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- EMDB-54397: Cryo-EM map of human MRE11-RAD50-NBS1 complex bound to ATPgammaS -

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Basic information

Entry
Database: EMDB / ID: EMD-54397
TitleCryo-EM map of human MRE11-RAD50-NBS1 complex bound to ATPgammaS
Map data
Sample
  • Complex: Human MRE11-RAD50-NBS1 complex bound to ATPgammaS
    • Protein or peptide: Human MRE11
    • Protein or peptide: Human RAD50
    • Protein or peptide: Human NBS1
KeywordsMRE11-RAD50-NBS1 / DNA double-strand break repair / open coiled-coil / HYDROLASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsCui HJ / Fan YL / Hopfner KP
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis for DNA break sensing by human MRE11-RAD50-NBS1 and its regulation by telomeric factor TRF2.
Authors: Yilan Fan / Filiz Kuybu / Hengjun Cui / Katja Lammens / Jia-Xuan Chen / Michael Kugler / Christophe Jung / Karl-Peter Hopfner /
Abstract: The MRE11-RAD50-NBS1 (MRN) complex is a central, multifunctional factor in the detection, signaling and nucleolytic processing of DNA double-strand breaks (DSBs). To clarify how human MRN binds ...The MRE11-RAD50-NBS1 (MRN) complex is a central, multifunctional factor in the detection, signaling and nucleolytic processing of DNA double-strand breaks (DSBs). To clarify how human MRN binds generic and telomeric DNA ends and can separate DNA end sensing from nuclease activities, we determined cryo-electron microscopy (cryo-EM) structures of human MRN bound to DNA and to DNA and the telomere protection factor TRF2. MRN senses DSBs through a tight clamp-like sensing state with closed coiled-coil domains, but auto-inhibited MRE11 nuclease. NBS1 wraps around the MRE11 dimer, with NBS1's ATM recruitment motif sequestered by binding to the regulatory RAD50 S site, necessitating a switch in the NBS1 C helix for ATM activation. At telomeric DNA, TRF2 blocks the second S site via the iDDR motif to prevent nuclease and ATM activation. Our results provide a structural framework for DNA sensing via a gating mechanism and separation of sensing, signaling and processing activities of mammalian MRN.
History
DepositionJul 15, 2025-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54397.png

Downloads & links

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Map

FileDownload / File: emd_54397.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 360 pix.
= 261.72 Å		0.73 Å/pix.
x 360 pix.
= 261.72 Å		0.73 Å/pix.
x 360 pix.
= 261.72 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.727 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.058
Minimum - Maximum-0.46768445 - 0.6154296
Average (Standard dev.)0.0002582782 (±0.012816818)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 261.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54397_msk_1.map
Projections & Slices
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Half map: #2

Fileemd_54397_half_map_1.map
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Half map: #1

Fileemd_54397_half_map_2.map
Projections & Slices
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Sample components

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Entire : Human MRE11-RAD50-NBS1 complex bound to ATPgammaS

EntireName: Human MRE11-RAD50-NBS1 complex bound to ATPgammaS
Components
  • Complex: Human MRE11-RAD50-NBS1 complex bound to ATPgammaS
    • Protein or peptide: Human MRE11
    • Protein or peptide: Human RAD50
    • Protein or peptide: Human NBS1

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Supramolecule #1: Human MRE11-RAD50-NBS1 complex bound to ATPgammaS

SupramoleculeName: Human MRE11-RAD50-NBS1 complex bound to ATPgammaS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 554 KDa

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Macromolecule #1: Human MRE11

MacromoleculeName: Human MRE11 / type: protein_or_peptide / ID: 1 / Details: H129N nuclease-dead mutant / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSTADALDDE NTFKILVATD IHLGFMEKDA VRGNDTFVTL DEILRLAQEN EVDFILLGGD LFHENKPSRK TLHTCLELLR KYCMGDRPVQ FEILSDQSVN FGFSKFPWVN YQDGNLNISI PVFSIHGNND DPTGADALCA LDILSCAGFV NHFGRSMSVE KIDISPVLLQ ...String:
MSTADALDDE NTFKILVATD IHLGFMEKDA VRGNDTFVTL DEILRLAQEN EVDFILLGGD LFHENKPSRK TLHTCLELLR KYCMGDRPVQ FEILSDQSVN FGFSKFPWVN YQDGNLNISI PVFSIHGNND DPTGADALCA LDILSCAGFV NHFGRSMSVE KIDISPVLLQ KGSTKIALYG LGSIPDERLY RMFVNKKVTM LRPKEDENSW FNLFVIHQNR SKHGSTNFIP EQFLDDFIDL VIWGHEHECK IAPTKNEQQL FYISQPGSSV VTSLSPGEAV KKHVGLLRIK GRKMNMHKIP LHTVRQFFME DIVLANHPDI FNPDNPKVTQ AIQSFCLEKI EEMLENAERE RLGNSHQPEK PLVRLRVDYS GGFEPFSVLR FSQKFVDRVA NPKDIIHFFR HREQKEKTGE EINFGKLITK PSEGTTLRVE DLVKQYFQTA EKNVQLSLLT ERGMGEAVQE FVDKEEKDAI EELVKYQLEK TQRFLKERHI DALEDKIDEE VRRFRETRQK NTNEEDDEVR EAMTRARALR SQSEESASAF SADDLMSIDL AEQMANDSDD SISAATNKGR GRGRGRRGGR GQNSASRGGS QRGRADTGLE TSTRSRNSKT AVSASRNMSI IDAFKSTRQQ PSRNVTTKNY SEVIEVDESD VEEDIFPTTS KTDQRWSSTS SSKIMSQSQV SKGVDFESSE DDDDDPFMNT SSLRRNRR

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Macromolecule #2: Human RAD50

MacromoleculeName: Human RAD50 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSRIEKMSIL GVRSFGIEDK DKQIITFFSP LTILVGPNGA GKTTIIECLK YICTGDFPPG TKGNTFVHDP KVAQETDVRA QIRLQFRDVN GELIAVQRSM VCTQKSKKTE FKTLEGVITR TKHGEKVSLS SKCAEIDREM ISSLGVSKAV LNNVIFCHQE DSNWPLSEGK ...String:
MSRIEKMSIL GVRSFGIEDK DKQIITFFSP LTILVGPNGA GKTTIIECLK YICTGDFPPG TKGNTFVHDP KVAQETDVRA QIRLQFRDVN GELIAVQRSM VCTQKSKKTE FKTLEGVITR TKHGEKVSLS SKCAEIDREM ISSLGVSKAV LNNVIFCHQE DSNWPLSEGK ALKQKFDEIF SATRYIKALE TLRQVRQTQG QKVKEYQMEL KYLKQYKEKA CEIRDQITSK EAQLTSSKEI VKSYENELDP LKNRLKEIEH NLSKIMKLDN EIKALDSRKK QMEKDNSELE EKMEKVFQGT DEQLNDLYHN HQRTVREKER KLVDCHRELE KLNKESRLLN QEKSELLVEQ GRLQLQADRH QEHIRARDSL IQSLATQLEL DGFERGPFSE RQIKNFHKLV RERQEGEAKT ANQLMNDFAE KETLKQKQID EIRDKKTGLG RIIELKSEIL SKKQNELKNV KYELQQLEGS SDRILELDQE LIKAERELSK AEKNSNVETL KMEVISLQNE KADLDRTLRK LDQEMEQLNH HTTTRTQMEM LTKDKADKDE QIRKIKSRHS DELTSLLGYF PNKKQLEDWL HSKSKEINQT RDRLAKLNKE LASSEQNKNH INNELKRKEE QLSSYEDKLF DVCGSQDFES DLDRLKEEIE KSSKQRAMLA GATAVYSQFI TQLTDENQSC CPVCQRVFQT EAELQEVISD LQSKLRLAPD KLKSTESELK KKEKRRDEML GLVPMRQSII DLKEKEIPEL RNKLQNVNRD IQRLKNDIEE QETLLGTIMP EEESAKVCLT DVTIMERFQM ELKDVERKIA QQAAKLQGID LDRTVQQVNQ EKQEKQHKLD TVSSKIELNR KLIQDQQEQI QHLKSTTNEL KSEKLQISTN LQRRQQLEEQ TVELSTEVQS LYREIKDAKE QVSPLETTLE KFQQEKEELI NKKNTSNKIA QDKLNDIKEK VKNIHGYMKD IENYIQDGKD DYKKQKETEL NKVIAQLSEC EKHKEKINED MRLMRQDIDT QKIQERWLQD NLTLRKRNEE LKEVEEERKQ HLKEMGQMQV LQMKSEHQKL EENIDNIKRN HNLALGRQKG YEEEIIHFKK ELREPQFRDA EEKYREMMIV MRTTELVNKD LDIYYKTLDQ AIMKFHSMKM EEINKIIRDL WRSTYRGQDI EYIEIRSDAD ENVSASDKRR NYNYRVVMLK GDTALDMRGR CSAGQKVLAS LIIRLALAET FCLNCGIIAL DEPTTNLDRE NIESLAHALV EIIKSRSQQR NFQLLVITHD EDFVELLGRS EYVEKFYRIK KNIDQCSEIV KCSVSSLGFN VH

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Macromolecule #3: Human NBS1

MacromoleculeName: Human NBS1 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MWKLLPAAGP AGGEPYRLLT GVEYVVGRKN CAILIENDQS ISRNHAVLTA NFSVTNLSQT DEIPVLTLKD NSKYGTFVNE EKMQNGFSRT LKSGDGITFG VFGSKFRIEY EPLVACSSCL DVSGKTALNQ AILQLGGFTV NNWTEECTHL VMVSVKVTIK TICALICGRP ...String:
MWKLLPAAGP AGGEPYRLLT GVEYVVGRKN CAILIENDQS ISRNHAVLTA NFSVTNLSQT DEIPVLTLKD NSKYGTFVNE EKMQNGFSRT LKSGDGITFG VFGSKFRIEY EPLVACSSCL DVSGKTALNQ AILQLGGFTV NNWTEECTHL VMVSVKVTIK TICALICGRP IVKPEYFTEF LKAVESKKQP PQIESFYPPL DEPSIGSKNV DLSGRQERKQ IFKGKTFIFL NAKQHKKLSS AVVFGGGEAR LITEENEEEH NFFLAPGTCV VDTGITNSQT LIPDCQKKWI QSIMDMLQRQ GLRPIPEAEI GLAVIFMTTK NYCDPQGHPS TGLKTTTPGP SLSQGVSVDE KLMPSAPVNT TTYVADTESE QADTWDLSER PKEIKVSKME QKFRMLSQDA PTVKESCKTS SNNNSMVSNT LAKMRIPNYQ LSPTKLPSIN KSKDRASQQQ QTNSIRNYFQ PSTKKRERDE ENQEMSSCKS ARIETSCSLL EQTQPATPSL WKNKEQHLSE NEPVDTNSDN NLFTDTDLKS IVKNSASKSH AAEKLRSNKK REMDDVAIED EVLEQLFKDT KPELEIDVKV QKQEEDVNVR KRPRMDIETN DTFSDEAVPE SSKISQENEI GKKRELKEDS LWSAKEISNN DKLQDDSEML PKKLLLTEFR SLVIKNSTSR NPSGINDDYG QLKNFKKFKK VTYPGAGKLP HIIGGSDLIA HHARKNTELE EWLRQEMEVQ NQHAKEESLA DDLFRYNPYL KRRR

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 75330
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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