9ZD1: ATR-ATRIP-TOPBP1 AAD

Cryo-EM structure of ATR-ATRIP-TOPBP1 AAD. Determined by electron microscopy at 3.2 Å resolution. Released 5 Aug 2026.

Method
Electron microscopy
Resolution
3.2 Å
Organism
Homo sapiens
Chains
6
Atoms
47,314
Mol. weight
834.34 kDa
Ligands
ANP, MG, ZN
Released
5 Aug 2026

Explore 9ZD1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9ZD1 contains 372 α-helices and 48 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 162 helices, 23 β-strands

ElementResiduesLengthSheet
α-helix8-103
α-helix11-2010
α-helix23-253
α-helix26-4419
α-helix48-569
α-helix62-632
α-helix64-7815
α-helix80-823
α-helix90-11122
α-helix114-1163
α-helix120-13718
α-helix139-16527
β-strand173-17421
α-helix184-1863
β-strand195-19621
α-helix199-21517
α-helix218-2203
α-helix225-23915
α-helix245-25915
α-helix263-27917
α-helix280-2823
α-helix286-30217
α-helix309-3113
α-helix315-33016
α-helix333-3364
α-helix340-35112
α-helix352-3565
α-helix365-38016
α-helix390-3923
α-helix393-41523
β-strand453-45532
α-helix456-4594
α-helix461-48020
α-helix486-50621
β-strand531-53332
α-helix537-55317
α-helix556-5583
α-helix561-57919
α-helix584-59411
α-helix597-6015
α-helix606-6094
α-helix618-6247
α-helix625-6273
α-helix630-64011
α-helix649-66012
α-helix665-6739
α-helix675-6806
α-helix690-6978
α-helix701-7099
α-helix711-7166
β-strand722-72653
α-helix741-7444
β-strand745-74953
α-helix753-7553
β-strand758-75924
α-helix760-77011
α-helix776-7838
α-helix786-7916
β-strand793-79424
α-helix800-81011
α-helix811-8144
α-helix818-83417
α-helix841-86020
α-helix863-87917
α-helix884-89613
α-helix901-91818
α-helix922-9287
α-helix930-94617
α-helix962-98120
α-helix987-100519
α-helix1008-102013
α-helix1025-10317
α-helix1033-104311
α-helix1046-106015
α-helix1064-10707
α-helix1072-10809
α-helix1087-109913
α-helix1116-11238
α-helix1124-11263
α-helix1127-113913
α-helix1141-11433
α-helix1145-116218
α-helix1164-11696
α-helix1171-118212
α-helix1189-120214
α-helix1209-121911
α-helix1222-12254
α-helix1227-12348
α-helix1235-12395
α-helix1246-12516
α-helix1259-12613
α-helix1262-127817
α-helix1281-129212
α-helix1297-131317
α-helix1315-13239
α-helix1330-134213
α-helix1348-136114
α-helix1366-13683
α-helix1382-13843
α-helix1390-140617
α-helix1411-142818
α-helix1438-14458
α-helix1448-14547
α-helix1455-14584
β-strand1463-146425
β-strand147916
β-strand148416
α-helix1487-150014
α-helix1505-15139
α-helix1517-15193
α-helix1522-153918
α-helix1542-155615
α-helix1573-160028
α-helix1623-163513
α-helix1638-164710
α-helix1651-166414
α-helix1670-16723
α-helix1673-168210
α-helix1686-169510
α-helix1699-17013
α-helix1702-171110
α-helix1715-172814
α-helix1734-174613
α-helix1749-176214
α-helix1764-17663
α-helix1771-178111
α-helix1784-17929
α-helix1800-181314
α-helix1816-183722
α-helix1843-18464
α-helix1848-186417
α-helix1865-18673
α-helix1883-18886
α-helix1894-191017
α-helix1916-193318
α-helix1937-194610
α-helix1952-196615
α-helix1970-198314
α-helix1989-19913
α-helix1994-201320
α-helix2018-203114
α-helix2036-205318
α-helix2062-207716
α-helix2083-210624
α-helix2113-213220
α-helix2135-21395
α-helix2142-21476
α-helix2154-217017
α-helix2172-218312
α-helix2188-220417
α-helix2208-222720
β-strand2236-223837
α-helix2244-22507
α-helix22581
β-strand225918
α-helix22601
α-helix2263-22653
β-strand229218
β-strand2293-229647
β-strand2299-230247
β-strand2310-231677
β-strand2321-232777
α-helix2332-235120
α-helix2353-23586
β-strand2367-236937
β-strand2375-237847
β-strand238519
α-helix2386-239712
α-helix2403-24097
α-helix2417-24237
α-helix2424-24285
α-helix2429-24313
α-helix2437-24437
α-helix2447-247125
β-strand2481-248339
β-strand2490-249239
α-helix2501-25044
α-helix2517-25237
α-helix2527-25293
α-helix2531-254515
α-helix2547-255812
α-helix2588-260013
α-helix2616-262813
α-helix2630-26334
α-helix2638-26403
Chain B: 162 helices, 23 β-strands
ElementResiduesLengthSheet
α-helix8-103
α-helix11-2010
α-helix23-253
α-helix26-4419
α-helix48-569
α-helix62-632
α-helix64-7815
α-helix80-823
α-helix90-11122
α-helix114-1163
α-helix120-13718
α-helix139-16527
β-strand173-174210
α-helix184-1863
β-strand195-196210
α-helix199-21517
α-helix218-2203
α-helix225-23915
α-helix245-25915
α-helix263-27917
α-helix280-2823
α-helix286-30217
α-helix309-3113
α-helix315-33016
α-helix333-3364
α-helix340-35112
α-helix352-3565
α-helix365-38016
α-helix390-3923
α-helix393-41523
β-strand453-455311
α-helix456-4594
α-helix461-48020
α-helix486-50621
β-strand531-533311
α-helix537-55317
α-helix556-5583
α-helix561-57919
α-helix584-59411
α-helix597-6015
α-helix606-6094
α-helix618-6247
α-helix625-6273
α-helix630-64112
α-helix649-66012
α-helix665-6739
α-helix675-6806
α-helix690-6978
α-helix701-7099
α-helix711-7166
β-strand722-726512
α-helix741-7444
β-strand745-749512
α-helix753-7553
β-strand758-759213
α-helix760-77011
α-helix776-7838
α-helix786-7916
β-strand793-794213
α-helix800-81011
α-helix811-8144
α-helix818-83417
α-helix841-86020
α-helix863-87917
α-helix884-89613
α-helix901-91818
α-helix922-9287
α-helix930-94617
α-helix962-98120
α-helix987-100519
α-helix1008-102013
α-helix1025-10317
α-helix1033-104311
α-helix1046-106015
α-helix1064-10707
α-helix1072-10809
α-helix1087-109913
α-helix1116-11238
α-helix1124-11263
α-helix1127-113913
α-helix1141-11433
α-helix1145-116218
α-helix1164-11696
α-helix1171-118212
α-helix1189-120214
α-helix1209-121911
α-helix1222-12254
α-helix1227-12348
α-helix1235-12395
α-helix1246-12516
α-helix1259-12613
α-helix1262-127817
α-helix1281-129212
α-helix1297-131317
α-helix1315-13239
α-helix1330-134213
α-helix1348-136114
α-helix1366-13683
α-helix1382-13843
α-helix1390-140617
α-helix1411-142818
α-helix1438-14458
α-helix1448-14547
α-helix1455-14584
β-strand1463-1464214
β-strand1479115
β-strand1484115
α-helix1487-150014
α-helix1505-15139
α-helix1517-15193
α-helix1522-153918
α-helix1542-155615
α-helix1573-160028
α-helix1623-163513
α-helix1638-164710
α-helix1651-166414
α-helix1670-16723
α-helix1673-168210
α-helix1686-169510
α-helix1699-17013
α-helix1702-171110
α-helix1715-172814
α-helix1734-174613
α-helix1749-176214
α-helix1764-17663
α-helix1771-178111
α-helix1784-17929
α-helix1800-181314
α-helix1816-183722
α-helix1843-18464
α-helix1848-186417
α-helix1865-18673
α-helix1883-18886
α-helix1894-191017
α-helix1916-193318
α-helix1937-194610
α-helix1952-196615
α-helix1970-198314
α-helix1989-19913
α-helix1994-201320
α-helix2018-203114
α-helix2036-205318
α-helix2062-207716
α-helix2083-210624
α-helix2113-213220
α-helix2135-21395
α-helix2142-21476
α-helix2154-217017
α-helix2172-218312
α-helix2188-220417
α-helix2208-222720
β-strand2236-2238316
α-helix2244-22507
α-helix22581
β-strand2259117
α-helix22601
α-helix2263-22653
β-strand2292117
β-strand2293-2296416
β-strand2299-2302416
β-strand2310-2316716
β-strand2321-2327716
α-helix2332-235120
α-helix2353-23586
β-strand2367-2369316
β-strand2375-2378416
β-strand2385118
α-helix2386-239712
α-helix2403-24097
α-helix2417-24237
α-helix2424-24285
α-helix2429-24313
α-helix2437-24437
α-helix2447-247125
β-strand2481-2483318
β-strand2490-2492318
α-helix2501-25044
α-helix2517-25237
α-helix2527-25293
α-helix2531-254515
α-helix2547-255812
α-helix2588-260013
α-helix2616-262813
α-helix2630-26334
α-helix2638-26403
Chains C and D: 21 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix306-31611
α-helix329-3335
α-helix372-39120
α-helix414-4196
α-helix420-44122
α-helix467-48822
α-helix490-4956
α-helix537-55115
α-helix555-57319
α-helix577-5859
α-helix586-5894
α-helix591-5944
α-helix600-61314
α-helix620-6245
α-helix631-64111
α-helix650-66819
α-helix682-70221
α-helix711-73323
α-helix737-7404
α-helix745-76117
α-helix767-77711
Chains I and J: 3 helices, 1 β-strand
ElementResiduesLengthSheet
α-helix1065-108218
α-helix1117-112610
β-strand1143-114425
α-helix1148-115912

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Serine/threonine-protein kinase ATRA, Bprotein2663Homo sapiensQ13535 (AlphaFold model)
ATR-interacting proteinC, Dprotein810Homo sapiensQ8WXE1 (AlphaFold model)
DNA topoisomerase 2-binding protein 1I, Jprotein219Homo sapiensQ92547 (AlphaFold model)
Sequence of entity 1 (A, B), FASTA
>9ZD1_1 Serine/threonine-protein kinase ATR (chains A, B)
MDYKDDDDKENLYFQGGGRMGEHGLELASMIPALRELGSATPEEYNTVVQKPRQILCQFI
DRILTDVNVVAVELVKKTDSQPTSVMLLDFIQHIMKSSPLMFVNVSGSHEAKGSCIEFSN
WIITRLLRIAATPSCHLLHKKICEVICSLLFLFKSKSPAIFGVLTKELLQLFEDLVYLHR
RNVMGHAVEWPVVMSRFLSQLDEHMGYLQSAPLQLMSMQNLEFIEVTLLMVLTRIIAIVF
FRRQELLLWQIGCVLLEYGSPKIKSLAISFLTELFQLGGLPAQPASTFFSSFLELLKHLV
EMDTDQLKLYEEPLSKLIKTLFPFEAEAYRNIEPVYLNMLLEKLCVMFEDGVLMRLKSDL
LKAALCHLLQYFLKFVPAGYESALQVRKVYVRNICKALLDVLGIEVDAEYLLGPLYAALK
MESMEIIEEIQCQTQQENLSSNSDGISPKRRRLSSSLNPSKRAPKQTEEIKHVDMNQKSI
LWSALKQKAESLQISLEYSGLKNPVIEMLEGIAVVLQLTALCTVHCSHQNMNCRTFKDCQ
HKSKKKPSVVITWMSLDFYTKVLKSCRSLLESVQKLDLEATIDKVVKIYDALIYMQVNSS
FEDHILEDLCGMLSLPWIYSHSDDGCLKLTTFAANLLTLSCRISDSYSPQAQSRCVFLLT
LFPRRIFLEWRTAVYNWALQSSHEVIRASCVSGFFILLQQQNSCNRVPKILIDKVKDDSD
IVKKEFASILGQLVCTLHGMFYLTSSLTEPFSEHGHVDLFCRNLKATSQHECSSSQLKAS
VCKPFLFLLKKKIPSPVKLAFIDNLHHLCKHLDFREDETDVKAVLGTLLNLMEDPDKDVR
VAFSGNIKHILESLDSEDGFIKELFVLRMKEAYTHAQISRNNELKDTLILTTGDIGRAAK
GDLVPFALLHLLHCLLSKSASVSGAAYTEIRALVAAKSVKLQSFFSQYKKPICQFLVESL
HSSQMTALPNTPCQNADVRKQDVAHQREMALNTLSEIANVFDFPDLNRFLTRTLQVLLPD
LAAKASPAASALIRTLGKQLNVNRREILINNFKYIFSHLVCSCSKDELERALHYLKNETE
IELGSLLRQDFQGLHNELLLRIGEHYQQVFNGLSILASFASSDDPYQGPRDIISPELMAD
YLQPKLLGILAFFNMQLLSSSVGIEDKKMALNSLMSLMKLMGPKHVSSVRVKMMTTLRTG
LRFKDDFPELCCRAWDCFVRCLDHACLGSLLSHVIVALLPLIHIQPKETAAIFHYLIIEN
RDAVQDFLHEIYFLPDHPELKKIKAVLQEYRKETSESTDLQTTLQLSMKAIQHENVDVRI
HALTSLKETLYKNQEKLIKYATDSETVEPIISQLVTVLLKGCQDANSQARLLCGECLGEL
GAIDPGRLDFSTTETQGKDFTFVTGVEDSSFAYGLLMELTRAYLAYADNSRAQDSAAYAI
QELLSIYDCREMETNGPGHQLWRRFPEHVREILEPHLNTRYKSSQKSTDWSGVKKPIYLS
KLGSNFAEWSASWAGYLITKVRHDLASKIFTCCSIMMKHDFKVTIYLLPHILVYVLLGCN
QEDQQEVYAEIMAVLKHDDQHTINTQDIASDLCQLSTQTVFSMLDHLTQWARHKFQALKA
EKCPHSKSNRNKVDSMVSTVDYEDYQSVTRFLDLIPQDTLAVASFRSKAYTRAVMHFESF
ITEKKQNIQEHLGFLQKLYAAMHEPDGVAGVSAIRKAEPSLKEQILEHESLGLLRDATAC
YDRAIQLEPDQIIHYHGVVKSMLGLGQLSTVITQVNGVHANRSEWTDELNTYRVEAAWKL
SQWDLVENYLAADGKSTTWSVRLGQLLLSAKKRDITAFYDSLKLVRAEQIVPLSAASFER
GSYQRGYEYIVRLHMLCELEHSIKPLFQHSPGDSSQEDSLNWVARLEMTQNSYRAKEPIL
ALRRALLSLNKRPDYNEMVGECWLQSARVARKAGHHQTAYNALLNAGESRLAELYVERAK
WLWSKGDVHQALIVLQKGVELCFPENETPPEGKNMLIHGRAMLLVGRFMEETANFESNAI
MKKYKDVTACLPEWEDGHFYLAKYYDKLMPMVTDNKMEKQGDLIRYIVLHFGRSLQYGNQ
FIYQSMPRMLTLWLDYGTKAYEWEKAGRSDRVQMRNDLGKINKVITEHTNYLAPYQFLTA
FSQLISRICHSHDEVFVVLMEIIAKVFLAYPQQAMWMMTAVSKSSYPMRVNRCKEILNKA
IHMKKSLEKFVGDATRLTDKLLELCNKPVDGSSSTLSMSTHFKMLKKLVEEATFSEILIP
LQSVMIPTLPSILGTHANHASHEPFPGHWAYIAGFDDMVEILASLQKPKKISLKGSDGKF
YIMMCKPKDDLRKDCRLMEFNSLINKCLRKDAESRRRELHIRTYAVIPLNDECGIIEWVN
NTAGLRPILTKLYKEKGVYMTGKELRQCMLPKSAALSEKLKVFREFLLPRHPPIFHEWFL
RTFPDPTSWYSSRSAYCRSTAVMSMVGYILGLGDRHGENILFDSLTGECVHVDFNCLFNK
GETFEVPEIVPFRLTHNMVNGMGPMGTEGLFRRACEVTMRLMRDQREPLMSVLKTFLHDP
LVEWSKPVKGHSKAPLNETGEVVNEKAKTHVLDIEQRLQGVIKTRNRVTGLPLSIEGHVH
YLIQEATDENLLCQMYLGWTPYM
Sequence of entity 2 (C, D), FASTA
>9ZD1_2 ATR-interacting protein (chains C, D)
MDYKDDDDKENLYFQGGGRMAGTSAPGSKRRSEPPAPRPGPPPGTGHPPSKRARGFSAAA
APDPDDPFGAHGDFTADDLEELDTLASQALSQCPAAARDVSSDHKVHRLLDGMSKNPSGK
NRETVPIKDNFELEVLQAQYKELKEKMKVMEEEVLIKNGEIKILRDSLHQTESVLEEQRR
SHFLLEQEKTQALSDKEKEFSKKLQSLQSELQFKDAEMNELRTKLQTSERANKLAAPSVS
HVSPRKNPSVVIKPEACSPQFGKTSFPTKESFSANMSLPHPCQTESGYKPLVGREDSKPH
SLRGDSIKQEEAQKSFVDSWRQRSNTQGSILINLLLKQPLIPGSSLSLCHLLSSSSESPA
GTPLQPPGFGSTLAGMSGLRTTGSYDGSFSLSALREAQNLAFTGLNLVARNECSRDGDPA
EGGRRAFPLCQLPGAVHFLPLVQFFIGLHCQALQDLAAAKRSGAPGDSPTHSSCVSSGVE
TNPEDSVCILEGFSVTALSILQHLVCHSGAVVSLLLSGVGADSAAGEGNRSLVHRLSDGD
MTSALRGVADDQGQHPLLKMLLHLLAFSSAATGHLQASVLTQCLKVLVKLAENTSCDFLP
RFQCVFQVLPKCLSPETPLPSVLLAVELLSLLADHDQLAPQLCSHSEGCLLLLLYMYITS
RPDRVALETQWLQLEQEVVWLLAKLGVQSPLPPVTGSNCQCNVEVVRALTVMLHRQWLTV
RRAGGPPRTDQQRRTVRCLRDTVLLLHGLSQKDKLFMMHCVEVLHQFDQVMPGVSMLIRG
LPDVTDCEEAALDDLCAAETDVEDPEVECG
Sequence of entity 3 (I, J), FASTA
>9ZD1_3 DNA topoisomerase 2-binding protein 1 (chains I, J)
GSGRAQECKHLPESLYPHTYNPKMSLDISAVQDGRLCNSRLLSAVSSTKDDEPDPLILEE
NDVDNMATNNKESAPSNGSGKNDSKGVLTQTLEMRENFQKQLQEIMSATSIVKPQGQRTS
LSRSGCNSASSTPDSTRSARSGRSRVLEALRQSRQTVPDVNTEPSQNEQIIWDDPTAREE
RARLASNLQWPSCPTQYSELQVDIQNLEDSPFQKPLHDS

Ligands and cofactors

IDNameFormulaCopies
ANPPhosphoaminophosphonic acid-adenylate esterC10 H17 N6 O12 P32
MGMagnesium ionMg4
ZNZinc ionZn4

Primary citation

Structural mechanism of TOPBP1 activating the ATR-ATRIP replication checkpoint kinase. Li, B., Yaseen, A., Pavletich, N.P. Nat Struct Mol Biol (2026) 33:1204-1213. DOI 10.1038/s41594-026-01844-1 · PubMed

Other PDB entries of the same protein (UniProt Q13535 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

About this viewer

MolViewer shows 9ZD1 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.