+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6708 | ||||||||||||
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Title | Intact ATR/Mec1-ATRIP/Ddc2 complex | ||||||||||||
Map data | |||||||||||||
Sample |
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Function / homology | Function and homology information ATR-ATRIP complex / positive regulation of DNA-templated DNA replication / telomere maintenance via recombination / regulation of double-strand break repair / reciprocal meiotic recombination / nucleobase-containing compound metabolic process / nuclear chromosome / telomere maintenance via telomerase / signal transduction in response to DNA damage / telomere maintenance ...ATR-ATRIP complex / positive regulation of DNA-templated DNA replication / telomere maintenance via recombination / regulation of double-strand break repair / reciprocal meiotic recombination / nucleobase-containing compound metabolic process / nuclear chromosome / telomere maintenance via telomerase / signal transduction in response to DNA damage / telomere maintenance / DNA damage checkpoint signaling / establishment of protein localization / chromosome / chromatin organization / DNA replication / DNA recombination / damaged DNA binding / non-specific serine/threonine protein kinase / protein kinase activity / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / mitochondrion / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Baker's yeast (brewer's yeast) | ||||||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 3.9 Å | ||||||||||||
Authors | Wang X / Ran T / Cai G | ||||||||||||
Funding support | China, 3 items
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Citation | Journal: Science / Year: 2017 Title: 3.9 Å structure of the yeast Mec1-Ddc2 complex, a homolog of human ATR-ATRIP. Authors: Xuejuan Wang / Tingting Ran / Xuan Zhang / Jiyu Xin / Zhihui Zhang / Tengwei Wu / Weiwu Wang / Gang Cai / Abstract: The ataxia telangiectasia-mutated and Rad3-related (ATR) kinase is a master regulator of DNA damage response and replication stress in humans, but the mechanism of its activation remains unclear. ATR ...The ataxia telangiectasia-mutated and Rad3-related (ATR) kinase is a master regulator of DNA damage response and replication stress in humans, but the mechanism of its activation remains unclear. ATR acts together with its partner ATRIP. Using cryo-electron microscopy, we determined the structure of intact Mec1-Ddc2 (the yeast homolog of ATR-ATRIP), which is poised for catalysis, at a resolution of 3.9 angstroms. Mec1-Ddc2 forms a dimer of heterodimers through the PRD and FAT domains of Mec1 and the coiled-coil domain of Ddc2. The PRD and Bridge domains in Mec1 constitute critical regulatory sites. The activation loop of Mec1 is inhibited by the PRD, revealing an allosteric mechanism of kinase activation. Our study clarifies the architecture of ATR-ATRIP and provides a structural framework for the understanding of ATR regulation. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6708.map.gz | 47.3 MB | EMDB map data format | |
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Header (meta data) | emd-6708-v30.xml emd-6708.xml | 13.4 KB 13.4 KB | Display Display | EMDB header |
Images | emd_6708.png | 264.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6708 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6708 | HTTPS FTP |
-Validation report
Summary document | emd_6708_validation.pdf.gz | 525.6 KB | Display | EMDB validaton report |
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Full document | emd_6708_full_validation.pdf.gz | 525.2 KB | Display | |
Data in XML | emd_6708_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | emd_6708_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6708 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6708 | HTTPS FTP |
-Related structure data
Related structure data | 5x6oMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6708.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : ATR/Mec1-ATRIP/Ddc2
Entire | Name: ATR/Mec1-ATRIP/Ddc2 |
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Components |
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-Supramolecule #1: ATR/Mec1-ATRIP/Ddc2
Supramolecule | Name: ATR/Mec1-ATRIP/Ddc2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: ATR/Mec1 "butterfly" |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Macromolecule #1: Serine/threonine-protein kinase MEC1
Macromolecule | Name: Serine/threonine-protein kinase MEC1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase |
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Source (natural) | Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 273.680812 KDa |
Sequence | String: MESHVKYLDE LILAIKDLNS GVDSKVQIKK VPTDPSSSQE YAKSLKILNT LIRNLKDQRR NNIMKNDTIF SKTVSALALL LEYNPFLLV MKDSNGNFEI QRLIDDFLNI SVLNYDNYHR IWFMRRKLGS WCKACVEFYG KPAKFQLTAH FENTMNLYEQ A LTEVLLGK ...String: MESHVKYLDE LILAIKDLNS GVDSKVQIKK VPTDPSSSQE YAKSLKILNT LIRNLKDQRR NNIMKNDTIF SKTVSALALL LEYNPFLLV MKDSNGNFEI QRLIDDFLNI SVLNYDNYHR IWFMRRKLGS WCKACVEFYG KPAKFQLTAH FENTMNLYEQ A LTEVLLGK TELLKFYDTL KGLYILLYWF TSEYSTFGNS IAFLDSSLGF TKFDFNFQRL IRIVLYVFDS CELAALEYAE IQ LKYISLV VDYVCNRTIS TALDAPALVC CEQLKFVLTT MHHFLDNKYG LLDNDPTMAK GILRLYSLCI SNDFSKCFVD HFP IDQWAD FSQSEHFPFT QLTNKALSIV YFDLKRRSLP VEALKYDNKF NIWVYQSEPD SSLKNVTSPF DDRYKQLEKL RLLV LKKFN KTERGTLLKY RVNQLSPGFF QRAGNDFKLI LNEASVSIQT CFKTNNITRL TSWTVILGRL ACLESEKFSG TLPNS TKDM DNWYVCHLCD IEKTGNPFVR INPNRPEAAG KSEIFRILHS NFLSHPNIDE FSESLLSGIL FSLHRIFSHF QPPKLT DGN GQINKSFKLV QKCFMNSNRY LRLLSTRIIP LFNISDSHNS EDEHTATLIK FLQSQKLPVV KENLVIAWTQ LTLTTSN DV FDTLLLKLID IFNSDDYSLR IMMTLQIKNM AKILKKTPYQ LLSPILPVLL RQLGKNLVER KVGFQNLIEL LGYSSKTI L DIFQRYIIPY AIIQYKSDVL SEIAKIMCDG DTSLINQMKV NLLKKNSRQI FAVALVKHGL FSLDILETLF LNRAPTFDK GYITAYLPDY KTLAEITKLY KNSVTKDASD SENANMILCS LRFLITNFEK DKRHGSKYKN INNWTDDQEQ AFQKKLQDNI LGIFQVFSS DIHDVEGRTT YYEKLRVING ISFLIIYAPK KSIISALAQI SICLQTGLGL KEVRYEAFRC WHLLVRHLND E ELSTVIDS LIAFILQKWS EFNGKLRNIV YSILDTLIKE KSDLILKLKP YTTLALVGKP ELGILARDGQ FARMVNKIRS TT DLIPIFA NNLKSSNKYV INQNLDDIEV YLRRKQTERS IDFTPKKVGQ TSDITLVLGA LLDTSHKFRN LDKDLCEKCA KCI SMIGVL DVTKHEFKRT TYSENEVYDL NDSVQTIKFL IWVINDILVP AFWQSENPSK QLFVALVIQE SLKYCGLSSE SWDM NHKEL YPNEAKLWEK FNSVSKTTIY PLLSSLYLAQ SWKEYVPLKY PSNNFKEGYK IWVKRFTLDL LKTGTTENHP LHVFS SLIR EDDGSLSNFL LPYISLDIII KAEKGTPYAD ILNGIIIEFD SIFTCNLEGM NNLQVDSLRM CYESIFRVFE YCKKWA TEF KQNYSKLHGT FIIKDTKTTN MLLRIDEFLR TTPSDLLAQR SLETDSFERS ALYLEQCYRQ NPHDKNQNGQ LLKNLQI TY EEIGDIDSLD GVLRTFATGN LVSKIEELQY SENWKLAQDC FNVLGKFSDD PKTTTRMLKS MYDHQLYSQI ISNSSFHS S DGKISLSPDV KEWYSIGLEA ANLEGNVQTL KNWVEQIESL RNIDDREVLL QYNIAKALIA ISNEDPLRTQ KYIHNSFRL IGTNFITSSK ETTLLKKQNL LMKLHSLYDL SFLSSAKDKF EYKSNTTILD YRMERIGADF VPNHYILSMR KSFDQLKMNE QADADLGKT FFTLAQLARN NARLDIASES LMHCLERRLP QAELEFAEIL WKQGENDRAL KIVQEIHEKY QENSSVNARD R AAVLLKFT EWLDLSNNSA SEQIIKQYQD IFQIDSKWDK PYYSIGLYYS RLLERKKAEG YITNGRFEYR AISYFLLAFE KN TAKVREN LPKVITFWLD IAAASISEAP GNRKEMLSKA TEDICSHVEE ALQHCPTYIW YFVLTQLLSR LLHSHQSSAQ IIM HILLSL AVEYPSHILW YITALVNSNS SKRVLRGKHI LEKYRQHSQN PHDLVSSALD LTKALTRVCL QDVKSITSRS GKSL EKDFK FDMNVAPSAM VVPVRKNLDI ISPLESNSMR GYQPFRPVVS IIRFGSSYKV FSSLKKPKQL NIIGSDGNIY GIMCK KEDV RQDNQYMQFA TTMDFLLSKD IASRKRSLGI NIYSVLSLRE DCGILEMVPN VVTLRSILST KYESLKIKYS LKSLHD RWQ HTAVDGKLEF YMEQVDKFPP ILYQWFLENF PDPINWFNAR NTYARSYAVM AMVGHILGLG DRHCENILLD IQTGKVL HV DFDCLFEKGK RLPVPEIVPF RLTPNLLDAL GIIGTEGTFK KSSEVTLALM RKNEVALMNV IETIMYDRNM DHSIQKAL K VLRNKIRGID PQDGLVLSVA GQTETLIQEA TSEDNLSKMY IGWLPFW |
-Macromolecule #2: DNA damage checkpoint protein LCD1
Macromolecule | Name: DNA damage checkpoint protein LCD1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 86.533594 KDa |
Sequence | String: MRRETVGEFS SDDDDDILLE LGTRPPRFTQ IPPSSAALQT QIPTTLEVTT TTLNNKQSKN DNQLVNQLNK AQGEASMLRD KINFLNIER EKEKNIQAVK VNELQVKHLQ ELAKLKQELQ KLEDEKKFLQ MEARGKSKRE VITNVKPPST TLSTNTNTIT P DSSSVAIE ...String: MRRETVGEFS SDDDDDILLE LGTRPPRFTQ IPPSSAALQT QIPTTLEVTT TTLNNKQSKN DNQLVNQLNK AQGEASMLRD KINFLNIER EKEKNIQAVK VNELQVKHLQ ELAKLKQELQ KLEDEKKFLQ MEARGKSKRE VITNVKPPST TLSTNTNTIT P DSSSVAIE AKPQSPQSKK RKISDNLLKK NMVPLNPNRI IPDETSLFLE SILLHQIIGA DLSTIEILNR LKLDYITEFK FK NFVIAKG APIGKSIVSL LLRCKKTLTL DRFIDTLLED IAVLIKEISV HPNESKLAVP FLVALMYQIV QFRPSATHNL ALK DCFLFI CDLIRIYHHV LKVPIHESNM NLHVEPQIFQ YELIDYLIIS YSFDLLEGIL RVLQSHPKQT YMEFFDENIL KSFE FVYKL ALTISYKPMV NVIFSAVEVV NIITSIILNM DNSSDLKSLI SGSWWRDCIT RLYALLEKEI KSGDVYNENV DTTTL HMSK YHDFFGLIRN IGDNELGGLI SKLIYTDRLQ SVPRVISKED IGMDSDKFTA PIIGYKMEKW LLKLKDEVLN IFENLL MIY GDDATIVNGE MLIHSSKFLS REQALMIERY VGQDSPNLDL RCHLIEHTLT IIYRLWKDHF KQLREEQIKQ VESQLIM SL WRFLVCQTET VTANEREMRD HRHLVDSLHD LTIKDQASYY EDAFEDLPEY IEEELKMQLN KRTGRIMQVK YDEKFQEM A RTILESKSFD LTTLEEADSL YISMGL |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Staining | Type: NONE / Material: Uranyl Formate |
Vitrification | Cryogen name: ETHANE |
Details | ATR/Mec1 "butterfly" |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 63132 |
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Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |