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- EMDB-74048: Cryo-EM structure of ATR-ATRIP-TOPBP1 AAD -

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Basic information

Entry
Database: EMDB / ID: EMD-74048
TitleCryo-EM structure of ATR-ATRIP-TOPBP1 AAD
Map data
Sample
  • Complex: ATR-ATRIP-TOPBP1 AAD
    • Protein or peptide: Serine/threonine-protein kinase ATR
    • Protein or peptide: ATR-interacting protein
    • Protein or peptide: DNA topoisomerase 2-binding protein 1
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Keywordskinase / PI3K-related kinase / complex / replication stress response / replication checkpoint / NUCLEAR PROTEIN
Function / homology
Function and homology information


broken chromosome clustering / ATR-ATRIP complex / BRCA1-B 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 / histone H2AXS139 kinase activity ...broken chromosome clustering / ATR-ATRIP complex / BRCA1-B 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 / histone H2AXS139 kinase activity / homologous recombination / DNA replication checkpoint signaling / MutLalpha complex binding / response to arsenic-containing substance / double-strand break repair via classical nonhomologous end joining / 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 / positive regulation of DNA damage response, signal transduction by p53 class mediator / protein localization to chromosome, telomeric region / K63-linked polyubiquitin modification-dependent protein binding / DNA metabolic process / response to ionizing radiation / HDR through Single Strand Annealing (SSA) / negative regulation of DNA replication / mitotic G2 DNA damage checkpoint signaling / replicative senescence / Impaired BRCA2 binding to RAD51 / male germ cell nucleus / replication fork processing / chromosome organization / 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 / regulation of cellular response to heat / positive regulation of telomere maintenance via telomerase / DNA damage checkpoint signaling / telomere maintenance / Meiotic synapsis / protein serine/threonine kinase activator activity / site of DNA damage / condensed nuclear chromosome / TP53 Regulates Transcription of DNA Repair Genes / Fanconi Anemia Pathway / cellular response to gamma radiation / PML body / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / spindle pole / cellular response to UV / nuclear envelope / double-strand break repair / chromosome / site of double-strand break / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / nuclear body / protein kinase activity / non-specific serine/threonine protein kinase / DNA replication / response to xenobiotic stimulus / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / centrosome / DNA damage response / DNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus
Similarity search - Function
: / : / TopBP1, BRCT0 domain / TopBP1, first BRCT domain / : / : / TopBP1/SLF1, BRCT domain / ATR-interacting protein / : / : ...: / : / TopBP1, BRCT0 domain / TopBP1, first BRCT domain / : / : / TopBP1/SLF1, BRCT domain / ATR-interacting protein / : / : / ATR-interacting protein N-terminal domain / ATRIP C-terminal domain / : / Serine/threonine-protein kinase ATR, N-HEAT region / Secretoglobin superfamily / : / Serine/threonine-protein kinase ATR, M-HEAT region / UME domain / UME (NUC010) domain / Domain in UVSB PI-3 kinase, MEI-41 and ESR-1 / : / Serine/threonine-protein kinase ATR-like, HEAT repeats / HEAT, type 2 / HEAT repeat profile. / : / FATC domain / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / 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 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase ATR / ATR-interacting protein / DNA topoisomerase 2-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLi B / Pavletich NP
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM149915 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA008748 United States
CitationJournal: Nat Struct Mol Biol / Year: 2026
Title: Structural mechanism of TOPBP1 activating the ATR-ATRIP replication checkpoint kinase.
Authors: Buren Li / Ayat Yaseen / Nikola P Pavletich /
Abstract: The ATR protein kinase preserves genomic integrity during DNA replication by controlling checkpoints needed for the orderly progression of S phase and for the responses to replication stress. ATR, ...The ATR protein kinase preserves genomic integrity during DNA replication by controlling checkpoints needed for the orderly progression of S phase and for the responses to replication stress. ATR, with its obligate partner ATRIP, is activated by the TOPBP1 and ETAA1 proteins, which control different branches of ATR signaling. TOPBP1 is essential for induction of the S phase checkpoint in response to stalled replication forks, while ETAA1 is required for timely progression to mitosis from an unperturbed S phase. TOPBP1 and ETAA1 contain ATR-activating domains (AADs) of limited homology, but how they activate ATR has not yet been fully elucidated. Here we present the 3.0-Å cryo-EM structure of the human ATR-ATRIP complex bound to the TOPBP1 AAD, showing that TOPBP1 activates ATR by inducing a global conformational change that allosterically realigns active site residues in the kinase domain ~70 Å away. We also present the 3.3-Å structure of the ATR-ATRIP-ETAA1 AAD complex, which reveals a binding mode distinct from TOPBP1. Our data suggest that the distinct binding modes of TOPBP1 and ETAA1 contribute to the different cellular contexts and outcomes of ATR-ATRIP activation.
History
DepositionNov 24, 2025-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74048.png

Downloads & links

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Map

FileDownload / File: emd_74048.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 320 pix.
= 340.48 Å		1.06 Å/pix.
x 320 pix.
= 340.48 Å		1.06 Å/pix.
x 320 pix.
= 340.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.064 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.07979648 - 0.12470938
Average (Standard dev.)0.00014967618 (±0.0033523538)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 340.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : ATR-ATRIP-TOPBP1 AAD

EntireName: ATR-ATRIP-TOPBP1 AAD
Components
  • Complex: ATR-ATRIP-TOPBP1 AAD
    • Protein or peptide: Serine/threonine-protein kinase ATR
    • Protein or peptide: ATR-interacting protein
    • Protein or peptide: DNA topoisomerase 2-binding protein 1
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

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Supramolecule #1: ATR-ATRIP-TOPBP1 AAD

SupramoleculeName: ATR-ATRIP-TOPBP1 AAD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 830 KDa

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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: 304.008312 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKE NLYFQGGGRM GEHGLELASM IPALRELGSA TPEEYNTVVQ KPRQILCQFI DRILTDVNVV AVELVKKTDS QPTSVMLLD FIQHIMKSSP LMFVNVSGSH EAKGSCIEFS NWIITRLLRI AATPSCHLLH KKICEVICSL LFLFKSKSPA I FGVLTKEL ...String:
MDYKDDDDKE NLYFQGGGRM GEHGLELASM IPALRELGSA TPEEYNTVVQ KPRQILCQFI DRILTDVNVV AVELVKKTDS QPTSVMLLD FIQHIMKSSP LMFVNVSGSH EAKGSCIEFS NWIITRLLRI AATPSCHLLH KKICEVICSL LFLFKSKSPA I FGVLTKEL LQLFEDLVYL HRRNVMGHAV EWPVVMSRFL SQLDEHMGYL QSAPLQLMSM QNLEFIEVTL LMVLTRIIAI VF FRRQELL LWQIGCVLLE YGSPKIKSLA ISFLTELFQL GGLPAQPAST FFSSFLELLK HLVEMDTDQL KLYEEPLSKL IKT LFPFEA EAYRNIEPVY LNMLLEKLCV MFEDGVLMRL KSDLLKAALC HLLQYFLKFV PAGYESALQV RKVYVRNICK ALLD VLGIE VDAEYLLGPL YAALKMESME IIEEIQCQTQ QENLSSNSDG ISPKRRRLSS SLNPSKRAPK QTEEIKHVDM NQKSI LWSA LKQKAESLQI SLEYSGLKNP VIEMLEGIAV VLQLTALCTV HCSHQNMNCR TFKDCQHKSK KKPSVVITWM SLDFYT KVL KSCRSLLESV QKLDLEATID KVVKIYDALI YMQVNSSFED HILEDLCGML SLPWIYSHSD DGCLKLTTFA ANLLTLS CR ISDSYSPQAQ SRCVFLLTLF PRRIFLEWRT AVYNWALQSS HEVIRASCVS GFFILLQQQN SCNRVPKILI DKVKDDSD I VKKEFASILG QLVCTLHGMF YLTSSLTEPF SEHGHVDLFC RNLKATSQHE CSSSQLKASV CKPFLFLLKK KIPSPVKLA FIDNLHHLCK HLDFREDETD VKAVLGTLLN LMEDPDKDVR VAFSGNIKHI LESLDSEDGF IKELFVLRMK EAYTHAQISR NNELKDTLI LTTGDIGRAA KGDLVPFALL HLLHCLLSKS ASVSGAAYTE IRALVAAKSV KLQSFFSQYK KPICQFLVES L HSSQMTAL PNTPCQNADV RKQDVAHQRE MALNTLSEIA NVFDFPDLNR FLTRTLQVLL PDLAAKASPA ASALIRTLGK QL NVNRREI LINNFKYIFS HLVCSCSKDE LERALHYLKN ETEIELGSLL RQDFQGLHNE LLLRIGEHYQ QVFNGLSILA SFA SSDDPY QGPRDIISPE LMADYLQPKL LGILAFFNMQ LLSSSVGIED KKMALNSLMS LMKLMGPKHV SSVRVKMMTT LRTG LRFKD DFPELCCRAW DCFVRCLDHA CLGSLLSHVI VALLPLIHIQ PKETAAIFHY LIIENRDAVQ DFLHEIYFLP DHPEL KKIK AVLQEYRKET SESTDLQTTL QLSMKAIQHE NVDVRIHALT SLKETLYKNQ EKLIKYATDS ETVEPIISQL VTVLLK GCQ DANSQARLLC GECLGELGAI DPGRLDFSTT ETQGKDFTFV TGVEDSSFAY GLLMELTRAY LAYADNSRAQ DSAAYAI QE LLSIYDCREM ETNGPGHQLW RRFPEHVREI LEPHLNTRYK SSQKSTDWSG VKKPIYLSKL GSNFAEWSAS WAGYLITK V RHDLASKIFT CCSIMMKHDF KVTIYLLPHI LVYVLLGCNQ EDQQEVYAEI MAVLKHDDQH TINTQDIASD LCQLSTQTV FSMLDHLTQW ARHKFQALKA EKCPHSKSNR NKVDSMVSTV DYEDYQSVTR FLDLIPQDTL AVASFRSKAY TRAVMHFESF ITEKKQNIQ EHLGFLQKLY AAMHEPDGVA GVSAIRKAEP SLKEQILEHE SLGLLRDATA CYDRAIQLEP DQIIHYHGVV K SMLGLGQL STVITQVNGV HANRSEWTDE LNTYRVEAAW KLSQWDLVEN YLAADGKSTT WSVRLGQLLL SAKKRDITAF YD SLKLVRA EQIVPLSAAS FERGSYQRGY EYIVRLHMLC ELEHSIKPLF QHSPGDSSQE DSLNWVARLE MTQNSYRAKE PIL ALRRAL LSLNKRPDYN EMVGECWLQS ARVARKAGHH QTAYNALLNA GESRLAELYV ERAKWLWSKG DVHQALIVLQ KGVE LCFPE NETPPEGKNM LIHGRAMLLV GRFMEETANF ESNAIMKKYK DVTACLPEWE DGHFYLAKYY DKLMPMVTDN KMEKQ GDLI RYIVLHFGRS LQYGNQFIYQ SMPRMLTLWL DYGTKAYEWE KAGRSDRVQM RNDLGKINKV ITEHTNYLAP YQFLTA FSQ LISRICHSHD EVFVVLMEII AKVFLAYPQQ AMWMMTAVSK SSYPMRVNRC KEILNKAIHM KKSLEKFVGD ATRLTDK LL ELCNKPVDGS SSTLSMSTHF KMLKKLVEEA TFSEILIPLQ SVMIPTLPSI LGTHANHASH EPFPGHWAYI AGFDDMVE I LASLQKPKKI SLKGSDGKFY IMMCKPKDDL RKDCRLMEFN SLINKCLRKD AESRRRELHI RTYAVIPLND ECGIIEWVN NTAGLRPILT KLYKEKGVYM TGKELRQCML PKSAALSEKL KVFREFLLPR HPPIFHEWFL RTFPDPTSWY SSRSAYCRST AVMSMVGYI LGLGDRHGEN ILFDSLTGEC VHVDFNCLFN KGETFEVPEI VPFRLTHNMV NGMGPMGTEG LFRRACEVTM R LMRDQREP LMSVLKTFLH DPLVEWSKPV KGHSKAPLNE TGEVVNEKAK THVLDIEQRL QGVIKTRNRV TGLPLSIEGH VH YLIQEAT DENLLCQMYL GWTPYM

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: 88.192039 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKE NLYFQGGGRM AGTSAPGSKR RSEPPAPRPG PPPGTGHPPS KRARGFSAAA APDPDDPFGA HGDFTADDLE ELDTLASQA LSQCPAAARD VSSDHKVHRL LDGMSKNPSG KNRETVPIKD NFELEVLQAQ YKELKEKMKV MEEEVLIKNG E IKILRDSL ...String:
MDYKDDDDKE NLYFQGGGRM AGTSAPGSKR RSEPPAPRPG PPPGTGHPPS KRARGFSAAA APDPDDPFGA HGDFTADDLE ELDTLASQA LSQCPAAARD VSSDHKVHRL LDGMSKNPSG KNRETVPIKD NFELEVLQAQ YKELKEKMKV MEEEVLIKNG E IKILRDSL HQTESVLEEQ RRSHFLLEQE KTQALSDKEK EFSKKLQSLQ SELQFKDAEM NELRTKLQTS ERANKLAAPS VS HVSPRKN PSVVIKPEAC SPQFGKTSFP TKESFSANMS LPHPCQTESG YKPLVGREDS KPHSLRGDSI KQEEAQKSFV DSW RQRSNT QGSILINLLL KQPLIPGSSL SLCHLLSSSS ESPAGTPLQP PGFGSTLAGM SGLRTTGSYD GSFSLSALRE AQNL AFTGL NLVARNECSR DGDPAEGGRR AFPLCQLPGA VHFLPLVQFF IGLHCQALQD LAAAKRSGAP GDSPTHSSCV SSGVE TNPE DSVCILEGFS VTALSILQHL VCHSGAVVSL LLSGVGADSA AGEGNRSLVH RLSDGDMTSA LRGVADDQGQ HPLLKM LLH LLAFSSAATG HLQASVLTQC LKVLVKLAEN TSCDFLPRFQ CVFQVLPKCL SPETPLPSVL LAVELLSLLA DHDQLAP QL CSHSEGCLLL LLYMYITSRP DRVALETQWL QLEQEVVWLL AKLGVQSPLP PVTGSNCQCN VEVVRALTVM LHRQWLTV R RAGGPPRTDQ QRRTVRCLRD TVLLLHGLSQ KDKLFMMHCV EVLHQFDQVM PGVSMLIRGL PDVTDCEEAA LDDLCAAET DVEDPEVECG

UniProtKB: ATR-interacting protein

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Macromolecule #3: DNA topoisomerase 2-binding protein 1

MacromoleculeName: DNA topoisomerase 2-binding protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.285584 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSGRAQECKH LPESLYPHTY NPKMSLDISA VQDGRLCNSR LLSAVSSTKD DEPDPLILEE NDVDNMATNN KESAPSNGSG KNDSKGVLT QTLEMRENFQ KQLQEIMSAT SIVKPQGQRT SLSRSGCNSA SSTPDSTRSA RSGRSRVLEA LRQSRQTVPD V NTEPSQNE ...String:
GSGRAQECKH LPESLYPHTY NPKMSLDISA VQDGRLCNSR LLSAVSSTKD DEPDPLILEE NDVDNMATNN KESAPSNGSG KNDSKGVLT QTLEMRENFQ KQLQEIMSAT SIVKPQGQRT SLSRSGCNSA SSTPDSTRSA RSGRSRVLEA LRQSRQTVPD V NTEPSQNE QIIWDDPTAR EERARLASNL QWPSCPTQYS ELQVDIQNLE DSPFQKPLHD S

UniProtKB: DNA topoisomerase 2-binding protein 1

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Macromolecule #4: ZINC ION

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

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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: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 6 / Number of copies: 2 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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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

Concentration0.7 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTris-HClTris-HCl
80.0 mMNaClsodium chloride
0.5 mMTCEPtris-(2-carboxyethyl) phosphine
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: SerialEM
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 479450
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)

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