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- EMDB-52961: Cryo-EM structure of human Mre11-Rad50-Nbs1 (MRN) complex bound t... -

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Basic information

Entry
Database: EMDB / ID: EMD-52961
TitleCryo-EM structure of human Mre11-Rad50-Nbs1 (MRN) complex bound to DNA and telomeric factor TRF2 fragment (438-542)
Map data
Sample
  • Complex: MRN-TRF2(438-542)-DNA complex
    • Protein or peptide: x 4 types
    • DNA: x 2 types
  • Ligand: x 5 types
KeywordsMre11-Rad50-Nbs1 complex / double-strand DNA break repair protein / nuclease / HYDROLASE
Function / homology
Function and homology information


telomere maintenance via telomere trimming / chromosomal region / axonal transport of messenger ribonucleoprotein complex / negative regulation of telomere single strand break repair / telomeric 3' overhang formation / negative regulation of telomere maintenance via recombination / telomeric loop formation / mitochondrial double-strand break repair via homologous recombination / Mre11 complex / negative regulation of telomere maintenance via semi-conservative replication ...telomere maintenance via telomere trimming / chromosomal region / axonal transport of messenger ribonucleoprotein complex / negative regulation of telomere single strand break repair / telomeric 3' overhang formation / negative regulation of telomere maintenance via recombination / telomeric loop formation / mitochondrial double-strand break repair via homologous recombination / Mre11 complex / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of telomeric D-loop disassembly / negative regulation of double-strand break repair via nonhomologous end joining / blastocyst growth / negative regulation of telomere capping / BRCA1-C complex / Sensing of DNA Double Strand Breaks / meiotic DNA double-strand break formation / protection from non-homologous end joining at telomere / regulation of mitotic recombination / RNA-templated DNA biosynthetic process / R-loop processing / Hydrolases; Acting on acid anhydrides / negative regulation of telomere maintenance / t-circle formation / negative regulation of t-circle formation / telomeric D-loop disassembly / single-stranded DNA endodeoxyribonuclease activity / chromosome organization involved in meiotic cell cycle / shelterin complex / phosphorylation-dependent protein binding / Telomere C-strand synthesis initiation / homologous chromosome pairing at meiosis / regulation of telomere maintenance via telomerase / double-stranded telomeric DNA binding / DNA strand resection involved in replication fork processing / nuclease activity / homologous recombination / G-quadruplex DNA binding / nuclear inclusion body / 3'-5'-DNA exonuclease activity / DNA double-strand break processing / Telomere C-strand (Lagging Strand) Synthesis / single-stranded telomeric DNA binding / nuclear telomere cap complex / Impaired BRCA2 binding to PALB2 / double-strand break repair via alternative nonhomologous end joining / chromatin-protein adaptor activity / G-rich strand telomeric DNA binding / protein localization to site of double-strand break / telomere capping / telomere maintenance via recombination / isotype switching / Cytosolic sensors of pathogen-associated DNA / mitotic G2/M transition checkpoint / HDR through MMEJ (alt-NHEJ) / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / IRF3-mediated induction of type I IFN / Removal of the Flap Intermediate from the C-strand / reciprocal meiotic recombination / mitotic intra-S DNA damage checkpoint signaling / regulation of telomere maintenance / regulation of DNA-templated DNA replication initiation / negative regulation of telomere maintenance via telomere lengthening / sister chromatid cohesion / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / protein localization to chromosome, telomeric region / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / neuromuscular process controlling balance / positive regulation of double-strand break repair / telomeric DNA binding / Impaired BRCA2 binding to RAD51 / negative regulation of telomere maintenance via telomerase / mitotic G2 DNA damage checkpoint signaling / positive regulation of telomere maintenance / telomere maintenance in response to DNA damage / Presynaptic phase of homologous DNA pairing and strand exchange / negative regulation of cellular senescence / Telomere Extension By Telomerase / protein K63-linked ubiquitination / neuroblast proliferation / telomere maintenance via telomerase / positive regulation of double-strand break repair via homologous recombination / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / 3'-5' exonuclease activity / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere maintenance / Inhibition of DNA recombination at telomere / intrinsic apoptotic signaling pathway / Meiotic synapsis / DNA damage checkpoint signaling / replication fork
Similarity search - Function
Nibrin, C-terminal / Nibrin / DNA damage repair protein Nbs1 / DNA damage repair protein Nbs1 / Nibrin, second BRCT domain / Nibrin, second BRCT domain superfamily / Second BRCT domain on Nijmegen syndrome breakage protein / DNA repair protein Rad50, eukaryotes / Nibrin-related / Telomeric repeat-binding factor 2, Rap1-binding domain ...Nibrin, C-terminal / Nibrin / DNA damage repair protein Nbs1 / DNA damage repair protein Nbs1 / Nibrin, second BRCT domain / Nibrin, second BRCT domain superfamily / Second BRCT domain on Nijmegen syndrome breakage protein / DNA repair protein Rad50, eukaryotes / Nibrin-related / Telomeric repeat-binding factor 2, Rap1-binding domain / Telomeric repeat-binding factor 2 Rap1-binding motif / Telomeric repeat-binding factor 2 / 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. / Telomeric repeat-binding factor 1/2 / Telomere repeat-binding factor, dimerisation domain superfamily / Telomere repeat-binding factor, dimerisation domain / Telomere repeat binding factor (TRF) / Mre11 nuclease, N-terminal metallophosphatase domain / SbcC/RAD50-like, Walker B motif / Rad50/SbcC-type AAA domain / AAA domain / Myb-type HTH DNA-binding domain profile. / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / Myb domain / Myb-like DNA-binding domain / SMAD/FHA domain superfamily / BRCA1 C Terminus (BRCT) domain / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / BRCT domain / BRCT domain superfamily / Homeobox-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Nibrin / Double-strand break repair protein MRE11 / Telomeric repeat-binding factor 2 / DNA repair protein RAD50
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.71 Å
AuthorsCui HJ / Lammens K / Hopfner KP / Fan YL / Kuybu F
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
DepositionFeb 26, 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_52961.png

Downloads & links

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Map

FileDownload / File: emd_52961.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.727 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.8097618 - 3.480737
Average (Standard dev.)0.000040351482 (±0.09268052)
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_52961_msk_1.map
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Half map: #2

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Sample components

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Entire : MRN-TRF2(438-542)-DNA complex

EntireName: MRN-TRF2(438-542)-DNA complex
Components
  • Complex: MRN-TRF2(438-542)-DNA complex
    • Protein or peptide: Telomeric repeat-binding factor 2
    • DNA: DNA (64-MER)
    • DNA: DNA (64-MER)
    • Protein or peptide: Nibrin
    • Protein or peptide: DNA repair protein RAD50
    • Protein or peptide: Double-strand break repair protein MRE11
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MANGANESE (II) ION
  • Ligand: water

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Supramolecule #1: MRN-TRF2(438-542)-DNA complex

SupramoleculeName: MRN-TRF2(438-542)-DNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 605 KDa

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Macromolecule #1: Telomeric repeat-binding factor 2

MacromoleculeName: Telomeric repeat-binding factor 2 / type: protein_or_peptide / ID: 1
Details: GP is the leftover sequence from PreScission cleavage site, and GGSSGGSSG is a linker sequence between the cleavage site and TRF2(438-542) fragment.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.931349 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPGGSSGGSS GQPLPGEKNP KVPKGKWNSS NGVEEKETWV EEDELFQVQA APDEDSTTNI TKKQKWTVEE SEWVKAGVQK YGEGNWAAI SKNYPFVNRT AVMIKDRWRT MKRLGMN

UniProtKB: Telomeric repeat-binding factor 2

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Macromolecule #4: Nibrin

MacromoleculeName: Nibrin / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 85.073023 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MWKLLPAAGP AGGEPYRLLT GVEYVVGRKN CAILIENDQS ISRNHAVLTA NFSVTNLSQT DEIPVLTLKD NSKYGTFVNE EKMQNGFSR TLKSGDGITF GVFGSKFRIE YEPLVACSSC LDVSGKTALN QAILQLGGFT VNNWTEECTH LVMVSVKVTI K TICALICG ...String:
MWKLLPAAGP AGGEPYRLLT GVEYVVGRKN CAILIENDQS ISRNHAVLTA NFSVTNLSQT DEIPVLTLKD NSKYGTFVNE EKMQNGFSR TLKSGDGITF GVFGSKFRIE YEPLVACSSC LDVSGKTALN QAILQLGGFT VNNWTEECTH LVMVSVKVTI K TICALICG RPIVKPEYFT EFLKAVESKK QPPQIESFYP PLDEPSIGSK NVDLSGRQER KQIFKGKTFI FLNAKQHKKL SS AVVFGGG EARLITEENE EEHNFFLAPG TCVVDTGITN SQTLIPDCQK KWIQSIMDML QRQGLRPIPE AEIGLAVIFM TTK NYCDPQ GHPSTGLKTT TPGPSLSQGV SVDEKLMPSA PVNTTTYVAD TESEQADTWD LSERPKEIKV SKMEQKFRML SQDA PTVKE SCKTSSNNNS MVSNTLAKMR IPNYQLSPTK LPSINKSKDR ASQQQQTNSI RNYFQPSTKK RERDEENQEM SSCKS ARIE TSCSLLEQTQ PATPSLWKNK EQHLSENEPV DTNSDNNLFT DTDLKSIVKN SASKSHAAEK LRSNKKREMD DVAIED EVL EQLFKDTKPE LEIDVKVQKQ EEDVNVRKRP RMDIETNDTF SDEAVPESSK ISQENEIGKK RELKEDSLWS AKEISNN DK LQDDSEMLPK KLLLTEFRSL VIKNSTSRNP SGINDDYGQL KNFKKFKKVT YPGAGKLPHI IGGSDLIAHH ARKNTELE E WLRQEMEVQN QHAKEESLAD DLFRYNPYLK RRR

UniProtKB: Nibrin

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Macromolecule #5: DNA repair protein RAD50

MacromoleculeName: DNA repair protein RAD50 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 154.150016 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSRIEKMSIL GVRSFGIEDK DKQIITFFSP LTILVGPNGA GKTTIIECLK YICTGDFPPG TKGNTFVHDP KVAQETDVRA QIRLQFRDV NGELIAVQRS MVCTQKSKKT EFKTLEGVIT RTKHGEKVSL SSKCAEIDRE MISSLGVSKA VLNNVIFCHQ E DSNWPLSE ...String:
MSRIEKMSIL GVRSFGIEDK DKQIITFFSP LTILVGPNGA GKTTIIECLK YICTGDFPPG TKGNTFVHDP KVAQETDVRA QIRLQFRDV NGELIAVQRS MVCTQKSKKT EFKTLEGVIT RTKHGEKVSL SSKCAEIDRE MISSLGVSKA VLNNVIFCHQ E DSNWPLSE GKALKQKFDE IFSATRYIKA LETLRQVRQT QGQKVKEYQM ELKYLKQYKE KACEIRDQIT SKEAQLTSSK EI VKSYENE LDPLKNRLKE IEHNLSKIMK LDNEIKALDS RKKQMEKDNS ELEEKMEKVF QGTDEQLNDL YHNHQRTVRE KER KLVDCH RELEKLNKES RLLNQEKSEL LVEQGRLQLQ ADRHQEHIRA RDSLIQSLAT QLELDGFERG PFSERQIKNF HKLV RERQE GEAKTANQLM NDFAEKETLK QKQIDEIRDK KTGLGRIIEL KSEILSKKQN ELKNVKYELQ QLEGSSDRIL ELDQE LIKA ERELSKAEKN SNVETLKMEV ISLQNEKADL DRTLRKLDQE MEQLNHHTTT RTQMEMLTKD KADKDEQIRK IKSRHS DEL TSLLGYFPNK KQLEDWLHSK SKEINQTRDR LAKLNKELAS SEQNKNHINN ELKRKEEQLS SYEDKLFDVC GSQDFES DL DRLKEEIEKS SKQRAMLAGA TAVYSQFITQ LTDENQSCCP VCQRVFQTEA ELQEVISDLQ SKLRLAPDKL KSTESELK K KEKRRDEMLG LVPMRQSIID LKEKEIPELR NKLQNVNRDI QRLKNDIEEQ ETLLGTIMPE EESAKVCLTD VTIMERFQM ELKDVERKIA QQAAKLQGID LDRTVQQVNQ EKQEKQHKLD TVSSKIELNR KLIQDQQEQI QHLKSTTNEL KSEKLQISTN LQRRQQLEE QTVELSTEVQ SLYREIKDAK EQVSPLETTL EKFQQEKEEL INKKNTSNKI AQDKLNDIKE KVKNIHGYMK D IENYIQDG KDDYKKQKET ELNKVIAQLS ECEKHKEKIN EDMRLMRQDI DTQKIQERWL QDNLTLRKRN EELKEVEEER KQ HLKEMGQ MQVLQMKSEH QKLEENIDNI KRNHNLALGR QKGYEEEIIH FKKELREPQF RDAEEKYREM MIVMRTTELV NKD LDIYYK TLDQAIMKFH SMKMEEINKI IRDLWRSTYR GQDIEYIEIR SDADENVSAS DKRRNYNYRV VMLKGDTALD MRGR CSAGQ KVLASLIIRL ALAETFCLNC GIIALDEPTT NLDRENIESL AHALVEIIKS RSQQRNFQLL VITHDEDFVE LLGRS EYVE KFYRIKKNID QCSEIVKCSV SSLGFNVH

UniProtKB: DNA repair protein RAD50

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Macromolecule #6: Double-strand break repair protein MRE11

MacromoleculeName: Double-strand break repair protein MRE11 / type: protein_or_peptide / ID: 6
Details: Following residue R708 is a short GS linker, a PreScission cleavage site, and two FLAG tags.
Number of copies: 2 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 84.03268 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSTADALDDE NTFKILVATD IHLGFMEKDA VRGNDTFVTL DEILRLAQEN EVDFILLGGD LFHENKPSRK TLHTCLELLR KYCMGDRPV QFEILSDQSV NFGFSKFPWV NYQDGNLNIS IPVFSIHGNH DDPTGADALC ALDILSCAGF VNHFGRSMSV E KIDISPVL ...String:
MSTADALDDE NTFKILVATD IHLGFMEKDA VRGNDTFVTL DEILRLAQEN EVDFILLGGD LFHENKPSRK TLHTCLELLR KYCMGDRPV QFEILSDQSV NFGFSKFPWV NYQDGNLNIS IPVFSIHGNH DDPTGADALC ALDILSCAGF VNHFGRSMSV E KIDISPVL LQKGSTKIAL YGLGSIPDER LYRMFVNKKV TMLRPKEDEN SWFNLFVIHQ NRSKHGSTNF IPEQFLDDFI DL VIWGHEH ECKIAPTKNE QQLFYISQPG SSVVTSLSPG EAVKKHVGLL RIKGRKMNMH KIPLHTVRQF FMEDIVLANH PDI FNPDNP KVTQAIQSFC LEKIEEMLEN AERERLGNSH QPEKPLVRLR VDYSGGFEPF SVLRFSQKFV DRVANPKDII HFFR HREQK EKTGEEINFG KLITKPSEGT TLRVEDLVKQ YFQTAEKNVQ LSLLTERGMG EAVQEFVDKE EKDAIEELVK YQLEK TQRF LKERHIDALE DKIDEEVRRF RETRQKNTNE EDDEVREAMT RARALRSQSE ESASAFSADD LMSIDLAEQM ANDSDD SIS AATNKGRGRG RGRRGGRGQN SASRGGSQRG RADTGLETST RSRNSKTAVS ASRNMSIIDA FKSTRQQPSR NVTTKNY SE VIEVDESDVE EDIFPTTSKT DQRWSSTSSS KIMSQSQVSK GVDFESSEDD DDDPFMNTSS LRRNRRSGGS LEVLFQGP D YKDDDDKGTD YKDDDDK

UniProtKB: Double-strand break repair protein MRE11

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Macromolecule #2: DNA (64-MER)

MacromoleculeName: DNA (64-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.423369 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)

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Macromolecule #3: DNA (64-MER)

MacromoleculeName: DNA (64-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.000281 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)

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #8: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #9: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 9 / Number of copies: 2 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Macromolecule #10: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 10 / Number of copies: 4 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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Macromolecule #11: water

MacromoleculeName: water / type: ligand / ID: 11 / Number of copies: 6 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 25mM Hepes-NaOH, pH 7.5, 150 mM NaCl, 1 mM DTT, 1 mM ATP, 1mM BeF3, 5 mM MgCl2, 1 mM MnCl2
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 12 sec. / Details: 20 mA, 12 s
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: LEICA PLUNGER

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Detector mode: COUNTING / 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 / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 129300
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC (ver. 4.6.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9q9j:
Cryo-EM structure of human Mre11-Rad50-Nbs1 (MRN) complex bound to DNA and telomeric factor TRF2 fragment (438-542)

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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

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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

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