8RD4: Telomeric RAP1:DNA-PK complex

Telomeric RAP1:DNA-PK complex. Determined by electron microscopy at 3.58 Å resolution. Released 5 Mar 2025.

Method
Electron microscopy
Resolution
3.58 Å
Organisms
Homo sapiens, synthetic construct
Chains
6
Atoms
40,711
Mol. weight
728.44 kDa
Released
5 Mar 2025

Explore 8RD4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8RD4 contains 272 α-helices and 80 β-strands across 4 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: 221 helices, 18 β-strands

ElementResiduesLengthSheet
α-helix11-155
α-helix18-203
α-helix28-4013
α-helix41-433
α-helix51-588
α-helix77-9115
α-helix104-11512
α-helix132-1365
α-helix147-1526
α-helix168-1714
α-helix173-1808
α-helix181-1833
α-helix186-1894
α-helix195-2039
α-helix217-22711
α-helix244-25613
α-helix267-27711
α-helix290-30112
α-helix306-32823
α-helix335-34915
α-helix356-37015
α-helix371-3733
α-helix380-3834
α-helix387-39610
α-helix410-42213
α-helix432-44514
α-helix446-4483
α-helix456-46813
α-helix477-49115
α-helix494-4952
α-helix524-5329
α-helix561-57818
β-strand58311
β-strand61411
α-helix617-63115
α-helix646-65914
α-helix666-67914
α-helix701-71717
α-helix723-73311
α-helix745-7484
α-helix749-7579
α-helix763-77917
α-helix786-7883
α-helix793-8008
α-helix818-8214
α-helix828-8347
α-helix848-86215
α-helix869-8724
α-helix879-8824
β-strand893-89532
β-strand904-90632
α-helix907-9093
α-helix911-9199
α-helix924-94522
α-helix959-97214
α-helix978-9825
α-helix985-99511
α-helix1004-101714
α-helix1023-104220
α-helix1046-10483
α-helix1056-106712
α-helix1072-108514
α-helix1096-111318
α-helix1119-11213
α-helix1123-114119
α-helix1165-117410
α-helix1181-119414
α-helix1195-11973
α-helix1204-121512
α-helix1218-12214
α-helix1223-12253
α-helix1250-127122
α-helix1278-12803
α-helix1294-12996
α-helix1300-13023
α-helix1326-135126
α-helix1353-13564
α-helix1368-13769
α-helix1389-13924
α-helix1395-140814
α-helix1412-14209
α-helix1425-14317
α-helix1445-146016
β-strand147213
β-strand147713
α-helix1478-149114
α-helix1505-152016
α-helix1525-15339
α-helix1558-15625
α-helix1566-15738
α-helix1578-15847
α-helix1590-160617
α-helix1614-162310
α-helix1627-16293
α-helix1642-165312
α-helix1668-167811
α-helix1686-16927
α-helix1693-16997
α-helix1706-172015
α-helix1734-175219
α-helix1756-176611
α-helix1777-17859
α-helix1791-180616
α-helix1814-18185
α-helix1819-18246
α-helix1825-18306
α-helix1834-18363
α-helix1837-18415
α-helix1844-18529
α-helix1854-18552
α-helix1860-188324
α-helix1895-18984
α-helix1912-192110
α-helix1935-195420
α-helix1971-19733
α-helix1978-19814
α-helix2088-20903
α-helix2094-210512
α-helix2123-21275
α-helix2128-21347
α-helix2140-215213
α-helix2154-21574
α-helix2165-21739
α-helix2183-219311
α-helix2194-21963
α-helix2206-222116
α-helix2228-224417
α-helix2253-22608
α-helix2269-228214
α-helix2296-23049
α-helix2305-23084
α-helix2313-233220
α-helix2338-235013
α-helix2358-236811
α-helix2379-23857
α-helix2386-23883
α-helix2392-240312
α-helix2411-24177
α-helix2420-24256
α-helix2429-244214
α-helix2443-24453
α-helix2448-245912
α-helix2467-248317
α-helix2495-250814
α-helix2509-25113
α-helix2515-252612
α-helix2535-25428
α-helix2543-25453
α-helix2554-256411
α-helix2565-25673
α-helix2788-279811
α-helix2802-282019
α-helix2826-284621
α-helix2852-286312
α-helix2873-288311
α-helix2886-289611
α-helix2920-293213
α-helix2936-294510
α-helix2952-296110
α-helix2967-297610
α-helix2988-300417
α-helix3008-30169
α-helix3035-305420
α-helix3061-30688
α-helix3076-30805
α-helix3084-30929
α-helix3096-311621
α-helix3125-31295
α-helix3132-314615
α-helix3148-31514
α-helix3155-316612
α-helix3176-319318
α-helix3231-324818
α-helix3254-32629
α-helix3264-32663
α-helix3273-328917
α-helix3293-32986
α-helix3301-33088
α-helix3315-33173
α-helix3322-334322
α-helix3353-33597
α-helix3371-339020
α-helix3410-342718
α-helix3442-345615
α-helix3459-34624
α-helix3466-34749
α-helix3480-34867
α-helix3492-34987
α-helix3499-35057
α-helix3511-35133
α-helix3516-35249
α-helix3530-35389
α-helix3546-35494
α-helix3552-356110
α-helix3568-357811
α-helix3581-359818
α-helix3606-36138
α-helix3614-36185
α-helix3633-36397
α-helix3645-36495
α-helix3661-36633
α-helix3664-36718
α-helix3681-36833
α-helix3685-36884
β-strand3727-372824
β-strand3736-373834
β-strand3741-374225
β-strand3746-374725
β-strand3750-375454
α-helix3759-377517
α-helix3779-37835
β-strand3793-379754
β-strand3800-380454
β-strand3810-381126
α-helix3812-38198
α-helix3822-38298
α-helix3835-384713
α-helix3855-38584
α-helix3859-38613
α-helix3864-387512
α-helix3882-38887
α-helix3897-391721
β-strand3928-393036
β-strand3937-393936
α-helix3965-39684
α-helix3969-39713
α-helix3980-399314
α-helix3997-400610
α-helix4016-40216
α-helix4033-40386
α-helix4042-405211
β-strand405417
α-helix4056-406712
α-helix4074-40829
α-helix4089-40913
β-strand409617
α-helix4100-411112
α-helix4114-41185
α-helix4122-41243
Chain D: 8 helices, 10 β-strands
ElementResiduesLengthSheet
β-strand2218
α-helix271
β-strand2818
α-helix291
β-strand30-3239
α-helix37-4812
β-strand52-5439
β-strand62-6329
β-strand64-65210
α-helix70-756
β-strand79-80210
α-helix82-909
α-helix96-994
β-strand100110
α-helix138-1458
α-helix155-1573
β-strand167111
β-strand171111
Chain E: 23 helices, 29 β-strands
ElementResiduesLengthSheet
β-strand35-42812
β-strand43113
α-helix46-494
α-helix57-582
α-helix59-7618
β-strand82-85412
β-strand86-88313
β-strand94113
β-strand102-104313
β-strand109112
α-helix113-1175
α-helix120-1223
α-helix124-13411
α-helix145-15511
β-strand161-169912
β-strand170114
α-helix180-19617
β-strand199-201312
β-strand204114
α-helix240-2423
β-strand258-262515
β-strand268-275815
β-strand277116
α-helix282-2854
β-strand288-289217
β-strand295117
β-strand297118
β-strand300-303419
β-strand316-322720
β-strand325-329520
α-helix331-3366
β-strand344-352915
α-helix353-3553
β-strand366-370515
α-helix378-39114
β-strand394-401815
β-strand409-416815
β-strand419-420221
β-strand426-428321
β-strand431-433315
β-strand436115
α-helix437-4393
α-helix440-4423
α-helix444-4485
α-helix459-4679
β-strand470122
α-helix481-49414
α-helix511-5188
α-helix521-5299
α-helix561-57010
α-helix578-58811
α-helix596-60813
Chain F: 20 helices, 23 β-strands
ElementResiduesLengthSheet
β-strand9-15723
α-helix18-214
α-helix30-4718
β-strand53-59723
β-strand81-84423
α-helix88-947
α-helix107-12115
β-strand130-135623
β-strand161-165523
α-helix201-21515
α-helix218-2236
β-strand225-226223
α-helix227-2304
α-helix242-2465
β-strand248-253622
β-strand257-2681222
β-strand277-280420
β-strand290-293419
β-strand296118
α-helix307-3093
β-strand310-311217
β-strand314-316324
β-strand319-321324
α-helix325-3306
β-strand339-346822
β-strand357-364822
α-helix373-38614
β-strand390-396722
α-helix402-4032
β-strand404-412922
β-strand417-423722
β-strand430116
α-helix445-4473
α-helix448-46013
β-strand462115
β-strand464-465225
α-helix467-4693
β-strand474-475225
α-helix485-49915
α-helix505-5095
α-helix510-5156
α-helix520-5256
α-helix527-53610

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
DNA-dependent protein kinase catalytic subunitAprotein4128Homo sapiensP78527
Telomeric repeat-binding factor 2-interacting protein 1Dprotein399Homo sapiensQ9NYB0 (AlphaFold model)
X-ray repair cross-complementing protein 6Eprotein609Homo sapiensP12956 (AlphaFold model)
X-ray repair cross-complementing protein 5Fprotein732Homo sapiensP13010 (AlphaFold model)
DNA (41-mer)XDNA100synthetic construct
DNA (41-mer)YDNA100synthetic construct
Sequence of entity 1 (A), FASTA
>8RD4_1 DNA-dependent protein kinase catalytic subunit (chains A)
MAGSGAGVRCSLLRLQETLSAADRCGAALAGHQLIRGLGQECVLSSSPAVLALQTSLVFS
RDFGLLVFVRKSLNSIEFRECREEILKFLCIFLEKMGQKIAPYSVEIKNTCTSVYTKDRA
AKCKIPALDLLIKLLQTFRSSRLMDEFKIGELFSKFYGELALKKKIPDTVLEKVYELLGL
LGEVHPSEMINNAENLFRAFLGELKTQMTSAVREPKLPVLAGCLKGLSSLLCNFTKSMEE
DPQTSREIFNFVLKAIRPQIDLKRYAVPSAGLRLFALHASQFSTCLLDNYVSLFEVLLKW
CAHTNVELKKAALSALESFLKQVSNMVAKNAEMHKNKLQYFMEQFYGIIRNVDSNNKELS
IAIRGYGLFAGPCKVINAKDVDFMYVELIQRCKQMFLTQTDTGDDRVYQMPSFLQSVASV
LLYLDTVPEVYTPVLEHLVVMQIDSFPQYSPKMQLVCCRAIVKVFLALAAKGPVLRNCIS
TVVHQGLIRICSKPVVLPKGPESESEDHRASGEVRTGKWKVPTYKDYVDLFRHLLSSDQM
MDSILADEAFFSVNSSSESLNHLLYDEFVKSVLKIVEKLDLTLEIQTVGEQENGDEAPGV
WMIPTSDPAANLHPAKPKDFSAFINLVEFCREILPEKQAEFFEPWVYSFSYELILQSTRL
PLISGFYKLLSITVRNAKKIKYFEGVSPKSLKHSPEDPEKYSCFALFVKFGKEVAVKMKQ
YKDELLASCLTFLLSLPHNIIELDVRAYVPALQMAFKLGLSYTPLAEVGLNALEEWSIYI
DRHVMQPYYKDILPCLDGYLKTSALSDETKNNWEVSALSRAAQKGFNKVVLKHLKKTKNL
SSNEAISLEEIRIRVVQMLGSLGGQINKNLLTVTSSDEMMKSYVAWDREKRLSFAVPFRE
MKPVIFLDVFLPRVTELALTASDRQTKVAACELLHSMVMFMLGKATQMPEGGQGAPPMYQ
LYKRTFPVLLRLACDVDQVTRQLYEPLVMQLIHWFTNNKKFESQDTVALLEAILDGIVDP
VDSTLRDFCGRCIREFLKWSIKQITPQQQEKSPVNTKSLFKRLYSLALHPNAFKRLGASL
AFNNIYREFREEESLVEQFVFEALVIYMESLALAHADEKSLGTIQQCCDAIDHLCRIIEK
KHVSLNKAKKRRLPRGFPPSASLCLLDLVKWLLAHCGRPQTECRHKSIELFYKFVPLLPG
NRSPNLWLKDVLKEEGVSFLINTFEGGGCGQPSGILAQPTLLYLRGPFSLQATLCWLDLL
LAALECYNTFIGERTVGALQVLGTEAQSSLLKAVAFFLESIAMHDIIAAEKCFGTGAAGN
RTSPQEGERYNYSKCTVVVRIMEFTTTLLNTSPEGWKLLKKDLCNTHLMRVLVQTLCEPA
SIGFNIGDVQVMAHLPDVCVNLMKALKMSPYKDILETHLREKITAQSIEELCAVNLYGPD
AQVDRSRLAAVVSACKQLHRAGLLHNILPSQSTDLHHSVGTELLSLVYKGIAPGDERQCL
PSLDLSCKQLASGLLELAFAFGGLCERLVSLLLNPAVLSTASLGSSQGSVIHFSHGEYFY
SLFSETINTELLKNLDLAVLELMQSSVDNTKMVSAVLNGMLDQSFRERANQKHQGLKLAT
TILQHWKKCDSWWAKDSPLETKMAVLALLAKILQIDSSVSFNTSHGSFPEVFTTYISLLA
DTKLDLHLKGQAVTLLPFFTSLTGGSLEELRRVLEQLIVAHFPMQSREFPPGTPRFNNYV
DCMKKFLDALELSQSPMLLELMTEVLCREQQHVMEELFQSSFRRIARRGSCVTQVGLLES
VYEMFRKDDPRLSFTRQSFVDRSLLTLLWHCSLDALREFFSTIVVDAIDVLKSRFTKLNE
STFDTQITKKMGYYKILDVMYSRLPKDDVHAKESKINQVFHGSCITEGNELTKTLIKLCY
DAFTENMAGENQLLERRRLYHCAAYNCAISVICCVFNELKFYQGFLFSEKPEKNLLIFEN
LIDLKRRYNFPVEVEVPMERKKKYIEIRKEAREAANGDSDGPSYMSSLSYLADSTLSEEM
SQFDFSTGVQSYSYSSQDPRPATGRFRRREQRDPTVHDDVLELEMDELNRHECMAPLTAL
VKHMHRSLGPPQGEEDSVPRDLPSWMKFLHGKLGNPIVPLNIRLFLAKLVINTEEVFRPY
AKHWLSPLLQLAASENNGGEGIHYMVVEIVATILSWTGLATPTGVPKDEVLANRLLNFLM
KHVFHPKRAVFRHNLEIIKTLVECWKDCLSIPYRLIFEKFSGKDPNSKDNSVGIQLLGIV
MANDLPPYDPQCGIQSSEYFQALVNNMSFVRYKEVYAAAAEVLGLILRYVMERKNILEES
LCELVAKQLKQHQNTMEDKFIVCLNKVTKSFPPLADRFMNAVFFLLPKFHGVLKTLCLEV
VLCRVEGMTELYFQLKSKDFVQVMRHRDDERQKVCLDIIYKMMPKLKPVELRELLNPVVE
FVSHPSTTCREQMYNILMWIHDNYRDPESETDNDSQEIFKLAKDVLIQGLIDENPGLQLI
IRNFWSHETRLPSNTLDRLLALNSLYSPKIEVHFLSLATNFLLEMTSMSPDYPNPMFEHP
LSECEFQEYTIDSDWRFRSTVLTPMFVETQASQGTLQTRTQEGSLSARWPVAGQIRATQQ
QHDFTLTQTADGRSSFDWLTGSSTDPLVDHTSPSSDSLLFAHKRSERLQRAPLKSVGPDF
GKKRLGLPGDEVDNKVKGAAGRTDLLRLRRRFMRDQEKLSLMYARKGVAEQKREKEIKSE
LKMKQDAQVVLYRSYRHGDLPDIQIKHSSLITPLQAVAQRDPIIAKQLFSSLFSGILKEM
DKFKTLSEKNNITQKLLQDFNRFLNTTFSFFPPFVSCIQDISCQHAALLSLDPAAVSAGC
LASLQQPVGIRLLEEALLRLLPAELPAKRVRGKARLPPDVLRWVELAKLYRSIGEYDVLR
GIFTSEIGTKQITQSALLAEARSDYSEAAKQYDEALNKQDWVDGEPTEAEKDFWELASLD
CYNHLAEWKSLEYCSTASIDSENPPDLNKIWSEPFYQETYLPYMIRSKLKLLLQGEADQS
LLTFIDKAMHGELQKAILELHYSQELSLLYLLQDDVDRAKYYIQNGIQSFMQNYSSIDVL
LHQSRLTKLQSVQALTEIQEFISFISKQGNLSSQVPLKRLLNTWTNRYPDAKMDPMNIWD
DIITNRCFFLSKIEEKLTPLPEDNSMNVDQDGDPSDRMEVQEQEEDISSLIRSCKFSMKM
KMIDSARKQNNFSLAMKLLKELHKESKTRDDWLVSWVQSYCRLSHCRSRSQGCSEQVLTV
LKTVSLLDENNVSSYLSKNILAFRDQNILLGTTYRIIANALSSEPACLAEIEEDKARRIL
ELSGSSSEDSEKVIAGLYQRAFQHLSEAVQAAEEEAQPPSWSCGPAAGVIDAYMTLADFC
DQQLRKEEENASVIDSAELQAYPALVVEKMLKALKLNSNEARLKFPRLLQIIERYPEETL
SLMTKEISSVPCWQFISWISHMVALLDKDQAVAVQHSVEEITDNYPQAIVYPFIISSESY
SFKDTSTGHKNKEFVARIKSKLDQGGVIQDFINALDQLSNPELLFKDWSNDVRAELAKTP
VNKKNIEKMYERMYAALGDPKAPGLGAFRRKFIQTFGKEFDKHFGKGGSKLLRMKLSDFN
DITNMLLLKMNKDSKPPGNLKECSPWMSDFKVEFLRNELEIPGQYDGRGKPLPEYHVRIA
GFDERVTVMASLRRPKRIIIRGHDEREHPFLVKGGEDLRQDQRVEQLFQVMNGILAQDSA
CSQRALQLRTYSVVPMTSRLGLIEWLENTVTLKDLLLNTMSQEEKAAYLSDPRAPPCEYK
DWLTKMSGKHDVGAYMLMYKGANRTETVTSFRKRESKVPADLLKRAFVRMSTSPEAFLAL
RSHFASSHALICISHWILGIGDRHLNNFMVAMETGGVIGIDFGHAFGSATQFLPVPELMP
FRLTRQFINLMLPMKETGLMYSIMVHALRAFRSDPGLLTNTMDVFVKEPSFDWKNFEQKM
LKKGGSWIQEINVAEKNWYPRQKICYAKRKLAGANPAVITCDELLLGHEKAPAFRDYVAV
ARGSKDHNIRAQEPESGLSEETQVKCLMDQATDPNILGRTWEGWEPWM
Sequence of entity 2 (D), FASTA
>8RD4_2 Telomeric repeat-binding factor 2-interacting protein 1 (chains D)
MAEAMDLGKDPNGPTHSSTLFVRDDGSSMSFYVRPSPAKRRLSTLILHGGGTVCRVQEPG
AVLLAQPGEALAEASGDFISTQYILDCVERNERLELEAYRLGPASAADTGSEAKPGALAE
GAAEPEPQRHAGRIAFTDADDVAILTYVKENARSPSSVTGNALWKAMEKSSLTQHSWQSL
KDRYLKHLRGQEHKYLLGDAPVSPSSQKLKRKAEEDPEAADSGEPQNKRTPDLPEEEYVK
EEIQENEEAVKKMLVEATREFEEVVVDESPPDFEIHITMCDDDPPTPEEDSETQPDEEEE
EEEEKVSQPEVGAAIKIIRQLMEKFNLDLSTVTQAFLKNSGELEATSAFLASGQRADGYP
IWSRQDDIDLQKDDEDTREALVKKFGAQNVARRIEFRKK
Sequence of entity 3 (E), FASTA
>8RD4_3 X-ray repair cross-complementing protein 6 (chains E)
MSGWESYYKTEGDEEAEEEQEENLEASGDYKYSGRDSLIFLVDASKAMFESQSEDELTPF
DMSIQCIQSVYISKIISSDRDLLAVVFYGTEKDKNSVNFKNIYVLQELDNPGAKRILELD
QFKGQQGQKRFQDMMGHGSDYSLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDNPHGNDS
AKASRARTKAGDLRDTGIFLDLMHLKKPGGFDISLFYRDIISIAEDEDLRVHFEESSKLE
DLLRKVRAKETRKRALSRLKLKLNKDIVISVGIYNLVQKALKPPPIKLYRETNEPVKTKT
RTFNTSTGGLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMGFKPLVLLKKHH
YLRPSLFVYPEESLVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVPQEEEL
DDQKIQVTPPGFQLVFLPFADDKRKMPFTEKIMATPEQVGKMKAIVEKLRFTYRSDSFEN
PVLQQHFRNLEALALDLMEPEQAVDLTLPKVEAMNKRLGSLVDEFKELVYPPDYNPEGKV
TKRKHDNEGSGSKRPKVEYSEEELKTHISKGTLGKFTVPMLKEACRAYGLKSGLKKQELL
EALTKHFQD
Sequence of entity 4 (F), FASTA
>8RD4_4 X-ray repair cross-complementing protein 5 (chains F)
MVRSGNKAAVVLCMDVGFTMSNSIPGIESPFEQAKKVITMFVQRQVFAENKDEIALVLFG
TDGTDNPLSGGDQYQNITVHRHLMLPDFDLLEDIESKIQPGSQQADFLDALIVSMDVIQH
ETIGKKFEKRHIEIFTDLSSRFSKSQLDIIIHSLKKCDISLQFFLPFSLGKEDGSGDRGD
GPFRLGGHGPSFPLKGITEQQKEGLEIVKMVMISLEGEDGLDEIYSFSESLRKLCVFKKI
ERHSIHWPCRLTIGSNLSIRIAAYKSILQERVKKTWTVVDAKTLKKEDIQKETVYCLNDD
DETEVLKEDIIQGFRYGSDIVPFSKVDEEQMKYKSEGKCFSVLGFCKSSQVQRRFFMGNQ
VLKVFAARDDEAAAVALSSLIHALDDLDMVAIVRYAYDKRANPQVGVAFPHIKHNYECLV
YVQLPFMEDLRQYMFSSLKNSKKYAPTEAQLNAVDALIDSMSLAKKDEKTDTLEDLFPTT
KIPNPRFQRLFQCLLHRALHPREPLPPIQQHIWNMLNPPAEVTTKSQIPLSKIKTLFPLI
EAKKKDQVTAQEIFQDNHEDGPTAKKLKTEQGGAHFSVSSLAEGSVTSVGSVNPAENFRV
LVKQKKASFEEASNQLINHIEQFLDTNETPYFMKSIDCIRAFREEAIKFSEEQRFNNFLK
ALQEKVEIKQLNHFWEIVVQDGITLITKEEASGSSVTAEEAKKFLAPKDKPSGDTAAVFE
EGGDVDDLLDMI
Sequence of entity 5 (X), FASTA
>8RD4_5 DNA (41-MER) (chains X)
CGTCTATATTCTATTGTCTCTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAG
GGTTAGGGTTAACATCAGTCTCACATAGATTAGCTCACGC
Sequence of entity 6 (Y), FASTA
>8RD4_6 DNA (41-MER) (chains Y)
GCGTGAGCTAATCTATGTGAGACTGATGTTAACCCTAACCCTAACCCTAACCCTAACCCT
AACCCTAACCCTAACCCTAAGAGACAATAGAATATAGACG

Primary citation

Chromosome end protection by RAP1-mediated inhibition of DNA-PK. Eickhoff, P., Sonmez, C., Fisher, C.E.L. et al. Nature (2025) 642:1090-1096. DOI 10.1038/s41586-025-08896-1 · PubMed

Other PDB entries of the same protein (UniProt P78527), best resolution first:

Browse structure collections

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