[English] 日本語
Yorodumi
- EMDB-14879: Mre11-Rad50-Nbs1 complex (Chaetomium thermophilum) lower coiled-coils -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-14879
TitleMre11-Rad50-Nbs1 complex (Chaetomium thermophilum) lower coiled-coils
Map dataLower CC, 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


mitochondrial double-strand break repair via homologous recombination / Mre11 complex / meiotic DNA double-strand break formation / single-stranded DNA endodeoxyribonuclease activity / 3'-5'-DNA exonuclease activity / mitotic intra-S DNA damage checkpoint signaling / mitotic G2 DNA damage checkpoint signaling / telomere maintenance / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining ...mitochondrial double-strand break repair via homologous recombination / Mre11 complex / meiotic DNA double-strand break formation / single-stranded DNA endodeoxyribonuclease activity / 3'-5'-DNA exonuclease activity / mitotic intra-S DNA damage checkpoint signaling / mitotic G2 DNA damage checkpoint signaling / telomere maintenance / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / manganese ion binding / site of double-strand break / Hydrolases; Acting on ester bonds / chromosome, telomeric region
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 MRE11
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus) / Thermochaetoides thermophila (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.57 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) releaseJan 11, 2023-
Map releaseJan 11, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_14879.png

Downloads & links

-
Map

FileDownload / File: emd_14879.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLower CC, main map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.8 Å/pix.
x 500 pix.
= 900.15 Å		1.8 Å/pix.
x 500 pix.
= 900.15 Å		1.8 Å/pix.
x 500 pix.
= 900.15 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.8003 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.2
Minimum - Maximum-9.366391999999999 - 18.678574000000001
Average (Standard dev.)-0.0008052135 (±0.10363971)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 900.15 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_14879_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Lower CC, half map B

Fileemd_14879_half_map_1.map
AnnotationLower CC, half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Lower CC, half map A

Fileemd_14879_half_map_2.map
AnnotationLower CC, half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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: all
Source (natural)Organism: Chaetomium thermophilum (fungus)

-
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 MRE11

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.27 mg/mL
BufferpH: 7.6
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 43.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.57 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 71734
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more