2025-10-01 REL PDBe INITIAL_RELEASE REPOSITORY PDBe PDBe 2025-02-26 2025-10-01 2025-10-01 2025-10-01 German Research Foundation (DFG) Germany Cryo-EM structure of human Mre11-Rad50 (MR) complex bound to DNA and telomeric factor TRF2 fragment (438-542) Cui HJ Lammens K Hopfner KP Fan YL Kuybu F Mre11-Rad50-TRF2 complex, double-strand DNA break repair protein, nuclease, HYDROLASE Fan Y Kuybu F Cui H Lammens K Chen JX Kugler M Jung C Hopfner KP Structural basis for DNA break sensing by human MRE11-RAD50-NBS1 and its regulation by telomeric factor TRF2. Nat Commun UK 16 8320 8320 2025 40968163 doi:10.1038/s41467-025-64082-x 2041-1723 9q9k FULLOVERLAP EMDB EMD-52962 associated EM volume
Cryo-EM structure of human Mre11-Rad50 (MR) complex bound to DNA and telomeric factor TRF2 fragment (438-542)
 MR-TRF2(438-542)-DNA complex MR-TRF2(438-542)-DNA complex 0 1 2 3 4 5 Homo sapiens 0.52 Telomeric repeat-binding factor 2 Homo sapiens 0.012931349
GP is the leftover sequence from PreScission cleavage site, and GGSSGGSSG is a linker sequence between the cleavage site and TRF2(438-542) fragment.
2 Trichoplusia ni LEVO GPGGSSGGSSGQPLPGEKNPKVPKGKWNSSNGVEEKETWVEEDELFQVQAAPDEDSTTNITKKQKWTVEESEWVKAGVQK YGEGNWAAISKNYPFVNRTAVMIKDRWRTMKRLGMN Q15554 DNA (64-MER) Homo sapiens 0.019423369 1 (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT) DNA DNA (64-MER) Homo sapiens 0.020000280999999998 1 (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA) DNA DNA repair protein RAD50 Homo sapiens 0.154150016 2 Trichoplusia ni LEVO MSRIEKMSILGVRSFGIEDKDKQIITFFSPLTILVGPNGAGKTTIIECLKYICTGDFPPGTKGNTFVHDPKVAQETDVRA QIRLQFRDVNGELIAVQRSMVCTQKSKKTEFKTLEGVITRTKHGEKVSLSSKCAEIDREMISSLGVSKAVLNNVIFCHQE DSNWPLSEGKALKQKFDEIFSATRYIKALETLRQVRQTQGQKVKEYQMELKYLKQYKEKACEIRDQITSKEAQLTSSKEI VKSYENELDPLKNRLKEIEHNLSKIMKLDNEIKALDSRKKQMEKDNSELEEKMEKVFQGTDEQLNDLYHNHQRTVREKER KLVDCHRELEKLNKESRLLNQEKSELLVEQGRLQLQADRHQEHIRARDSLIQSLATQLELDGFERGPFSERQIKNFHKLV RERQEGEAKTANQLMNDFAEKETLKQKQIDEIRDKKTGLGRIIELKSEILSKKQNELKNVKYELQQLEGSSDRILELDQE LIKAERELSKAEKNSNVETLKMEVISLQNEKADLDRTLRKLDQEMEQLNHHTTTRTQMEMLTKDKADKDEQIRKIKSRHS DELTSLLGYFPNKKQLEDWLHSKSKEINQTRDRLAKLNKELASSEQNKNHINNELKRKEEQLSSYEDKLFDVCGSQDFES DLDRLKEEIEKSSKQRAMLAGATAVYSQFITQLTDENQSCCPVCQRVFQTEAELQEVISDLQSKLRLAPDKLKSTESELK KKEKRRDEMLGLVPMRQSIIDLKEKEIPELRNKLQNVNRDIQRLKNDIEEQETLLGTIMPEEESAKVCLTDVTIMERFQM ELKDVERKIAQQAAKLQGIDLDRTVQQVNQEKQEKQHKLDTVSSKIELNRKLIQDQQEQIQHLKSTTNELKSEKLQISTN LQRRQQLEEQTVELSTEVQSLYREIKDAKEQVSPLETTLEKFQQEKEELINKKNTSNKIAQDKLNDIKEKVKNIHGYMKD IENYIQDGKDDYKKQKETELNKVIAQLSECEKHKEKINEDMRLMRQDIDTQKIQERWLQDNLTLRKRNEELKEVEEERKQ HLKEMGQMQVLQMKSEHQKLEENIDNIKRNHNLALGRQKGYEEEIIHFKKELREPQFRDAEEKYREMMIVMRTTELVNKD LDIYYKTLDQAIMKFHSMKMEEINKIIRDLWRSTYRGQDIEYIEIRSDADENVSASDKRRNYNYRVVMLKGDTALDMRGR CSAGQKVLASLIIRLALAETFCLNCGIIALDEPTTNLDRENIESLAHALVEIIKSRSQQRNFQLLVITHDEDFVELLGRS EYVEKFYRIKKNIDQCSEIVKCSVSSLGFNVH Q92878 Double-strand break repair protein MRE11 Homo sapiens 0.08403267999999998
Following residue R708 is a short GS linker, a PreScission cleavage site, and two FLAG tags.
2 Trichoplusia ni LEVO MSTADALDDENTFKILVATDIHLGFMEKDAVRGNDTFVTLDEILRLAQENEVDFILLGGDLFHENKPSRKTLHTCLELLR KYCMGDRPVQFEILSDQSVNFGFSKFPWVNYQDGNLNISIPVFSIHGNHDDPTGADALCALDILSCAGFVNHFGRSMSVE KIDISPVLLQKGSTKIALYGLGSIPDERLYRMFVNKKVTMLRPKEDENSWFNLFVIHQNRSKHGSTNFIPEQFLDDFIDL VIWGHEHECKIAPTKNEQQLFYISQPGSSVVTSLSPGEAVKKHVGLLRIKGRKMNMHKIPLHTVRQFFMEDIVLANHPDI FNPDNPKVTQAIQSFCLEKIEEMLENAERERLGNSHQPEKPLVRLRVDYSGGFEPFSVLRFSQKFVDRVANPKDIIHFFR HREQKEKTGEEINFGKLITKPSEGTTLRVEDLVKQYFQTAEKNVQLSLLTERGMGEAVQEFVDKEEKDAIEELVKYQLEK TQRFLKERHIDALEDKIDEEVRRFRETRQKNTNEEDDEVREAMTRARALRSQSEESASAFSADDLMSIDLAEQMANDSDD SISAATNKGRGRGRGRRGGRGQNSASRGGSQRGRADTGLETSTRSRNSKTAVSASRNMSIIDAFKSTRQQPSRNVTTKNY SEVIEVDESDVEEDIFPTTSKTDQRWSSTSSSKIMSQSQVSKGVDFESSEDDDDDPFMNTSSLRRNRRSGGSLEVLFQGP DYKDDDDKGTDYKDDDDK P49959 3.1.-.- ADENOSINE-5'-DIPHOSPHATE 0.000427201 2 ADP MAGNESIUM ION 2.4305e-05 2 MG BERYLLIUM TRIFLUORIDE ION 6.600700000000001e-05 2 BEF MANGANESE (II) ION 5.4938e-05 4 MN water 1.8015e-05 6 HOH singleParticle particle 7.5
25mM Hepes-NaOH, pH 7.5, 150 mM NaCl, 1 mM DTT, 1 mM ATP, 1mM BeF3, 5 mM MgCl2, 1 mM MnCl2
 Quantifoil R2/1 COPPER 200 CARBON HOLEY GLOW DISCHARGE
20 mA, 7 s
 ETHANE 95 283 LEICA PLUNGER TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.5 2.6 NITROGEN GIF Bioquantum 20 FEI FALCON IV (4k x 4k) COUNTING 40.0 1 cryoSPARC 4.6.2 PHASE FLIPPING AND AMPLITUDE CORRECTION 2.59 FSC 0.143 CUT-OFF cryoSPARC 4.6.2 274928 MAXIMUM LIKELIHOOD cryoSPARC 4.6.2 MAXIMUM LIKELIHOOD cryoSPARC 4.6.2 5 cryoSPARC 4.6.2 emd_52962.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 261.72 261.72 261.72 90.0 90.0 90.0 X Y Z -2.4693701 4.954583 0.00049310754 0.08304975 0.727 0.727 0.727 0.3 AUTHOR AlphaFold in silico model RIGID BODY FIT REAL emd_52962_msk_1.map emd_52962_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 261.72 261.72 261.72 90.0 90.0 90.0 X Y Z -0.51526386 1.3413396 0.0011346845 0.04783289 0.727 0.727 0.727 AUTHOR emd_52962_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 261.72 261.72 261.72 90.0 90.0 90.0 X Y Z -0.50943017 1.4444592 0.0011108797 0.043588415 0.727 0.727 0.727 AUTHOR