6S85

Cutting state of the E. coli Mre11-Rad50 (SbcCD) head complex bound to ADP and dsDNA.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Mechanism of DNA End Sensing and Processing by the Mre11-Rad50 Complex.

Kashammer, L.Saathoff, J.H.Lammens, K.Gut, F.Bartho, J.Alt, A.Kessler, B.Hopfner, K.P.

(2019) Mol Cell 76: 382

  • DOI: https://doi.org/10.1016/j.molcel.2019.07.035
  • Primary Citation of Related Structures:  
    6S6V, 6S85

  • PubMed Abstract: 

    DNA double-strand breaks (DSBs) threaten genome stability throughout life and are linked to tumorigenesis in humans. To initiate DSB repair by end joining or homologous recombination, the Mre11-nuclease Rad50-ATPase complex detects and processes diverse and obstructed DNA ends, but a structural mechanism is still lacking. Here we report cryo-EM structures of the E. coli Mre11-Rad50 homolog SbcCD in resting and DNA-bound cutting states. In the resting state, Mre11's nuclease is blocked by ATP-Rad50, and the Rad50 coiled coils appear flexible. Upon DNA binding, the two coiled coils zip up into a rod and, together with the Rad50 nucleotide-binding domains, form a clamp around dsDNA. Mre11 moves to the side of Rad50, binds the DNA end, and assembles a DNA cutting channel for the nuclease reactions. The structures reveal how Mre11-Rad50 can detect and process diverse DNA ends and uncover a clamping and gating function for the coiled coils.


  • Organizational Affiliation

    Department of Biochemistry, Ludwig-Maximilians-Universität, 81377 Munich, Germany; Gene Center, Ludwig-Maximilians-Universität, 81377 Munich, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclease SbcCD subunit CA [auth C],
B [auth D]
1,048Escherichia coliMutation(s): 0 
Gene Names: 
UniProt
Find proteins for P13458 (Escherichia coli (strain K12))
Explore P13458 
Go to UniProtKB:  P13458
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13458
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclease SbcCD subunit DC [auth A],
D [auth B]
407Escherichia coliMutation(s): 0 
Gene Names: 
sbcDA9R57_08515ACU90_20930AM270_02320AM464_18970AMK83_08850AML07_05375APZ14_19360ARC77_21640AU473_24540AUQ13_18520AUS26_08295AW106_10255AWF80_027335B1K96_09895BANRA_00933BANRA_02010BANRA_03599BB545_15570BHS81_02440BHS87_02165BJJ90_20270BK292_14605BMT53_08385BMT91_05280BN17_02021BTQ04_02895BTQ06_17755BUE81_15560BVL39_00845BW690_06610BWP17_02185C2U48_08075C4J69_09475C5N07_12775C5P01_16270C5P43_02310C6986_02395C7235_18845C7B08_06215C9E25_04545CA593_01150CG691_03340CG705_03245CG706_02645COD30_16020COD46_04825CR538_19460CRE06_07850CVH05_20670CWS33_22910D0X26_07455D2184_11480D3821_12865D3822_22430D3O91_15270D3Y67_14385D4M06_05505D7K63_09095D7K66_05465D9H94_07055D9I87_03345D9I97_02300D9J44_05860D9L89_06325D9X97_05375DIV22_26320DL455_04405DL545_19095DL800_03920DMI04_05300DMZ31_02500DNB37_05400DNQ41_05900DOY56_05885DQF57_07710DQO13_05535DS732_06955DTL43_07380E2855_00535E2863_00431EAI44_12705EAI52_02980EB509_06820EB510_01660EB515_09310EC1094V2_3455EC3234A_4c00670EC3426_01235EC95NR1_04617ECs0448ED225_07565ED287_10145ED600_06285ED607_18305ED611_06615ED903_13690ED944_09545EEA45_02820EEP23_01080EF173_10600EFV01_15655EFV11_06690EFV17_08300EIA13_09680EL75_3353EL79_3448EL80_3402ERS085365_01835ERS085379_01210ERS085416_01963ERS139211_01257ERS150873_01853ERS150876_00572FORC28_4694HW43_05600NCTC10090_01877NCTC10429_03756NCTC11022_05144NCTC13125_01885NCTC13127_05149NCTC13462_01931NCTC8009_07006NCTC8179_01650NCTC8960_01309NCTC9036_03833NCTC9037_03951NCTC9045_04425NCTC9055_00697NCTC9058_03126NCTC9062_04472NCTC9111_03972NCTC9703_03216NCTC9706_01107PU06_02925RG28_02875RK56_026670RX35_02069SAMEA3446340_01461SAMEA3472043_02687SAMEA3472044_00460SAMEA3472047_02108SAMEA3472055_02158SAMEA3472070_02276SAMEA3472114_01252SAMEA3484427_03538SAMEA3484429_01894SAMEA3752553_00281SAMEA3752559_02892SAMEA3753064_01241SAMEA3753097_00507SAMEA3753290_01730SAMEA3753300_00463SK85_00423WR15_04330

UniProt
Find proteins for P0AG76 (Escherichia coli (strain K12))
Explore P0AG76 
Go to UniProtKB:  P0AG76
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AG76
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (31-MER)60synthetic construct
Sequence Annotations
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (32-MER)60synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
G [auth C],
I [auth D]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
K [auth A],
L [auth A],
M [auth B],
N [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth C],
J [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council--
German Research FoundationGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-04
    Type: Initial release
  • Version 1.1: 2019-09-18
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-20
    Changes: Database references, Derived calculations
  • Version 1.3: 2024-05-22
    Changes: Data collection, Database references, Derived calculations, Refinement description