVRDTR TLSGGESFLV S LALALALS DLVSHKTRID SLFLDEGFGT LDSETLDTAL DALDALNASG KTIGVISHVE AMKERIPVQI KVKKINGLGY SK LESTFAV K UniProtKB: Nuclease SbcCD subunit C |
-Macromolecule #2: Nuclease SbcCD subunit D
Macromolecule | Name: Nuclease SbcCD subunit D / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 45.640277 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MRILHTSDWH LGQNFYSKSR EAEHQAFLDW LLETAQTHQV DAIIVAGDVF DTGSPPSYAR TLYNRFVVNL QQTGCHLVVL AGNQDSVAT LNESRDIMAF LNTTVVASAG HAPQILPRRD GTPGAVLCPI PFLRPRDIIT SQAGLNGIEK QQHLLAAITD Y YQQHYADA ...String: MRILHTSDWH LGQNFYSKSR EAEHQAFLDW LLETAQTHQV DAIIVAGDVF DTGSPPSYAR TLYNRFVVNL QQTGCHLVVL AGNQDSVAT LNESRDIMAF LNTTVVASAG HAPQILPRRD GTPGAVLCPI PFLRPRDIIT SQAGLNGIEK QQHLLAAITD Y YQQHYADA CKLRGDQPLP IIATGHLTTV GASKSDAVRD IYIGTLDAFP AQNFPPADYI ALGHIHRAQI IGGMEHVRYC GS PIPLSFD ECGKSKYVHL VTFSNGKLES VENLNVPVTQ PMAVLKGDLA SITAQLEQWR DVSQEPPVWL DIEITTDEYL HDI QRKIQA LTESLPVEVL LVRRSREQRE RVLASQQRET LSELSVEEVF NRRLALEELD ESQQQRLQHL FTTTLHTLAG EHEA GHHHH HH UniProtKB: Nuclease SbcCD subunit D |
-Macromolecule #3: DNA (39-MER)
Macromolecule | Name: DNA (39-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 37.099617 KDa |
Sequence | String: (DC)(DC)(DA)(DG)(DT)(DT)(DG)(DA)(DT)(DC) (DG)(DG)(DC)(DG)(DC)(DG)(DA)(DG)(DA)(DT) (DT)(DT)(DA)(DA)(DT)(DC)(DG)(DC)(DC) (DG)(DC)(DG)(DA)(DC)(DA)(DA)(DT)(DT)(DT) (DG) (DC)(DG)(DA)(DC)(DG)(DG) ...String: (DC)(DC)(DA)(DG)(DT)(DT)(DG)(DA)(DT)(DC) (DG)(DG)(DC)(DG)(DC)(DG)(DA)(DG)(DA)(DT) (DT)(DT)(DA)(DA)(DT)(DC)(DG)(DC)(DC) (DG)(DC)(DG)(DA)(DC)(DA)(DA)(DT)(DT)(DT) (DG) (DC)(DG)(DA)(DC)(DG)(DG)(DC)(DG) (DC)(DG)(DT)(DG)(DC)(DA)(DG)(DG)(DG)(DC) (DC)(DA) (DG)(DA)(DC)(DT)(DG)(DG)(DA) (DG)(DG)(DT)(DG)(DG)(DC)(DA)(DA)(DC)(DG) (DC)(DC)(DA) (DA)(DT)(DC)(DA)(DG)(DC) (DA)(DA)(DC)(DG)(DA)(DC)(DT)(DG)(DT)(DT) (DT)(DG)(DC)(DC) (DC)(DG)(DC)(DC)(DA) (DG)(DT)(DT)(DG)(DT)(DT)(DG)(DT)(DG)(DC) (DC)(DA)(DC)(DG)(DC) GENBANK: GENBANK: MN982376.1 |
-Macromolecule #4: DNA (39-MER)
Macromolecule | Name: DNA (39-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 36.970527 KDa |
Sequence | String: (DG)(DC)(DG)(DT)(DG)(DG)(DC)(DA)(DC)(DA) (DA)(DC)(DA)(DA)(DC)(DT)(DG)(DG)(DC)(DG) (DG)(DG)(DC)(DA)(DA)(DA)(DC)(DA)(DG) (DT)(DC)(DG)(DT)(DT)(DG)(DC)(DT)(DG)(DA) (DT) (DT)(DG)(DG)(DC)(DG)(DT) ...String: (DG)(DC)(DG)(DT)(DG)(DG)(DC)(DA)(DC)(DA) (DA)(DC)(DA)(DA)(DC)(DT)(DG)(DG)(DC)(DG) (DG)(DG)(DC)(DA)(DA)(DA)(DC)(DA)(DG) (DT)(DC)(DG)(DT)(DT)(DG)(DC)(DT)(DG)(DA) (DT) (DT)(DG)(DG)(DC)(DG)(DT)(DT)(DG) (DC)(DC)(DA)(DC)(DC)(DT)(DC)(DC)(DA)(DG) (DT)(DC) (DT)(DG)(DG)(DC)(DC)(DC)(DT) (DG)(DC)(DA)(DC)(DG)(DC)(DG)(DC)(DC)(DG) (DT)(DC)(DG) (DC)(DA)(DA)(DA)(DT)(DT) (DG)(DT)(DC)(DG)(DC)(DG)(DG)(DC)(DG)(DA) (DT)(DT)(DA)(DA) (DA)(DT)(DC)(DT)(DC) (DG)(DC)(DG)(DC)(DC)(DG)(DA)(DT)(DC)(DA) (DA)(DC)(DT)(DG)(DG) GENBANK: GENBANK: MN982376.1 |
-Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ![]() ChemComp-ADP: |
-Macromolecule #6: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #7: MANGANESE (II) ION
Macromolecule | Name: MANGANESE (II) ION / type: ligand / ID: 7 / Number of copies: 4 / Formula: MN |
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Molecular weight | Theoretical: 54.938 Da |
-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) / Detector mode: COUNTING / Average electron dose: 43.19 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 57747 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |