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- EMDB-14881: Chaetomium thermophilum Mre11-Rad50-Nbs1 complex bound to ATPyS (... -

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Basic information

Entry
Database: EMDB / ID: EMD-14881
TitleChaetomium thermophilum Mre11-Rad50-Nbs1 complex bound to ATPyS (composite structure)
Map dataComposite 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
  • Ligand: MANGANESE (II) ION
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
KeywordsDNA repair / complex / ATPase / coiled-coils / HYDROLASE
Function / homology
Function and homology information


Mre11 complex / 3'-5'-DNA exonuclease activity / mitotic G2 DNA damage checkpoint signaling / telomere maintenance / guanyl-nucleotide exchange factor activity / DNA endonuclease activity / meiotic cell cycle / double-strand break repair / manganese ion binding / ATP hydrolysis activity / metal ion binding
Similarity search - Function
DNA repair protein Rad50, eukaryotes / Nibrin, second BRCT domain / Nibrin, second BRCT domain superfamily / Second BRCT domain on Nijmegen syndrome breakage protein / Nibrin-related / DNA double-strand break repair protein Mre11 / Mre11, DNA-binding / Mre11, capping domain / Mre11 DNA-binding presumed domain / Mre11 DNA-binding presumed domain ...DNA repair protein Rad50, eukaryotes / Nibrin, second BRCT domain / Nibrin, second BRCT domain superfamily / Second BRCT domain on Nijmegen syndrome breakage protein / Nibrin-related / DNA double-strand break repair protein Mre11 / Mre11, DNA-binding / Mre11, capping domain / Mre11 DNA-binding presumed domain / Mre11 DNA-binding presumed domain / SbcC/RAD50-like, Walker B motif / Rad50/SbcC-type AAA domain / AAA domain / Mre11 nuclease, N-terminal metallophosphatase domain / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / SMAD/FHA domain superfamily / Metallo-dependent phosphatase-like / BRCT domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Double-strand break repair protein / FHA domain-containing protein / DH domain-containing protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus) / Thermochaetoides thermophila (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsRotheneder M / Stakyte K / 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) releaseJan 11, 2023-
Map releaseJan 11, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14881.png

Downloads & links

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Map

FileDownload / File: emd_14881.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.03 Å/pix.
x 400 pix.
= 813.312 Å		2.03 Å/pix.
x 400 pix.
= 813.312 Å		2.03 Å/pix.
x 400 pix.
= 813.312 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.03328 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.1863173 - 3.1334965
Average (Standard dev.)0.0002549034 (±0.010006834)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 813.3121 Å
α=β=γ: 90.0 °

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Supplemental data

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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
  • Ligand: MANGANESE (II) ION
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

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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-#3
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 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 83.036273 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MPQTAGPDTI RILVSTDNHV GYEERDPIRK DDSWRTFDEI MQLARTKDVD MVLLGGDLFH DNKPSRKAMY QVMRSLRKNC LGMKPCELE FLSDPAEVFE GAFPHVNYYD PDINVSIPVF SIHGNHDDPS GDGHLCSLDL LQVAGLVNYF GRVPEADNIH V KPILLQKG ...String:
MPQTAGPDTI RILVSTDNHV GYEERDPIRK DDSWRTFDEI MQLARTKDVD MVLLGGDLFH DNKPSRKAMY QVMRSLRKNC LGMKPCELE FLSDPAEVFE GAFPHVNYYD PDINVSIPVF SIHGNHDDPS GDGHLCSLDL LQVAGLVNYF GRVPEADNIH V KPILLQKG KTKLALYGMS NVRDERIHRT FRDNKVRFYR PSQQTGDWFN LLTLHQNHYA HTPTGYLSEN MLPDFLDLVI WG HEHECLI DPKKNPETGF HVMQPGSSIA TSLVPGEAVP KHIAILSITG KSFEVEKIPL RTVRPFVIRE ITLATDKRFK GLE KKQDNR QEVTKRLMQI VEEMIAEANE MWRSLHEDSQ DDEDEEQPLP LIRLKVEYSS PEGTKFEVEN PQRFSNRFAG KVAN QNDVV HFYRKKTGTT RKPKEGKREL PEGIAEALED SDSISVDALV QEFFAQQSLK ILPQAPFGDA VNQFVSKDDK HAVEM FVMD SLSSQVRGLL QLDDDKINEG LDSHIEDFRK VMEKNFLSGQ QKQAQRRRRF KEKPEGWDSD LNGHWTLQPE AIEELS SSP EPAKEGGRVR PASRITVGDE DNLFEEEEFV QKTTAKRAPT TRATRKTAAA TRATTATKAS APAKKSIAAP RGRKRAN PF QDSAEEEEDV IMDDDDDYKP APPVKAPPPK PARETQTRGA PKTRQTTLNF SQAERPTRTT QKAIEISDDE ISEDDAFE S MPARKSKRY

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 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 152.229906 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSKIEKLSIL GVRSFGPHHP ETIAFNTPLT LIVGYNGSGK TTVIECLKYA TTGELPPNST RNGAFIHDPD LVGEKEVRAQ VKLSFRSTI GESYVVTRNI QLLVQRNNKR TQKTLEGSLL LRNNGERTVI STRVAELDKL VSEKLGVPPA ILDAVIFCHQ D DSLWPMSE ...String:
MSKIEKLSIL GVRSFGPHHP ETIAFNTPLT LIVGYNGSGK TTVIECLKYA TTGELPPNST RNGAFIHDPD LVGEKEVRAQ VKLSFRSTI GESYVVTRNI QLLVQRNNKR TQKTLEGSLL LRNNGERTVI STRVAELDKL VSEKLGVPPA ILDAVIFCHQ D DSLWPMSE PAALKKRFDE IFEAQKYTKV IENIRLLKKK KGDELKILKE REVQDKANKE RAEKVDRLMA QLTREILEAR EK CNELSKQ MEEESAKIKD KYEQANSFLK IMNDLQTKTE KLEYKKDAIV ELRSRIEELP DPDEVLRNTL DEYEQTINRI VAD RDHKAA QFHDLQAELK SARDQHTAKA AEQGKHQSDK EKYERQLVAR ERMIREAAER HEIRGYNGDL DDRRIAIFNE RIQK ILNDK RRELERLQRE NQEELDRKTA VIAERESRKQ SVIRDRKAAK DRIISLGKDM ASIQGELSSI DIDEGTEEML RAEMK ELQA RIEAAKADEQ NANLDAQIKE VNEEIWKLES LSAKLARELV ECTRLASERA QLDLRRKQLA ERKRELEIMT NTWNEQ FST LLGEGWRPET LERDFSDVLK QQQLLVGEHR KKKDATQQEL KQAEYQLSNA RNLHNKLTNE MEACMRAVQT AMKEARD LD SAPPVDEYIT MLETDEKELA EVETALKLYD ELKKHYSTIK DRALRFNKCY ICDRDFTNQE AAKTRLLEKV AKRLGDEE K KELLEDQAAF MKSLDILRAV RVKYDTYQRL SSELPQLSRE IDSETNRRED LVRRLEDQDL AFREADNKLQ EMETLNKHV MKITQLLKDI SDAEKQVERS QQLSNIETRS ADEINEEQTT CAEQTRAAQA KLTKLTAEKQ RLKDLVRQLE VERLQLENKI SSAVQQLER KKRLQESIAR HKEDQNQARN AVQEADEELE RLEPEIAGAR AALDEARQAC RAKEQKVAAE RDAIAQTVSE L NMINSEIQ EYLDRGGPSS LAANQRAIAN LETQMANLEG EMRELTVQIN KLNKEIDNSD AKKRNIADNL TYRKNLREKD AL EREIAEL EARNAQEDYD RLIKEAHYLE AHRSKLNADR ERLMGMMSTK DEEFRRLNEE YELDLKDAKA KYKETHIKVE TTK AAIEDL GRGMAAVDHA IMQYHSKMME QINRTIAELW QSTYQGTDID TIQIRSDVES TTSSDSGTRR NYNYRVSMVK GDTE MDMRG RCSAGQKVLA SIIIRLALAE SFCANCGLIA LDEPTTNLDS DNIRSLAESL HGIIKARQAQ GNLQLIVITH DEEFL KYMQ CSDFCDDFYR VKRDEKQNSV IVRESITRIT E

UniProtKB: DH domain-containing protein

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Macromolecule #3: FHA domain-containing protein

MacromoleculeName: FHA domain-containing protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 105.980812 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MWILESELFD GKRLWLRPGK TYLFGRTVAE AGQLTISDKT VSRKHLTIHI DNVPEGGGRN LRSRSNVIVE DLESKKGTLV NGVQIRGQK TTLTEDVNEI KLGLCPKTLK IRWHPIVLSF SFTSKELRAD PWTNLRDSLE QLDIKYSAEY EPTTTHVVSK K RNTSKGLQ ...String:
MWILESELFD GKRLWLRPGK TYLFGRTVAE AGQLTISDKT VSRKHLTIHI DNVPEGGGRN LRSRSNVIVE DLESKKGTLV NGVQIRGQK TTLTEDVNEI KLGLCPKTLK IRWHPIVLSF SFTSKELRAD PWTNLRDSLE QLDIKYSAEY EPTTTHVVSK K RNTSKGLQ ALINGRYIVT DSFINAIVQA TEIPEGEEGA SSALEQDFEA NWPNPLDHLP PRGEEPGNHT TETYAPDARR QE VFDGYTF IFYEKKQYDN LFPAISAGKG KALLKEVVPN RTRVDEFVRY VKSVAGEKGL GSFEDGSEGK GVVVVRYTPK GED SAWYAE FFTKFAQQLD HRPIDQKEFL EAILACDASM LRRPLEAMSQ PVSVSASVEP QSSEKVRPAV EDRKEVEQSA PKQL QPSAE VPATEESAPA PHRRERRTGR SRFKGFDFDD DDIIIETPQA QSSTQVPALP QVPSASQDSL FVSQREPSLA PSEPM LEEE APCNTRTTRQ THRKRVLSPL PEHDNSALLD EIAPITAAVK RRRIEAGQDP VPPLPEPEPE REDEDVEMVE ESPPRK GKK GAATTAKGKG KKIKQEDEEN VLELARRRRE EAEAAAAAER QRLAQLGDDD IDYAAIRRLH IIEEIEVRQP EPHGPNR TR EQDIADGRWD PRWNGRKNFK RFRRQGETGV RMPVQSVIVP LEEVRTKEYG IGDDYWLEDE EGRVPRRPKE TQTQERST I GSVRDGSGFA AAAASGKGKE KDKENEKEVG RPGSSAAAAK QRSKPAPRRT VLTLDSSDED EDEPSPHAPG IDTISDSEP EVVSSFPSVI PASEPSRSRA AKAAERANAL RSSAHSSQSQ TQQHRESQLS TGSSKIQLTL APGSSSLSFS RSGTAAGRNE NGKRPFGSF VSGESTASGR GMSVESGSVR GESASKRQKQ GSSGGGSFLA TRRKDDGSEE ESEDDELKFR FGRRR

UniProtKB: FHA domain-containing protein

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Macromolecule #4: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 6 / Number of copies: 2 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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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

Concentration0.27 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
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
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: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 288443

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