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- EMDB-14882: Chaetomium thermophilum Rad50 zinc-hook tetramer -

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Basic information

Entry
Database: EMDB / ID: EMD-14882
TitleChaetomium thermophilum Rad50 zinc-hook tetramer
Map dataZinc hook. the main map
Sample
  • Complex: Chaetomium thermophilum Mre11-Rad50-Nbs1 complex bound to ATPyS
    • Protein or peptide: Double-strand break repair protein
  • Protein or peptide: DH domain-containing protein
  • Protein or peptide: FHA domain-containing protein
KeywordsDNA repair / complex / ATPase / coiled-coils / HYDROLASE
Function / homology
Function and homology information


Mre11 complex / 3'-5'-DNA exonuclease activity / DNA endonuclease activity / meiotic cell cycle / double-strand break repair / manganese ion binding
Similarity search - Function
DNA double-strand break repair protein Mre11 / Mre11, DNA-binding / Mre11, capping domain / Mre11 DNA-binding presumed domain / Mre11 DNA-binding presumed domain / Mre11 nuclease, N-terminal metallophosphatase domain / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
Double-strand break repair protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus) / Thermochaetoides thermophila (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsStakyte K / Rotheneder M / Bartho JD / Lammens K / Hopfner KP
Funding support Germany, 3 items
OrganizationGrant numberCountry
German Research Foundation (DFG)CRC1361 Germany
German Research Foundation (DFG)SFB1361 Germany
German Research Foundation (DFG)GRK1721 Germany
CitationJournal: Mol Cell / Year: 2023
Title: Cryo-EM structure of the Mre11-Rad50-Nbs1 complex reveals the molecular mechanism of scaffolding functions.
Authors: Matthias Rotheneder / Kristina Stakyte / Erik van de Logt / Joseph D Bartho / Katja Lammens / Yilan Fan / Aaron Alt / Brigitte Kessler / Christophe Jung / Wynand P Roos / Barbara ...Authors: Matthias Rotheneder / Kristina Stakyte / Erik van de Logt / Joseph D Bartho / Katja Lammens / Yilan Fan / Aaron Alt / Brigitte Kessler / Christophe Jung / Wynand P Roos / Barbara Steigenberger / Karl-Peter Hopfner /
Abstract: The DNA double-strand break repair complex Mre11-Rad50-Nbs1 (MRN) detects and nucleolytically processes DNA ends, activates the ATM kinase, and tethers DNA at break sites. How MRN can act both as ...The DNA double-strand break repair complex Mre11-Rad50-Nbs1 (MRN) detects and nucleolytically processes DNA ends, activates the ATM kinase, and tethers DNA at break sites. How MRN can act both as nuclease and scaffold protein is not well understood. The cryo-EM structure of MRN from Chaetomium thermophilum reveals a 2:2:1 complex with a single Nbs1 wrapping around the autoinhibited Mre11 nuclease dimer. MRN has two DNA-binding modes, one ATP-dependent mode for loading onto DNA ends and one ATP-independent mode through Mre11's C terminus, suggesting how it may interact with DSBs and intact DNA. MRNs two 60-nm-long coiled-coil domains form a linear rod structure, the apex of which is assembled by the two joined zinc-hook motifs. Apices from two MRN complexes can further dimerize, forming 120-nm spanning MRN-MRN structures. Our results illustrate the architecture of MRN and suggest how it mechanistically integrates catalytic and tethering functions.
History
DepositionMay 3, 2022-
Header (metadata) releaseDec 28, 2022-
Map releaseDec 28, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14882.png

Downloads & links

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Map

FileDownload / File: emd_14882.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationZinc hook. the main map
Voxel sizeX=Y=Z: 1.059 Å
Density
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.063769735 - 0.45774072
Average (Standard dev.)-0.0001591245 (±0.012502395)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 372.768 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14882_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Zinc hook. half map a

Fileemd_14882_half_map_1.map
AnnotationZinc hook. half map a
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Zinc hook. half map b

Fileemd_14882_half_map_2.map
AnnotationZinc hook. half map b
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Chaetomium thermophilum Mre11-Rad50-Nbs1 complex bound to ATPyS

EntireName: Chaetomium thermophilum Mre11-Rad50-Nbs1 complex bound to ATPyS
Components
  • Complex: Chaetomium thermophilum Mre11-Rad50-Nbs1 complex bound to ATPyS
    • Protein or peptide: Double-strand break repair protein
  • Protein or peptide: DH domain-containing protein
  • Protein or peptide: FHA domain-containing protein

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Supramolecule #1: Chaetomium thermophilum Mre11-Rad50-Nbs1 complex bound to ATPyS

SupramoleculeName: Chaetomium thermophilum Mre11-Rad50-Nbs1 complex bound to ATPyS
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Chaetomium thermophilum (fungus)

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Macromolecule #1: Double-strand break repair protein

MacromoleculeName: Double-strand break repair protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MPQTAGPDTI RILVSTDNHV GYEERDPIRK DDSWRTFDEI MQLARTKDVD MVLLGGDLFH DNKPSRKAMY QVMRSLRKNC LGMKPCELEF LSDPAEVFEG AFPHVNYYDP DINVSIPVFS IHGNHDDPSG DGHLCSLDLL QVAGLVNYFG RVPEADNIHV KPILLQKGKT ...String:
MPQTAGPDTI RILVSTDNHV GYEERDPIRK DDSWRTFDEI MQLARTKDVD MVLLGGDLFH DNKPSRKAMY QVMRSLRKNC LGMKPCELEF LSDPAEVFEG AFPHVNYYDP DINVSIPVFS IHGNHDDPSG DGHLCSLDLL QVAGLVNYFG RVPEADNIHV KPILLQKGKT KLALYGMSNV RDERIHRTFR DNKVRFYRPS QQTGDWFNLL TLHQNHYAHT PTGYLSENML PDFLDLVIWG HEHECLIDPK KNPETGFHVM QPGSSIATSL VPGEAVPKHI AILSITGKSF EVEKIPLRTV RPFVIREITL ATDKRFKGLE KKQDNRQEVT KRLMQIVEEM IAEANEMWRS LHEDSQDDED EEQPLPLIRL KVEYSSPEGT KFEVENPQRF SNRFAGKVAN QNDVVHFYRK KTGTTRKPKE GKRELPEGIA EALEDSDSIS VDALVQEFFA QQSLKILPQA PFGDAVNQFV SKDDKHAVEM FVMDSLSSQV RGLLQLDDDK INEGLDSHIE DFRKVMEKNF LSGQQKQAQR RRRFKEKPEG WDSDLNGHWT LQPEAIEELS SSPEPAKEGG RVRPASRITV GDEDNLFEEE EFVQKTTAKR APTTRATRKT AAATRATTAT KASAPAKKSI AAPRGRKRAN PFQDSAEEEE DVIMDDDDDY KPAPPVKAPP PKPARETQTR GAPKTRQTTL NFSQAERPTR TTQKAIEISD DEISEDDAFE SMPARKSKRY

UniProtKB: Double-strand break repair protein

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Macromolecule #2: DH domain-containing protein

MacromoleculeName: DH domain-containing protein / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSKIEKLSIL GVRSFGPHHP ETIAFNTPLT LIVGYNGSGK TTVIECLKYA TTGELPPNST RNGAFIHDPD LVGEKEVRAQ VKLSFRSTIG ESYVVTRNIQ LLVQRNNKRT QKTLEGSLLL RNNGERTVIS TRVAELDKLV SEKLGVPPAI LDAVIFCHQD DSLWPMSEPA ...String:
MSKIEKLSIL GVRSFGPHHP ETIAFNTPLT LIVGYNGSGK TTVIECLKYA TTGELPPNST RNGAFIHDPD LVGEKEVRAQ VKLSFRSTIG ESYVVTRNIQ LLVQRNNKRT QKTLEGSLLL RNNGERTVIS TRVAELDKLV SEKLGVPPAI LDAVIFCHQD DSLWPMSEPA ALKKRFDEIF EAQKYTKVIE NIRLLKKKKG DELKILKERE VQDKANKERA EKVDRLMAQL TREILEAREK CNELSKQMEE ESAKIKDKYE QANSFLKIMN DLQTKTEKLE YKKDAIVELR SRIEELPDPD EVLRNTLDEY EQTINRIVAD RDHKAAQFHD LQAELKSARD QHTAKAAEQG KHQSDKEKYE RQLVARERMI REAAERHEIR GYNGDLDDRR IAIFNERIQK ILNDKRRELE RLQRENQEEL DRKTAVIAER ESRKQSVIRD RKAAKDRIIS LGKDMASIQG ELSSIDIDEG TEEMLRAEMK ELQARIEAAK ADEQNANLDA QIKEVNEEIW KLESLSAKLA RELVECTRLA SERAQLDLRR KQLAERKREL EIMTNTWNEQ FSTLLGEGWR PETLERDFSD VLKQQQLLVG EHRKKKDATQ QELKQAEYQL SNARNLHNKL TNEMEACMRA VQTAMKEARD LDSAPPVDEY ITMLETDEKE LAEVETALKL YDELKKHYST IKDRALRFNK CYICDRDFTN QEAAKTRLLE KVAKRLGDEE KKELLEDQAA FMKSLDILRA VRVKYDTYQR LSSELPQLSR EIDSETNRRE DLVRRLEDQD LAFREADNKL QEMETLNKHV MKITQLLKDI SDAEKQVERS QQLSNIETRS ADEINEEQTT CAEQTRAAQA KLTKLTAEKQ RLKDLVRQLE VERLQLENKI SSAVQQLERK KRLQESIARH KEDQNQARNA VQEADEELER LEPEIAGARA ALDEARQACR AKEQKVAAER DAIAQTVSEL NMINSEIQEY LDRGGPSSLA ANQRAIANLE TQMANLEGEM RELTVQINKL NKEIDNSDAK KRNIADNLTY RKNLREKDAL EREIAELEAR NAQEDYDRLI KEAHYLEAHR SKLNADRERL MGMMSTKDEE FRRLNEEYEL DLKDAKAKYK ETHIKVETTK AAIEDLGRGM AAVDHAIMQY HSKMMEQINR TIAELWQSTY QGTDIDTIQI RSDVESTTSS DSGTRRNYNY RVSMVKGDTE MDMRGRCSAG QKVLASIIIR LALAESFCAN CGLIALDEPT TNLDSDNIRS LAESLHGIIK ARQAQGNLQL IVITHDEEFL KYMQCSDFCD DFYRVKRDEK QNSVIVRESI TRITE

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Macromolecule #3: FHA domain-containing protein

MacromoleculeName: FHA domain-containing protein / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MWILESELFD GKRLWLRPGK TYLFGRTVAE AGQLTISDKT VSRKHLTIHI DNVPEGGGRN LRSRSNVIVE DLESKKGTLV NGVQIRGQKT TLTEDVNEIK LGLCPKTLKI RWHPIVLSFS FTSKELRADP WTNLRDSLEQ LDIKYSAEYE PTTTHVVSKK RNTSKGLQAL ...String:
MWILESELFD GKRLWLRPGK TYLFGRTVAE AGQLTISDKT VSRKHLTIHI DNVPEGGGRN LRSRSNVIVE DLESKKGTLV NGVQIRGQKT TLTEDVNEIK LGLCPKTLKI RWHPIVLSFS FTSKELRADP WTNLRDSLEQ LDIKYSAEYE PTTTHVVSKK RNTSKGLQAL INGRYIVTDS FINAIVQATE IPEGEEGASS ALEQDFEANW PNPLDHLPPR GEEPGNHTTE TYAPDARRQE VFDGYTFIFY EKKQYDNLFP AISAGKGKAL LKEVVPNRTR VDEFVRYVKS VAGEKGLGSF EDGSEGKGVV VVRYTPKGED SAWYAEFFTK FAQQLDHRPI DQKEFLEAIL ACDASMLRRP LEAMSQPVSV SASVEPQSSE KVRPAVEDRK EVEQSAPKQL QPSAEVPATE ESAPAPHRRE RRTGRSRFKG FDFDDDDIII ETPQAQSSTQ VPALPQVPSA SQDSLFVSQR EPSLAPSEPM LEEEAPCNTR TTRQTHRKRV LSPLPEHDNS ALLDEIAPIT AAVKRRRIEA GQDPVPPLPE PEPEREDEDV EMVEESPPRK GKKGAATTAK GKGKKIKQED EENVLELARR RREEAEAAAA AERQRLAQLG DDDIDYAAIR RLHIIEEIEV RQPEPHGPNR TREQDIADGR WDPRWNGRKN FKRFRRQGET GVRMPVQSVI VPLEEVRTKE YGIGDDYWLE DEEGRVPRRP KETQTQERST IGSVRDGSGF AAAAASGKGK EKDKENEKEV GRPGSSAAAA KQRSKPAPRR TVLTLDSSDE DEDEPSPHAP GIDTISDSEP EVVSSFPSVI PASEPSRSRA AKAAERANAL RSSAHSSQSQ TQQHRESQLS TGSSKIQLTL APGSSSLSFS RSGTAAGRNE NGKRPFGSFV SGESTASGRG MSVESGSVRG ESASKRQKQG SSGGGSFLAT RRKDDGSEEE SEDDELKFRF GRRR

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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

Concentration2.7 mg/mL
BufferpH: 7.6
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 43.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 32603
FSC plot (resolution estimation)

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