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- EMDB-44558: cryo EM structure of dsDNA bound Mre11-Rad50 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-44558
Titlecryo EM structure of dsDNA bound Mre11-Rad50 complex
Map dataSharpen Map
Sample
  • Complex: dsDNA bound yeast Mre11-Rad50 complex
    • Protein or peptide: DNA repair protein RAD50
    • Protein or peptide: Double-strand break repair protein MRE11
    • DNA: one strand of dsDNA
    • DNA: second strand of dsDNA
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: MANGANESE (II) ION
KeywordsMRN / Mre11 / Rad50 / Nbs1 / DNA binding / DNA damage / DNA repair / DNA BINDING PROTEIN
Function / homology
Function and homology information


DNA double-strand break processing involved in repair via synthesis-dependent strand annealing / nucleoside monophosphate phosphorylation / Cytosolic sensors of pathogen-associated DNA / meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / : / mitochondrial double-strand break repair via homologous recombination / DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / Mre11 complex / chromatin extrusion motor activity ...DNA double-strand break processing involved in repair via synthesis-dependent strand annealing / nucleoside monophosphate phosphorylation / Cytosolic sensors of pathogen-associated DNA / meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / : / mitochondrial double-strand break repair via homologous recombination / DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / Mre11 complex / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / meiotic DNA double-strand break formation / ascospore formation / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / R-loop processing / Hydrolases; Acting on acid anhydrides / chromosome organization involved in meiotic cell cycle / single-stranded DNA endodeoxyribonuclease activity / homologous chromosome pairing at meiosis / AMP kinase activity / double-stranded telomeric DNA binding / maintenance of DNA trinucleotide repeats / G-quadruplex DNA binding / 3'-5'-DNA exonuclease activity / DNA double-strand break processing / DNA clamp loader activity / single-stranded telomeric DNA binding / telomere maintenance via recombination / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / double-strand break repair via break-induced replication / reciprocal meiotic recombination / mitotic intra-S DNA damage checkpoint signaling / telomeric DNA binding / mitotic G2 DNA damage checkpoint signaling / telomere maintenance via telomerase / 3'-5' exonuclease activity / telomere maintenance / condensed nuclear chromosome / DNA endonuclease activity / meiotic cell cycle / double-strand break repair via homologous recombination / base-excision repair / double-strand break repair via nonhomologous end joining / double-strand break repair / manganese ion binding / site of double-strand break / double-stranded DNA binding / endonuclease activity / molecular adaptor activity / Hydrolases; Acting on ester bonds / chromosome, telomeric region / DNA repair / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / nucleoplasm / ATP binding / metal ion binding / nucleus
Similarity search - Function
DNA repair protein Rad50, eukaryotes / DNA double-strand break repair protein Mre11 / Mre11, DNA-binding / Mre11, capping domain / Mre11 DNA-binding presumed domain / Mre11 DNA-binding presumed domain / Rad50 zinc hook motif / RAD50, zinc hook / Rad50 zinc-hook domain profile. / Mre11 nuclease, N-terminal metallophosphatase domain ...DNA repair protein Rad50, eukaryotes / DNA double-strand break repair protein Mre11 / Mre11, DNA-binding / Mre11, capping domain / Mre11 DNA-binding presumed domain / Mre11 DNA-binding presumed domain / Rad50 zinc hook motif / RAD50, zinc hook / Rad50 zinc-hook domain profile. / Mre11 nuclease, N-terminal metallophosphatase domain / SbcC/RAD50-like, Walker B motif / Rad50/SbcC-type AAA domain / AAA domain / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA repair protein RAD50 / Double-strand break repair protein MRE11
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsYu Y / Patel DJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM136278 United States
CitationJournal: Res Sq / Year: 2024
Title: Structure guided functional analysis of the S. cerevisiae Mre11 complex.
Authors: John Petrini / Marcel Hohl / You Yu / Vitaly Kuryavyi / Dinshaw Patel
Abstract: The Mre11 complex comprises Mre11, Rad50 and Nbs1 (Xrs2 in ). The core components, Mre11 and Rad50 are highly conserved, with readily identifiable orthologs in all clades of life, whereas Nbs1/Xrs2 ...The Mre11 complex comprises Mre11, Rad50 and Nbs1 (Xrs2 in ). The core components, Mre11 and Rad50 are highly conserved, with readily identifiable orthologs in all clades of life, whereas Nbs1/Xrs2 are present only in eukaryotes. In eukaryotes, the complex is integral to the DNA damage response, acting in DNA double strand break (DSB) detection and repair, and the activation of DNA damage signaling. We present here a 3.2 Å cryo-EM structure of the Mre11-Rad50 complex with bound dsDNA. The structure provided a foundation for detailed mutational analyses regarding homo and heterotypic protein interfaces, as well as DNA binding properties of Rad50. We define several conserved residues in Rad50 and Mre11 that are critical to complex assembly as well as for DNA binding. In addition, the data reveal that the Rad50 coiled coil domain influences ATP hydrolysis over long distances.
History
DepositionApr 22, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44558.png

Downloads & links

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Map

FileDownload / File: emd_44558.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpen Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 280 pix.
= 303.24 Å		1.08 Å/pix.
x 280 pix.
= 303.24 Å		1.08 Å/pix.
x 280 pix.
= 303.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.083 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.28
Minimum - Maximum-1.8372029 - 3.8090835
Average (Standard dev.)0.0012663357 (±0.08582862)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 303.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_44558_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_44558_half_map_2.map
AnnotationHalf 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 : dsDNA bound yeast Mre11-Rad50 complex

EntireName: dsDNA bound yeast Mre11-Rad50 complex
Components
  • Complex: dsDNA bound yeast Mre11-Rad50 complex
    • Protein or peptide: DNA repair protein RAD50
    • Protein or peptide: Double-strand break repair protein MRE11
    • DNA: one strand of dsDNA
    • DNA: second strand of dsDNA
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: MANGANESE (II) ION

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Supramolecule #1: dsDNA bound yeast Mre11-Rad50 complex

SupramoleculeName: dsDNA bound yeast Mre11-Rad50 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 460 KDa

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Macromolecule #1: DNA repair protein RAD50

MacromoleculeName: DNA repair protein RAD50 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: Hydrolases; Acting on acid anhydrides
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 152.797688 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSAIYKLSIQ GIRSFDSNDR ETIEFGKPLT LIVGMNGSGK TTIIECLKYA TTGDLPPNSK GGVFIHDPKI TGEKDIRAQV KLAFTSANG LNMIVTRNIQ LLMKKTTTTF KTLEGQLVAI NNSGDRSTLS TRSLELDAQV PLYLGVPKAI LEYVIFCHQE D SLWPLSEP ...String:
MSAIYKLSIQ GIRSFDSNDR ETIEFGKPLT LIVGMNGSGK TTIIECLKYA TTGDLPPNSK GGVFIHDPKI TGEKDIRAQV KLAFTSANG LNMIVTRNIQ LLMKKTTTTF KTLEGQLVAI NNSGDRSTLS TRSLELDAQV PLYLGVPKAI LEYVIFCHQE D SLWPLSEP SNLKKKFDEI FQAMKFTKAL DNLKSIKKDM SVDIKLLKQS VEHLKLDKDR SKAMKLNIHQ LQTKIDQYNE EV SEIESQL NEITEKSDKL FKSNQDFQKI LSKVENLKNT KLSISDQVKR LSNSIDILDL SKPDLQNLLA NFSKVLMDKN NQL RDLETD ISSLKDRQSS LQSLSNSLIR RQGELEAGKE TYEKNRNHLS SLKEAFQHKF QGLSNIENSD MAQVNHEMSQ FKAF ISQDL TDTIDQFAKD IQLKETNLSD LIKSITVDSQ NLEYNKKDRS KLIHDSEELA EKLKSFKSLS TQDSLNHELE NLKTY KEKL QSWESENIIP KLNQKIEEKN NEMIILENQI EKFQDRIMKT NQQADLYAKL GLIKKSINTK LDELQKITEK LQNDSR IRQ VFPLTQEFQR ADLEMDFQKL FINMQKNIAI NNKKMHELDR RYTNALYNLN TIEKDLQDNQ KSKEKVIQLL SENLPED CT IDEYNDVLEE TELSYKTALE NLKMHQTTLE FNRKALEIAE RDSCCYLCSR KFENESFKSK LLQELKTKTD ANFEKTLK D TVQNEKEYLH SLRLLEKHII TLNSINEKID NSQKCLEKAK EETKTSKSKL DELEVDSTKL KDEKELAESE IRPLIEKFT YLEKELKDLE NSSKTISEEL SIYNTSEDGI QTVDELRDQQ RKMNDSLREL RKTISDLQME KDEKVRENSR MINLIKEKEL TVSEIESSL TQKQNIDDSI RSKRENINDI DSRVKELEAR IISLKNKKDE AQSVLDKVKN ERDIQVRNKQ KTVADINRLI D RFQTIYNE VVDFEAKGFD ELQTTIKELE LNKAQMLELK EQLDLKSNEV NEEKRKLADS NNEEKNLKQN LELIELKSQL QH IESEISR LDVQNAEAER DKYQEESLRL RTRFEKLSSE NAGKLGEMKQ LQNQIDSLTH QLRTDYKDIE KNYHKEWVEL QTR SFVTDD IDVYSKALDS AIMKYHGLKM QDINRIIDEL WKRTYSGTDI DTIKIRSDEV SSTVKGKSYN YRVVMYKQDV ELDM RGRCS AGQKVLASII IRLALSETFG ANCGVIALDQ PTTNLDEENI ESLAKSLHNI INMRRHQKNF QLIVITHDEK FLGHM NAAA FTDHFFKVKR DDRQKSQIEW VDINRVTY

UniProtKB: DNA repair protein RAD50

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Macromolecule #2: Double-strand break repair protein MRE11

MacromoleculeName: Double-strand break repair protein MRE11 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 79.607297 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MDYPDPDTIR ILITTDNHVG YNENDPITGD DSWKTFHEVM MLAKNNNVDM VVQSGDLFHV NKPSKKSLYQ VLKTLRLCCM GDKPCELEL LSDPSQVFHY DEFTNVNYED PNFNISIPVF GISGNHDDAS GDSLLCPMDI LHATGLINHF GKVIESDKIK V VPLLFQKG ...String:
MDYPDPDTIR ILITTDNHVG YNENDPITGD DSWKTFHEVM MLAKNNNVDM VVQSGDLFHV NKPSKKSLYQ VLKTLRLCCM GDKPCELEL LSDPSQVFHY DEFTNVNYED PNFNISIPVF GISGNHDDAS GDSLLCPMDI LHATGLINHF GKVIESDKIK V VPLLFQKG STKLALYGLA AVRDERLFRT FKDGGVTFEV PTMREGEWFN LMCVHQNHTG HTNTAFLPEQ FLPDFLDMVI WG HEHECIP NLVHNPIKNF DVLQPGSSVA TSLCEAEAQP KYVFILDIKY GEAPKMTPIP LETIRTFKMK SISLQDVPHL RPH DKDATS KYLIEQVEEM IRDANEETKQ KLADDGEGDM VAELPKPLIR LRVDYSAPSN TQSPIDYQVE NPRRFSNRFV GRVA NGNNV VQFYKKRSPV TRSKKSGING TSISDRDVEK LFSESGGELE VQTLVNDLLN KMQLSLLPEV GLNEAVKKFV DKDEK TALK EFISHEISNE VGILSTNEEF LRTDDAEEMK ALIKQVKRAN SVRPTPPKEN DETNFAFNGN GLDSFRSSNR EVRTGS PDI TQSHVDNESR ITHISQAESS KPTSKPKRVR TATKKKIPAF SDSTVISDAE NELGDNNDAQ DDVDIDENDI IMVSTDE ED ASYGLLNGRK TKTKTRPAAS TKTASRRGKG RASRTPKTDI LGSLLAKKRK YDYKDDDDKH HHHH

UniProtKB: Double-strand break repair protein MRE11

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Macromolecule #3: one strand of dsDNA

MacromoleculeName: one strand of dsDNA / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 25.951223 KDa
SequenceString: (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) ...String:
(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)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA) (DA)(DA)(DA)

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Macromolecule #4: second strand of dsDNA

MacromoleculeName: second strand of dsDNA / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 25.203014 KDa
SequenceString: (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) ...String:
(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)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT) (DT)(DT)(DT)

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Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 7 / Number of copies: 4 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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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
Details: 50 mM Hepes, pH 7.5, 200 mM NaCl, 2 mM DTT, 2% Glycerol, 0.025% (w/v) CHAPSO (3-([3-Cholamidopropyl]dimethylammonio)-2-hydroxy-1-propanesulfonate)
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.22 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 242558
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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