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Yorodumi- EMDB-68920: Cryo-EM structure of human ATR-ATRIP complex with ATPgammaS, Chk1... -
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Basic information
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| Title | Cryo-EM structure of human ATR-ATRIP complex with ATPgammaS, Chk1 and TopBp1 | |||||||||
Map data | local resolution filtered map | |||||||||
Sample |
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Keywords | ATR / TopBp1 / Chk1 / DNA repair / NUCLEAR PROTEIN | |||||||||
| Function / homology | Function and homology informationbroken chromosome clustering / BRCA1-B complex / ATR-ATRIP complex / establishment of RNA localization to telomere / positive regulation of telomerase catalytic core complex assembly / nuclear membrane disassembly / establishment of protein-containing complex localization to telomere / MutSalpha complex binding / phosphorylation-dependent protein binding / negative regulation of mitotic nuclear division ...broken chromosome clustering / BRCA1-B complex / ATR-ATRIP complex / establishment of RNA localization to telomere / positive regulation of telomerase catalytic core complex assembly / nuclear membrane disassembly / establishment of protein-containing complex localization to telomere / MutSalpha complex binding / phosphorylation-dependent protein binding / negative regulation of mitotic nuclear division / histone H2AXS139 kinase activity / negative regulation of G0 to G1 transition / homologous recombination / histone H3T11 kinase activity / DNA replication checkpoint signaling / regulation of mitotic centrosome separation / negative regulation of DNA replication / MutLalpha complex binding / double-strand break repair via classical nonhomologous end joining / response to arsenic-containing substance / double-strand break repair via alternative nonhomologous end joining / mitotic DNA replication checkpoint signaling / protein localization to site of double-strand break / mitotic G2/M transition checkpoint / regulation of double-strand break repair / nucleobase-containing compound metabolic process / chromatin-protein adaptor activity / chromosome organization / DNA metabolic process / protein localization to chromosome, telomeric region / positive regulation of DNA damage response, signal transduction by p53 class mediator / K63-linked polyubiquitin modification-dependent protein binding / regulation of double-strand break repair via homologous recombination / male germ cell nucleus / response to ionizing radiation / peptidyl-threonine phosphorylation / HDR through Single Strand Annealing (SSA) / negative regulation of gene expression, epigenetic / mitotic G2 DNA damage checkpoint signaling / Transcriptional Regulation by E2F6 / Impaired BRCA2 binding to RAD51 / replicative senescence / Regulation of HSF1-mediated heat shock response / DNA replication initiation / response to mechanical stimulus / Presynaptic phase of homologous DNA pairing and strand exchange / Activation of ATR in response to replication stress / interstrand cross-link repair / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / regulation of cellular response to heat / DNA damage checkpoint signaling / signal transduction in response to DNA damage / positive regulation of telomere maintenance via telomerase / positive regulation of cell cycle / replication fork / protein serine/threonine kinase activator activity / telomere maintenance / replication fork processing / regulation of signal transduction by p53 class mediator / Meiotic synapsis / condensed nuclear chromosome / site of DNA damage / TP53 Regulates Transcription of DNA Repair Genes / cellular response to gamma radiation / cellular response to mechanical stimulus / Fanconi Anemia Pathway / Signaling by SCF-KIT / double-strand break repair via homologous recombination / PML body / G2/M DNA damage checkpoint / spindle pole / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / cellular response to UV / double-strand break repair / nuclear envelope / site of double-strand break / chromosome / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / nuclear body / DNA replication / protein kinase activity / protein phosphorylation / non-specific serine/threonine protein kinase / response to xenobiotic stimulus / chromatin remodeling / protein domain specific binding / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / apoptotic process / centrosome / DNA damage response / chromatin / protein-containing complex / DNA binding / : / nucleoplasm / ATP binding / identical protein binding Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Wang L / Wang M / Zhao L / Rao Q / Wu H / Ma B / Wang J / Zheng J / Li Y / Xu Y ...Wang L / Wang M / Zhao L / Rao Q / Wu H / Ma B / Wang J / Zheng J / Li Y / Xu Y / Guo J / Cheng J / Qiao S | |||||||||
| Funding support | China, 2 items
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Citation | Journal: To Be PublishedTitle: Mechanistic insights into phosphorylation-driven activation and therapeutic inhibition of human ATR-ATRIP Authors: Wang L / Wang M / Zhao L / Rao Q / Wu H / Ma B / Wang J / Zheng J / Li Y / Xu Y / Guo J / Cheng J / Qiao S | |||||||||
| History |
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_68920.map.gz | 12.2 MB | EMDB map data format | |
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| Header (meta data) | emd-68920-v30.xml emd-68920.xml | 28.6 KB 28.6 KB | Display Display | EMDB header |
| Images | emd_68920.png | 138.3 KB | ||
| Filedesc metadata | emd-68920.cif.gz | 8.7 KB | ||
| Others | emd_68920_additional_1.map.gz emd_68920_additional_2.map.gz emd_68920_additional_3.map.gz emd_68920_half_map_1.map.gz emd_68920_half_map_2.map.gz | 4.3 MB 7 MB 7.5 MB 285.1 MB 285.1 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-68920 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-68920 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 23fdMC ![]() 23ewC ![]() 23exC ![]() 23eyC ![]() 23faC ![]() 23fbC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_68920.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | local resolution filtered map | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.93 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Additional map: focusing on second ATR KD
| File | emd_68920_additional_1.map | ||||||||||||
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| Annotation | focusing on second ATR KD | ||||||||||||
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| Density Histograms |
-Additional map: focusing on tail domain
| File | emd_68920_additional_2.map | ||||||||||||
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| Annotation | focusing on tail domain | ||||||||||||
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| Density Histograms |
-Additional map: focusing on one ATR KD
| File | emd_68920_additional_3.map | ||||||||||||
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| Annotation | focusing on one ATR KD | ||||||||||||
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| Density Histograms |
-Half map: #1
| File | emd_68920_half_map_1.map | ||||||||||||
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| Density Histograms |
-Half map: #2
| File | emd_68920_half_map_2.map | ||||||||||||
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| Density Histograms |
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Sample components
-Entire : human ATR-ATRIP complex
| Entire | Name: human ATR-ATRIP complex |
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| Components |
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-Supramolecule #1: human ATR-ATRIP complex
| Supramolecule | Name: human ATR-ATRIP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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| Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Serine/threonine-protein kinase ATR
| Macromolecule | Name: Serine/threonine-protein kinase ATR / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase |
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| Source (natural) | Organism: Homo sapiens (human) |
| Molecular weight | Theoretical: 301.756781 KDa |
| Recombinant expression | Organism: Homo sapiens (human) |
| Sequence | String: MGEHGLELAS MIPALRELGS ATPEEYNTVV QKPRQILCQF IDRILTDVNV VAVELVKKTD SQPTSVMLLD FIQHIMKSSP LMFVNVSGS HEAKGSCIEF SNWIITRLLR IAATPSCHLL HKKICEVICS LLFLFKSKSP AIFGVLTKEL LQLFEDLVYL H RRNVMGHA ...String: MGEHGLELAS MIPALRELGS ATPEEYNTVV QKPRQILCQF IDRILTDVNV VAVELVKKTD SQPTSVMLLD FIQHIMKSSP LMFVNVSGS HEAKGSCIEF SNWIITRLLR IAATPSCHLL HKKICEVICS LLFLFKSKSP AIFGVLTKEL LQLFEDLVYL H RRNVMGHA VEWPVVMSRF LSQLDEHMGY LQSAPLQLMS MQNLEFIEVT LLMVLTRIIA IVFFRRQELL LWQIGCVLLE YG SPKIKSL AISFLTELFQ LGGLPAQPAS TFFSSFLELL KHLVEMDTDQ LKLYEEPLSK LIKTLFPFEA EAYRNIEPVY LNM LLEKLC VMFEDGVLMR LKSDLLKAAL CHLLQYFLKF VPAGYESALQ VRKVYVRNIC KALLDVLGIE VDAEYLLGPL YAAL KMESM EIIEEIQCQT QQENLSSNSD GISPKRRRLS SSLNPSKRAP KQTEEIKHVD MNQKSILWSA LKQKAESLQI SLEYS GLKN PVIEMLEGIA VVLQLTALCT VHCSHQNMNC RTFKDCQHKS KKKPSVVITW MSLDFYTKVL KSCRSLLESV QKLDLE ATI DKVVKIYDAL IYMQVNSSFE DHILEDLCGM LSLPWIYSHS DDGCLKLTTF AANLLTLSCR ISDSYSPQAQ SRCVFLL TL FPRRIFLEWR TAVYNWALQS SHEVIRASCV SGFFILLQQQ NSCNRVPKIL IDKVKDDSDI VKKEFASILG QLVCTLHG M FYLTSSLTEP FSEHGHVDLF CRNLKATSQH ECSSSQLKAS VCKPFLFLLK KKIPSPVKLA FIDNLHHLCK HLDFREDET DVKAVLGTLL NLMEDPDKDV RVAFSGNIKH ILESLDSEDG FIKELFVLRM KEAYTHAQIS RNNELKDTLI LTTGDIGRAA KGDLVPFAL LHLLHCLLSK SASVSGAAYT EIRALVAAKS VKLQSFFSQY KKPICQFLVE SLHSSQMTAL PNTPCQNADV R KQDVAHQR EMALNTLSEI ANVFDFPDLN RFLTRTLQVL LPDLAAKASP AASALIRTLG KQLNVNRREI LINNFKYIFS HL VCSCSKD ELERALHYLK NETEIELGSL LRQDFQGLHN ELLLRIGEHY QQVFNGLSIL ASFASSDDPY QGPRDIISPE LMA DYLQPK LLGILAFFNM QLLSSSVGIE DKKMALNSLM SLMKLMGPKH VSSVRVKMMT TLRTGLRFKD DFPELCCRAW DCFV RCLDH ACLGSLLSHV IVALLPLIHI QPKETAAIFH YLIIENRDAV QDFLHEIYFL PDHPELKKIK AVLQEYRKET SESTD LQTT LQLSMKAIQH ENVDVRIHAL TSLKETLYKN QEKLIKYATD SETVEPIISQ LVTVLLKGCQ DANSQARLLC GECLGE LGA IDPGRLDFST TETQGKDFTF VTGVEDSSFA YGLLMELTRA YLAYADNSRA QDSAAYAIQE LLSIYDCREM ETNGPGH QL WRRFPEHVRE ILEPHLNTRY KSSQKSTDWS GVKKPIYLSK LGSNFAEWSA SWAGYLITKV RHDLASKIFT CCSIMMKH D FKVTIYLLPH ILVYVLLGCN QEDQQEVYAE IMAVLKHDDQ HTINTQDIAS DLCQLSTQTV FSMLDHLTQW ARHKFQALK AEKCPHSKSN RNKVDSMVST VDYEDYQSVT RFLDLIPQDT LAVASFRSKA YTRAVMHFES FITEKKQNIQ EHLGFLQKLY AAMHEPDGV AGVSAIRKAE PSLKEQILEH ESLGLLRDAT ACYDRAIQLE PDQIIHYHGV VKSMLGLGQL STVITQVNGV H ANRSEWTD ELNTYRVEAA WKLSQWDLVE NYLAADGKST TWSVRLGQLL LSAKKRDITA FYDSLKLVRA EQIVPLSAAS FE RGSYQRG YEYIVRLHML CELEHSIKPL FQHSPGDSSQ EDSLNWVARL EMTQNSYRAK EPILALRRAL LSLNKRPDYN EMV GECWLQ SARVARKAGH HQTAYNALLN AGESRLAELY VERAKWLWSK GDVHQALIVL QKGVELCFPE NETPPEGKNM LIHG RAMLL VGRFMEETAN FESNAIMKKY KDVTACLPEW EDGHFYLAKY YDKLMPMVTD NKMEKQGDLI RYIVLHFGRS LQYGN QFIY QSMPRMLTLW LDYGTKAYEW EKAGRSDRVQ MRNDLGKINK VITEHTNYLA PYQFLTAFSQ LISRICHSHD EVFVVL MEI IAKVFLAYPQ QAMWMMTAVS KSSYPMRVNR CKEILNKAIH MKKSLEKFVG DATRLTDKLL ELCNKPVDGS SSTLSMS TH FKMLKKLVEE ATFSEILIPL QSVMIPTLPS ILGTHANHAS HEPFPGHWAY IAGFDDMVEI LASLQKPKKI SLKGSDGK F YIMMCKPKDD LRKDCRLMEF NSLINKCLRK DAESRRRELH IRTYAVIPLN DECGIIEWVN NTAGLRPILT KLYKEKGVY MTGKELRQCM LPKSAALSEK LKVFREFLLP RHPPIFHEWF LRTFPDPTSW YSSRSAYCRS TAVMSMVGYI LGLGDRHGEN ILFDSLTGE CVHVDFNCLF NKGETFEVPE IVPFRLTHNM VNGMGPMGTE GLFRRACEVT MRLMRDQREP LMSVLKTFLH D PLVEWSKP VKGHSKAPLN ETGEVVNEKA KTHVLDIEQR LQGVIKTRNR VTGLPLSIEG HVHYLIQEAT DENLLCQMYL GW TPYM UniProtKB: Serine/threonine-protein kinase ATR |
-Macromolecule #2: ATR-interacting protein
| Macromolecule | Name: ATR-interacting protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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| Source (natural) | Organism: Homo sapiens (human) |
| Molecular weight | Theoretical: 85.940664 KDa |
| Recombinant expression | Organism: Homo sapiens (human) |
| Sequence | String: MAGTSAPGSK RRSEPPAPRP GPPPGTGHPP SKRARGFSAA AAPDPDDPFG AHGDFTADDL EELDTLASQA LSQCPAAARD VSSDHKVHR LLDGMSKNPS GKNRETVPIK DNFELEVLQA QYKELKEKMK VMEEEVLIKN GEIKILRDSL HQTESVLEEQ R RSHFLLEQ ...String: MAGTSAPGSK RRSEPPAPRP GPPPGTGHPP SKRARGFSAA AAPDPDDPFG AHGDFTADDL EELDTLASQA LSQCPAAARD VSSDHKVHR LLDGMSKNPS GKNRETVPIK DNFELEVLQA QYKELKEKMK VMEEEVLIKN GEIKILRDSL HQTESVLEEQ R RSHFLLEQ EKTQALSDKE KEFSKKLQSL QSELQFKDAE MNELRTKLQT SERANKLAAP SVSHVSPRKN PSVVIKPEAC SP QFGKTSF PTKESFSANM SLPHPCQTES GYKPLVGRED SKPHSLRGDS IKQEEAQKSF VDSWRQRSNT QGSILINLLL KQP LIPGSS LSLCHLLSSS SESPAGTPLQ PPGFGSTLAG MSGLRTTGSY DGSFSLSALR EAQNLAFTGL NLVARNECSR DGDP AEGGR RAFPLCQLPG AVHFLPLVQF FIGLHCQALQ DLAAAKRSGA PGDSPTHSSC VSSGVETNPE DSVCILEGFS VTALS ILQH LVCHSGAVVS LLLSGVGADS AAGEGNRSLV HRLSDGDMTS ALRGVADDQG QHPLLKMLLH LLAFSSAATG HLQASV LTQ CLKVLVKLAE NTSCDFLPRF QCVFQVLPKC LSPETPLPSV LLAVELLSLL ADHDQLAPQL CSHSEGCLLL LLYMYIT SR PDRVALETQW LQLEQEVVWL LAKLGVQSPL PPVTGSNCQC NVEVVRALTV MLHRQWLTVR RAGGPPRTDQ QRRTVRCL R DTVLLLHGLS QKDKLFMMHC VEVLHQFDQV MPGVSMLIRG LPDVTDCEEA ALDDLCAAET DVEDPEVECG UniProtKB: ATR-interacting protein |
-Macromolecule #3: Serine/threonine-protein kinase Chk1
| Macromolecule | Name: Serine/threonine-protein kinase Chk1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase |
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| Source (natural) | Organism: Homo sapiens (human) |
| Molecular weight | Theoretical: 1.550712 KDa |
| Sequence | String: VKYSSSQPEP RTGL UniProtKB: Serine/threonine-protein kinase Chk1 |
-Macromolecule #4: DNA topoisomerase 2-binding protein 1
| Macromolecule | Name: DNA topoisomerase 2-binding protein 1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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| Source (natural) | Organism: Homo sapiens (human) |
| Molecular weight | Theoretical: 61.099613 KDa |
| Recombinant expression | Organism: ![]() |
| Sequence | String: AQECKHLPES LYPHTYNPKM SLDISAVQDG RLCNSRLLSA VSSTKDDEPD PLILEENDVD NMATNNKESA PSNGSGKNDS KGVLTQTLE MRENFQKQLQ EIMSATSIVK PQGQRTSLSR SGCNSASSTP DSTRSARSGR SRVLEALRQS RQTVPDVNTE P SQNEQIIW ...String: AQECKHLPES LYPHTYNPKM SLDISAVQDG RLCNSRLLSA VSSTKDDEPD PLILEENDVD NMATNNKESA PSNGSGKNDS KGVLTQTLE MRENFQKQLQ EIMSATSIVK PQGQRTSLSR SGCNSASSTP DSTRSARSGR SRVLEALRQS RQTVPDVNTE P SQNEQIIW DDPTAREERA RLASNLQWPS CPTQYSELQV DIQNLEDSPF QKPLHDSEIA KQAVCDPGNI RVTEAPKHPI SE ELETPIK DSHLIPTPQA PSIAFPLANP PVAPHPREKI ITIEETHEEL KKQYIFQLSS LNPQERIDYC HLIEKLGGLV IEK QCFDPT CTHIVVGHPL RNEKYLASVA AGKWVLHRSY LEACRTAGHF VQEEDYEWGS SSILDVLTGI NVQQRRLALA AMRW RKKIQ QRQESGIVEG AFSGWKVILH VDQSREAGFK RLLQSGGAKV LPGHSVPLFK EATHLFSDLN KLKPDDSGVN IAEAA AQNV YCLRTEYIAD YLMQESPPHV ENYCLPEAIS FIQNNKELGT GLSQKRKAPT EKNKIKRPRV H UniProtKB: DNA topoisomerase 2-binding protein 1 |
-Macromolecule #5: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
| Macromolecule | Name: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 5 / Number of copies: 2 / Formula: AGS |
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| Molecular weight | Theoretical: 523.247 Da |
| Chemical component information | ![]() ChemComp-AGS: |
-Macromolecule #6: MAGNESIUM ION
| Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: MG |
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| Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #7: ZINC ION
| Macromolecule | Name: ZINC ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: ZN |
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| Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.4 |
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| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination 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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Keywords
Homo sapiens (human)
Authors
China, 2 items
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Processing
FIELD EMISSION GUN
