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- EMDB-68919: Cryo-EM structure of human ATR-ATRIP complex with ATPgammaS and Chk1 -

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Basic information

Entry
Database: EMDB / ID: EMD-68919
TitleCryo-EM structure of human ATR-ATRIP complex with ATPgammaS and Chk1
Map datalocal. resolution filtered map
Sample
  • Complex: human ATR-ATRIP complex
    • Protein or peptide: Serine/threonine-protein kinase ATR
    • Protein or peptide: ATR-interacting protein
  • Protein or peptide: Serine/threonine-protein kinase Chk1
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
KeywordsATR / TopBp1 / Chk1 / DNA repair / NUCLEAR PROTEIN
Function / homology
Function and homology information


ATR-ATRIP complex / establishment of RNA localization to telomere / positive regulation of telomerase catalytic core complex assembly / establishment of protein-containing complex localization to telomere / MutSalpha complex binding / nuclear membrane disassembly / histone H2AXS139 kinase activity / negative regulation of mitotic nuclear division / apoptotic process involved in development / negative regulation of G0 to G1 transition ...ATR-ATRIP complex / establishment of RNA localization to telomere / positive regulation of telomerase catalytic core complex assembly / establishment of protein-containing complex localization to telomere / MutSalpha complex binding / nuclear membrane disassembly / histone H2AXS139 kinase activity / negative regulation of mitotic nuclear division / apoptotic process involved in development / negative regulation of G0 to G1 transition / histone H3T11 kinase activity / regulation of mitotic centrosome separation / MutLalpha complex binding / mitotic G2/M transition checkpoint / response to arsenic-containing substance / regulation of double-strand break repair / nucleobase-containing compound metabolic process / positive regulation of DNA damage response, signal transduction by p53 class mediator / protein localization to chromosome, telomeric region / peptidyl-threonine phosphorylation / inner cell mass cell proliferation / K63-linked polyubiquitin modification-dependent protein binding / regulation of double-strand break repair via homologous recombination / HDR through Single Strand Annealing (SSA) / nucleus organization / negative regulation of DNA replication / negative regulation of gene expression, epigenetic / mitotic G2 DNA damage checkpoint signaling / Transcriptional Regulation by E2F6 / Impaired BRCA2 binding to RAD51 / replication fork processing / replicative senescence / Regulation of HSF1-mediated heat shock response / Presynaptic phase of homologous DNA pairing and strand exchange / response to mechanical stimulus / Activation of ATR in response to replication stress / interstrand cross-link repair / regulation of cellular response to heat / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / site of DNA damage / signal transduction in response to DNA damage / positive regulation of telomere maintenance via telomerase / positive regulation of cell cycle / telomere maintenance / DNA damage checkpoint signaling / Meiotic synapsis / regulation of signal transduction by p53 class mediator / replication fork / condensed nuclear chromosome / TP53 Regulates Transcription of DNA Repair Genes / Fanconi Anemia Pathway / cellular response to mechanical stimulus / Signaling by SCF-KIT / cellular response to gamma radiation / PML body / G2/M DNA damage checkpoint / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / G2/M transition of mitotic cell cycle / cellular response to UV / nuclear envelope / double-strand break repair / regulation of cell population proliferation / chromosome / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / protein phosphorylation / protein kinase activity / DNA replication / non-specific serine/threonine protein kinase / chromatin remodeling / response to xenobiotic stimulus / protein domain specific binding / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / apoptotic process / DNA damage response / centrosome / chromatin / Golgi apparatus / protein-containing complex / : / DNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
ATR-interacting protein / : / Serine/threonine-protein kinase ATR, N-HEAT region / : / Serine/threonine-protein kinase ATR, M-HEAT region / UME domain / UME (NUC010) domain / Domain in UVSB PI-3 kinase, MEI-41 and ESR-1 / Checkpoint kinase 1, catalytic domain / : ...ATR-interacting protein / : / Serine/threonine-protein kinase ATR, N-HEAT region / : / Serine/threonine-protein kinase ATR, M-HEAT region / UME domain / UME (NUC010) domain / Domain in UVSB PI-3 kinase, MEI-41 and ESR-1 / Checkpoint kinase 1, catalytic domain / : / Serine/threonine-protein kinase ATR-like, HEAT repeats / HEAT repeat profile. / HEAT, type 2 / : / FATC domain / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / 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 / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase Chk1 / Serine/threonine-protein kinase ATR / ATR-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsWang 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
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
Ministry of Science and Technology (MoST, China) China
CitationJournal: To Be Published
Title: Cryo-EM structure of human ATR-ATRIP complex with ATPgammaS and Chk1
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
DepositionFeb 4, 2026-
Header (metadata) releaseMay 13, 2026-
Map releaseMay 13, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68919.png

Downloads & links

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Map

FileDownload / File: emd_68919.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocal. resolution filtered map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 432 pix.
= 401.76 Å		0.93 Å/pix.
x 432 pix.
= 401.76 Å		0.93 Å/pix.
x 432 pix.
= 401.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-1.3384057 - 2.0080853
Average (Standard dev.)0.0010637821 (±0.025642589)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 401.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: focusing on one ATR monomer

Fileemd_68919_additional_1.map
Annotationfocusing on one ATR monomer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: focusing on ATR tail

Fileemd_68919_additional_2.map
Annotationfocusing on ATR tail
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: focusing on the second ATR monomer

Fileemd_68919_additional_3.map
Annotationfocusing on the second ATR monomer
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: focusing on ATR head

Fileemd_68919_additional_4.map
Annotationfocusing on ATR head
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_68919_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_68919_half_map_2.map
Projections & Slices
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Sample components

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Entire : human ATR-ATRIP complex

EntireName: human ATR-ATRIP complex
Components
  • Complex: human ATR-ATRIP complex
    • Protein or peptide: Serine/threonine-protein kinase ATR
    • Protein or peptide: ATR-interacting protein
  • Protein or peptide: Serine/threonine-protein kinase Chk1
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: human ATR-ATRIP complex

SupramoleculeName: human ATR-ATRIP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Serine/threonine-protein kinase ATR

MacromoleculeName: 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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 301.756781 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #2: ATR-interacting protein

MacromoleculeName: ATR-interacting protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 85.940664 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #3: Serine/threonine-protein kinase Chk1

MacromoleculeName: Serine/threonine-protein kinase Chk1 / type: protein_or_peptide / ID: 3 / Details: VKYSSSQPEPRTGL / Number of copies: 2 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.550712 KDa
SequenceString:
VKYSSSQPEP RTGL

UniProtKB: Serine/threonine-protein kinase Chk1

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Macromolecule #4: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 4 / Number of copies: 2 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 256654
Initial angle assignmentType: OTHER / Details: cryoSPARC
Final angle assignmentType: OTHER / Details: cryoSPARC

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