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- EMDB-32913: Cryo-EM structure of MEC1-DDC2-MMS -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-32913
TitleCryo-EM structure of MEC1-DDC2-MMS
Map data
Sample
  • Complex: MEC1-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 / protein serine kinase activity / DNA repair / 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) / Saccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsZhang Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Discov / Year: 2022
Title: Structures of Mec1/ATR kinase endogenously stimulated by different genotoxins.
Authors: Qingjun Zhang / Po Wang / Tengwei Wu / Yueyue Zhang / Zexuan Zheng / Shangzhi Zhou / Dong Qian / Xuejuan Wang / Gang Cai /
History
DepositionFeb 19, 2022-
Header (metadata) releaseMar 1, 2023-
Map releaseMar 1, 2023-
UpdateMar 8, 2023-
Current statusMar 8, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32913.png

Downloads & links

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Map

FileDownload / File: emd_32913.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.5 Å
Density
Contour LevelBy AUTHOR: 0.019
Minimum - Maximum-0.06769305 - 0.12814954
Average (Standard dev.)0.00018214904 (±0.0043424326)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 390.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : MEC1-DDC2

EntireName: MEC1-DDC2
Components
  • Complex: MEC1-DDC2
    • Protein or peptide: Serine/threonine-protein kinase MEC1
    • Protein or peptide: DNA damage checkpoint protein LCD1DNA repair

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Supramolecule #1: MEC1-DDC2

SupramoleculeName: MEC1-DDC2 / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Details: MEC1-DDC2 EXPRESSED AND PURIFIED FROM YEAST INDUCED BY MMS
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: 2 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 273.680812 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
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: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 86.533594 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
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

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 81000
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 20185 / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing #1

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12000
Image processing ID1

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Image processing #2

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12000
Image processing ID2

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Image processing #3

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12000
Image processing ID3

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Image processing #4

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12000
Image processing ID4

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Image processing #5

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12000
Image processing ID5

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Image processing #6

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12000
Image processing ID6

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Image processing #7

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12000
Image processing ID7

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Image processing #8

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12000
Image processing ID8

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Image processing #9

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12000
Image processing ID9

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Image processing #10

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12000
Image processing ID10

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Image processing #11

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12000
Image processing ID11

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Image processing #12

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12000
Image processing ID12

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Image processing #13

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12000
Image processing ID13

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7wzw:
Cryo-EM structure of MEC1-DDC2-MMS

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