6S6V

Resting state of the E. coli Mre11-Rad50 (SbcCD) head complex bound to ATPgS

PDB DOI: https://doi.org/10.2210/pdb6S6V/pdb
EM Map EMD-10107: EMDB EMDataResource

Classification: DNA BINDING PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-07-03 Released: 2019-09-04
Deposition Author(s): Kaeshammer, L., Saathoff, J.H., Gut, F., Bartho, J., Alt, A., Kessler, B., Lammens, K., Hopfner, K.P.
Funding Organization(s): European Research Council, German Research Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 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

PubMed: 31492634 Search on PubMed
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.

Macromolecule Content

Total Structure Weight: 330.32 kDa
Atom Count: 11,820
Modelled Residue Count: 1,498
Deposited Residue Count: 2,910
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclease SbcCD subunit D	A, B	407	Escherichia coli	Mutation(s): 0 Gene Names: sbcD, A9R57_08515, ACU90_20930, AM270_02320, AM464_18970, AMK83_08850, AML07_05375, APZ14_19360, ARC77_21640, AU473_24540... sbcD, A9R57_08515, ACU90_20930, AM270_02320, AM464_18970, AMK83_08850, AML07_05375, APZ14_19360, ARC77_21640, AU473_24540, AUQ13_18520, AUS26_08295, AW106_10255, AWF80_027335, B1K96_09895, BANRA_00933, BANRA_02010, BANRA_03599, BB545_15570, BHS81_02440, BHS87_02165, BJJ90_20270, BK292_14605, BMT53_08385, BMT91_05280, BN17_02021, BTQ04_02895, BTQ06_17755, BUE81_15560, BVL39_00845, BW690_06610, BWP17_02185, C2U48_08075, C4J69_09475, C5N07_12775, C5P01_16270, C5P43_02310, C6986_02395, C7235_18845, C7B08_06215, C9E25_04545, CA593_01150, CG691_03340, CG705_03245, CG706_02645, COD30_16020, COD46_04825, CR538_19460, CRE06_07850, CVH05_20670, CWS33_22910, D0X26_07455, D2184_11480, D3821_12865, D3822_22430, D3O91_15270, D3Y67_14385, D4M06_05505, D7K63_09095, D7K66_05465, D9H94_07055, D9I87_03345, D9I97_02300, D9J44_05860, D9L89_06325, D9X97_05375, DIV22_26320, DL455_04405, DL545_19095, DL800_03920, DMI04_05300, DMZ31_02500, DNB37_05400, DNQ41_05900, DOY56_05885, DQF57_07710, DQO13_05535, DS732_06955, DTL43_07380, E2855_00535, E2863_00431, EAI44_12705, EAI52_02980, EB509_06820, EB510_01660, EB515_09310, EC1094V2_3455, EC3234A_4c00670, EC3426_01235, EC95NR1_04617, ECs0448, ED225_07565, ED287_10145, ED600_06285, ED607_18305, ED611_06615, ED903_13690, ED944_09545, EEA45_02820, EEP23_01080, EF173_10600, EFV01_15655, EFV11_06690, EFV17_08300, EIA13_09680, EL75_3353, EL79_3448, EL80_3402, ERS085365_01835, ERS085379_01210, ERS085416_01963, ERS139211_01257, ERS150873_01853, ERS150876_00572, FORC28_4694, HW43_05600, NCTC10090_01877, NCTC10429_03756, NCTC11022_05144, NCTC13125_01885, NCTC13127_05149, NCTC13462_01931, NCTC8009_07006, NCTC8179_01650, NCTC8960_01309, NCTC9036_03833, NCTC9037_03951, NCTC9045_04425, NCTC9055_00697, NCTC9058_03126, NCTC9062_04472, NCTC9111_03972, NCTC9703_03216, NCTC9706_01107, PU06_02925, RG28_02875, RK56_026670, RX35_02069, SAMEA3446340_01461, SAMEA3472043_02687, SAMEA3472044_00460, SAMEA3472047_02108, SAMEA3472055_02158, SAMEA3472070_02276, SAMEA3472114_01252, SAMEA3484427_03538, SAMEA3484429_01894, SAMEA3752553_00281, SAMEA3752559_02892, SAMEA3753064_01241, SAMEA3753097_00507, SAMEA3753290_01730, SAMEA3753300_00463, SK85_00423, WR15_04330
UniProt
Find proteins for P0AG76 (Escherichia coli (strain K12)) Explore P0AG76 Go to UniProtKB: P0AG76
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0AG76
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclease SbcCD subunit C	C, D	1,048	Escherichia coli	Mutation(s): 0 Gene Names: sbcC, A9R57_08510, ACU57_12010, AM464_18965, AUQ13_18525, BANRA_02011, BANRA_03598, BHS87_02160, BJJ90_20275, BUE81_15555... sbcC, A9R57_08510, ACU57_12010, AM464_18965, AUQ13_18525, BANRA_02011, BANRA_03598, BHS87_02160, BJJ90_20275, BUE81_15555, BW690_06605, C4J69_09480, C5N07_12770, C9E25_04550, CA593_01155, D0X26_07450, D3821_12870, D3Y67_14380, D9D20_11475, D9F57_05650, DNQ41_05895, EAI52_02975, EC3426_01234, EL75_3354, EL79_3449, EL80_3403, ERS085365_01836, ERS085416_01964, ERS139211_01256, ERS150873_01854, NCTC13462_01932, NCTC9037_03952, RK56_026675, SAMEA3446340_01460, SAMEA3472047_02107, SAMEA3484427_03539, SAMEA3484429_01893, SAMEA3752559_02893, SAMEA3753300_00462, SK85_00422
UniProt
Find proteins for P13458 (Escherichia coli (strain K12)) Explore P13458 Go to UniProtKB: P13458
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13458
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGS Query on AGS Download Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	I [auth C], K [auth D]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain I [auth C] Focus chain K [auth D]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B]	E [auth A], F [auth A], G [auth B], H [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C]	J [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain J [auth C] Focus chain L [auth D]