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- EMDB-6708: Intact ATR/Mec1-ATRIP/Ddc2 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-6708
TitleIntact ATR/Mec1-ATRIP/Ddc2 complex
Map data
Sample
  • Complex: ATR/Mec1-ATRIP/Ddc2
    • Protein or peptide: Serine/threonine-protein kinase MEC1
    • Protein or peptide: DNA damage checkpoint protein LCD1DNA repair
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 / chromatin organization / DNA recombination / DNA replication / damaged DNA binding / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / mitochondrion / ATP binding / nucleus / cytoplasm
Similarity search - Function
UME domain / UME (NUC010) domain / Domain in UVSB PI-3 kinase, MEI-41 and ESR-1 / DNA damage checkpoint protein, Lcd1 / DNA damage checkpoint protein / PIK-related kinase, FAT / FAT domain / FATC domain / FATC / FATC domain ...UME domain / UME (NUC010) domain / Domain in UVSB PI-3 kinase, MEI-41 and ESR-1 / DNA damage checkpoint protein, Lcd1 / DNA damage checkpoint protein / PIK-related kinase, FAT / FAT domain / FATC domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase MEC1 / DNA damage checkpoint protein LCD1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Baker's yeast (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 3.9 Å
AuthorsWang X / Ran T / Cai G
Funding support China, 3 items
OrganizationGrant numberCountry
National Basic Research Program2014CB910700 China
National Natural Science Foundation of China31222017 China
National Basic Research Program2013CB910200 China
CitationJournal: 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
DepositionFeb 22, 2017-
Header (metadata) releaseDec 20, 2017-
Map releaseDec 20, 2017-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0518
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0518
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5x6o
  • Surface level: 0.0518
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5x6o
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6708.png

Downloads & links

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Map

FileDownload / File: emd_6708.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.0518 / Movie #1: 0.0518
Minimum - Maximum-0.15051116 - 0.24395004
Average (Standard dev.)0.000500057 (±0.010790058)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z345.600345.600345.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1510.2440.001

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Supplemental data

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Sample components

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Entire : ATR/Mec1-ATRIP/Ddc2

EntireName: ATR/Mec1-ATRIP/Ddc2
Components
  • Complex: ATR/Mec1-ATRIP/Ddc2
    • Protein or peptide: Serine/threonine-protein kinase MEC1
    • Protein or peptide: DNA damage checkpoint protein LCD1DNA repair

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Supramolecule #1: ATR/Mec1-ATRIP/Ddc2

SupramoleculeName: ATR/Mec1-ATRIP/Ddc2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: ATR/Mec1 "butterfly"
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Serine/threonine-protein kinase MEC1

MacromoleculeName: 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
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 273.680812 KDa
SequenceString: 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

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Macromolecule #2: DNA damage checkpoint protein LCD1

MacromoleculeName: DNA damage checkpoint protein LCD1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 86.533594 KDa
SequenceString: 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

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
StainingType: NONE / Material: Uranyl Formate
VitrificationCryogen name: ETHANE
DetailsATR/Mec1 "butterfly"

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 63132

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