7ONB: U2 5' module of the A3'-SSA complex

Structure of the U2 5' module of the A3'-SSA complex. Determined by electron microscopy at 3.1 Å resolution. Released 4 Aug 2021.

Method
Electron microscopy
Resolution
3.1 Å
Organisms
Homo sapiens, unidentified adenovirus
Chains
11
Atoms
20,140
Mol. weight
693.83 kDa
Ligands
SJT, ZN
Released
4 Aug 2021

Explore 7ONB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7ONB contains 118 α-helices and 126 β-strands across 9 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: 20 helices, 99 β-strands

ElementResiduesLengthSheet
β-strand3-971
β-strand16-2052
β-strand29-3352
β-strand37-4372
β-strand50-5782
β-strand62-6873
β-strand77-8263
β-strand86-9383
β-strand98-10693
β-strand120-12344
β-strand129-13354
β-strand13615
β-strand139-14354
β-strand144-14526
β-strand153-15426
α-helix156-1572
β-strand158-15924
β-strand166-17385
β-strand181-18775
α-helix190-1934
α-helix199-2035
β-strand207-21485
β-strand219-22795
β-strand232-23767
α-helix238-2392
β-strand248-25257
β-strand255-25957
α-helix265-2662
β-strand267-27047
α-helix271-2722
β-strand273-27428
β-strand289-29359
β-strand300-30459
β-strand309-31689
β-strand324-33299
β-strand336-341610
β-strand346-351610
β-strand356-361610
β-strand372-37439
β-strand386-38728
β-strand395-401710
α-helix405-4062
β-strand407-413711
β-strand422-427611
α-helix430-4323
β-strand434-440711
β-strand442-443212
β-strand444-450713
β-strand474114
β-strand477115
β-strand482115
β-strand485114
β-strand486-487216
β-strand491-492216
β-strand509117
β-strand515-519517
β-strand524-528517
β-strand535-536217
α-helix537-5382
β-strand546-549418
β-strand554-557418
β-strand563-566418
β-strand587-592619
β-strand605-609519
β-strand613-617519
α-helix621-6233
β-strand629-631319
β-strand637-643720
β-strand664-669620
β-strand673-678620
β-strand687-690420
β-strand700-706721
β-strand709-715721
β-strand720-724521
β-strand729-732421
β-strand734-735212
β-strand741-745513
β-strand753-758613
β-strand761-767713
β-strand774-780711
β-strand785-790622
β-strand797-804822
α-helix809-82719
α-helix833-84412
α-helix849-8524
β-strand862-869822
β-strand876-881622
β-strand886-894923
β-strand904-911823
β-strand914124
β-strand919124
β-strand924-928523
α-helix931-9344
β-strand936125
β-strand939-944623
β-strand949-955726
β-strand958-963626
β-strand966-972726
β-strand977-983726
β-strand990-996727
β-strand999-1004627
β-strand1009-1015727
β-strand1020-1027827
β-strand1036-1038328
β-strand1043-1047528
β-strand1052-1057628
α-helix1058-10592
β-strand1087-1089327
β-strand1090-1096728
β-strand1101-110771
β-strand1116-112161
β-strand1126-113161
α-helix1135-115016
α-helix1160-11634
β-strand1171128
β-strand1173-117531
α-helix1176-11794
α-helix1187-11948
α-helix1201-121313
Chain B: 4 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix28-4518
α-helix47-5610
α-helix61-7111
α-helix79-813
Chain C: 63 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix489-50618
α-helix511-52111
α-helix523-5264
α-helix528-53912
α-helix546-56217
α-helix565-5706
α-helix571-5788
α-helix579-5835
α-helix587-60418
α-helix606-6138
α-helix614-6163
α-helix622-63918
α-helix641-65212
α-helix658-67518
α-helix676-6827
α-helix683-6908
α-helix691-6955
α-helix699-71618
α-helix722-7243
α-helix725-73410
α-helix740-75314
α-helix754-7563
α-helix759-77618
α-helix782-79615
α-helix803-8053
α-helix806-8105
α-helix811-8188
α-helix823-8253
α-helix827-84418
α-helix846-8505
α-helix855-8584
α-helix862-87918
α-helix886-90116
α-helix908-92114
α-helix922-9287
α-helix929-94012
α-helix945-96420
α-helix968-98013
α-helix987-100418
α-helix1013-10208
α-helix1021-10255
α-helix1029-104517
α-helix1047-10493
α-helix1052-106211
α-helix1063-10675
α-helix1071-108717
α-helix1090-110415
α-helix1108-112215
α-helix1125-11273
α-helix1129-11346
α-helix1135-11373
α-helix1142-115817
α-helix1159-11646
α-helix1166-117712
α-helix1182-119817
α-helix1205-121511
α-helix1216-12205
α-helix1224-124118
α-helix1243-12508
α-helix1253-12553
α-helix1259-127517
α-helix1279-12824
α-helix1299-13013
Chain D: 4 helices, 12 β-strands
ElementResiduesLengthSheet
β-strand10129
β-strand18-19230
α-helix201
β-strand21-22231
β-strand30132
β-strand39-42432
β-strand44-45230
α-helix48-503
α-helix52-543
β-strand57133
β-strand58131
β-strand64133
β-strand67-68231
β-strand70-72332
α-helix73-775
β-strand88129
Chain F: 1 helix, 0 β-strands
ElementResiduesLengthSheet
α-helix165-17915
Chain I: 14 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix459-4613
α-helix462-4687
α-helix478-4814
α-helix485-4928
α-helix498-5014
α-helix502-5043
α-helix523-5253
α-helix526-5294
α-helix568-5769
α-helix580-5823
α-helix611-6166
α-helix632-6387
α-helix648-6503
β-strand651134
β-strand655134
α-helix681-6822
Chain K: 3 helices, 6 β-strands
ElementResiduesLengthSheet
β-strand14-18538
α-helix26-327
β-strand39-43538
β-strand56-61638
α-helix64-7310
α-helix74-763
β-strand78-79239
β-strand82-83239
β-strand85-87338
Chain M: 2 helices, 3 β-strands
ElementResiduesLengthSheet
β-strand46-48335
β-strand54-56335
β-strand61-63335
α-helix66-738
α-helix76-8611

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Splicing factor 3B subunit 3Aprotein1217Homo sapiensQ15393 (AlphaFold model)
Splicing factor 3B subunit 5Bprotein86Homo sapiensQ9BWJ5 (AlphaFold model)
Splicing factor 3B subunit 1Cprotein1304Homo sapiensO75533 (AlphaFold model)
PHD finger-like domain-containing protein 5ADprotein110Homo sapiensQ7RTV0 (AlphaFold model)
UNKFprotein21Homo sapiens
MinxGRNA229unidentified adenovirus
RNU2HRNA188Homo sapiens
Splicing factor 3B subunit 2Iprotein895Homo sapiensQ13435
Splicing factor 3A subunit 2Mprotein464Homo sapiensQ15428
Splicing factor 3A subunit 3Nprotein501Homo sapiensQ12874
Splicing factor 3B subunit 4Kprotein424Homo sapiensQ15427
Sequence of entity 1 (A), FASTA
>7ONB_1 Splicing factor 3B subunit 3 (chains A)
MFLYNLTLQRATGISFAIHGNFSGTKQQEIVVSRGKILELLRPDPNTGKVHTLLTVEVFG
VIRSLMAFRLTGGTKDYIVVGSDSGRIVILEYQPSKNMFEKIHQETFGKSGCRRIVPGQF
LAVDPKGRAVMISAIEKQKLVYILNRDAAARLTISSPLEAHKANTLVYHVVGVDVGFENP
MFACLEMDYEEADNDPTGEAAANTQQTLTFYELDLGLNHVVRKYSEPLEEHGNFLITVPG
GSDGPSGVLICSENYITYKNFGDQPDIRCPIPRRRNDLDDPERGMIFVCSATHKTKSMFF
FLAQTEQGDIFKITLETDEDMVTEIRLKYFDTVPVAAAMCVLKTGFLFVASEFGNHYLYQ
IAHLGDDDEEPEFSSAMPLEEGDTFFFQPRPLKNLVLVDELDSLSPILFCQIADLANEDT
PQLYVACGRGPRSSLRVLRHGLEVSEMAVSELPGNPNAVWTVRRHIEDEFDAYIIVSFVN
ATLVLSIGETVEEVTDSGFLGTTPTLSCSLLGDDALVQVYPDGIRHIRADKRVNEWKTPG
KKTIVKCAVNQRQVVIALTGGELVYFEMDPSGQLNEYTERKEMSADVVCMSLANVPPGEQ
RSRFLAVGLVDNTVRIISLDPSDCLQPLSMQALPAQPESLCIVEMGGTEKQDELGERGSI
GFLYLNIGLQNGVLLRTVLDPVTGDLSDTRTRYLGSRPVKLFRVRMQGQEAVLAMSSRSW
LSYSYQSRFHLTPLSYETLEFASGFASEQCPEGIVAISTNTLRILALEKLGAVFNQVAFP
LQYTPRKFVIHPESNNLIIIETDHNAYTEATKAQRKQQMAEEMVEAAGEDERELAAEMAA
AFLNENLPESIFGAPKAGNGQWASVIRVMNPIQGNTLDLVQLEQNEAAFSVAVCRFSNTG
EDWYVLVGVAKDLILNPRSVAGGFVYTYKLVNNGEKLEFLHKTPVEEVPAAIAPFQGRVL
IGVGKLLRVYDLGKKKLLRKCENKHIANYISGIQTIGHRVIVSDVQESFIWVRYKRNENQ
LIIFADDTYPRWVTTASLLDYDTVAGADKFGNICVVRLPPNTNDEVDEDPTGNKALWDRG
LLNGASQKAEVIMNYHVGETVLSLQKTTLIPGGSESLVYTTLSGGIGILVPFTSHEDHDF
FQHVEMHLRSEHPPLCGRDHLSFRSYYFPVKNVIDGDLCEQFNSMEPNKQKNVSEELDRT
PPEVSKKLEDIRTRYAF
Sequence of entity 2 (B), FASTA
>7ONB_2 Splicing factor 3B subunit 5 (chains B)
MTDRYTIHSQLEHLQSKYIGTGHADTTKWEWLVNQHRDSYCSYMGHFDLLNYFAIAENES
KARVRFNLMEKMLQPCGPPADKPEEN
Sequence of entity 3 (C), FASTA
>7ONB_3 Splicing factor 3B subunit 1 (chains C)
MAKIAKTHEDIEAQIREIQGKKAALDEAQGVGLDSTGYYDQEIYGGSDSRFAGYVTSIAA
TELEDDDDDYSSSTSLLGQKKPGYHAPVALLNDIPQSTEQYDPFAEHRPPKIADREDEYK
KHRRTMIISPERLDPFADGGKTPDPKMNARTYMDVMREQHLTKEEREIRQQLAEKAKAGE
LKVVNGAAASQPPSKRKRRWDQTADQTPGATPKKLSSWDQAETPGHTPSLRWDETPGRAK
GSETPGATPGSKIWDPTPSHTPAGAATPGRGDTPGHATPGHGGATSSARKNRWDETPKTE
RDTPGHGSGWAETPRTDRGGDSIGETPTPGASKRKSRWDETPASQMGGSTPVLTPGKTPI
GTPAMNMATPTPGHIMSMTPEQLQAWRWEREIDERNRPLSDEELDAMFPEGYKVLPPPAG
YVPIRTPARKLTATPTPLGGMTGFHMQTEDRTMKSVNDQPSGNLPFLKPDDIQYFDKLLV
DVDESTLSPEEQKERKIMKLLLKIKNGTPPMRKAALRQITDKAREFGAGPLFNQILPLLM
SPTLEDQERHLLVKVIDRILYKLDDLVRPYVHKILVVIEPLLIDEDYYARVEGREIISNL
AKAAGLATMISTMRPDIDNMDEYVRNTTARAFAVVASALGIPSLLPFLKAVCKSKKSWQA
RHTGIKIVQQIAILMGCAILPHLRSLVEIIEHGLVDEQQKVRTISALAIAALAEAATPYG
IESFDSVLKPLWKGIRQHRGKGLAAFLKAIGYLIPLMDAEYANYYTREVMLILIREFQSP
DEEMKKIVLKVVKQCCGTDGVEANYIKTEILPPFFKHFWQHRMALDRRNYRQLVDTTVEL
ANKVGAAEIISRIVDDLKDEAEQYRKMVMETIEKIMGNLGAADIDHKLEEQLIDGILYAF
QEQTTEDSVMLNGFGTVVNALGKRVKPYLPQICGTVLWRLNNKSAKVRQQAADLISRTAV
VMKTCQEEKLMGHLGVVLYEYLGEEYPEVLGSILGALKAIVNVIGMHKMTPPIKDLLPRL
TPILKNRHEKVQENCIDLVGRIADRGAEYVSAREWMRICFELLELLKAHKKAIRRATVNT
FGYIAKAIGPHDVLATLLNNLKVQERQNRVCTTVAIAIVAETCSPFTVLPALMNEYRVPE
LNVQNGVLKSLSFLFEYIGEMGKDYIYAVTPLLEDALMDRDLVHRQTASAVVQHMSLGVY
GFGCEDSLNHLLNYVWPNVFETSPHVIQAVMGALEGLRVAIGPCRMLQYCLQGLFHPARK
VRDVYWKIYNSIYIGSQDALIAHYPRIYNDDKNTYIRYELDYIL
Sequence of entity 4 (D), FASTA
>7ONB_4 PHD finger-like domain-containing protein 5A (chains D)
MAKHHPDLIFCRKQAGVAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVI
CGGPGVSDAYYCKECTIQEKDRDGCPKIVNLGSSKTDLFYERKKYGFKKR
Sequence of entity 5 (F), FASTA
>7ONB_5 UNK (chains F)
AAAAARAARAAAWRAEQAAAA
Sequence of entity 6 (G), FASTA
>7ONB_6 MINX (chains G)
GGGCGCAGUAGUCCAGGGUUUCCUUGAUGAUGUCAUACUUAUCCUGUCCCUUUUUUUUCC
ACAGCUCGCGGUUGAGGACAAACUCUUCGCGGUCUUUCCACAGGUAAGUUGGAAGCAUGU
AGAACCUUGGAUCCGAUAUCCGUACACCAUCAGGGUACGAGCUAGCCCAUGGCGUACACC
AUCAGGGUACGACUAGUAGAUCUCGUACACCAUCAGGGUACGGAAUUCU
Sequence of entity 7 (H), FASTA
>7ONB_7 RNU2 (chains H)
AUCGCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGUAUCUGUUCUUAUCAGUUUAAUAU
CUGAUACGUCCUCUAUCCGAGGACAAUAUAUUAAAUGGAUUUUUGGAGCAGGGAGAUGGA
AUAGGAGCUUGCUCCGUCCACUCCACGCAUCGACCUGGUAUUGCAGUACCUCCAGGAACG
GUGCACCC
Sequence of entity 8 (I), FASTA
>7ONB_8 Splicing factor 3B subunit 2 (chains I)
MATEHPEPPKAELQLPPPPPPGHYGAWAAQELQAKLAEIGAPIQGNREELVERLQSYTRQ
TGIVLNRPVLRGEDGDKAAPPPMSAQLPGIPMPPPPLGLPPLQPPPPPPPPPPGLGLGFP
MAHPPNLGPPPPLRVGEPVALSEEERLKLAQQQAALLMQQEERAKQQGDHSLKEHELLEQ
QKRAAVLLEQERQQEIAKMGTPVPRPPQDMGQIGVRTPLGPRVAAPVGPVGPTPTVLPMG
APVPRPRGPPPPPGDENREMDDPSVGPKIPQALEKILQLKESRQEEMNSQQEEEEMETDA
RSSLGQSASETEEDTVSVSKKEKNRKRRNRKKKKKPQRVRGVSSESSGDREKDSTRSRGS
DSPAADVEIEYVTEEPEIYEPNFIFFKRIFEAFKLTDDVKKEKEKEPEKLDKLENSAAPK
KKGFEEEHKDSDDDSSDDEQEKKPEAPKLSKKKLRRMNRFTVAELKQLVARPDVVEMHDV
TAQDPKLLVHLKATRNSVPVPRHWCFKRKYLQGKRGIEKPPFELPDFIKRTGIQEMREAL
QEKEEQKTMKSKMREKVRPKMGKIDIDYQKLHDAFFKWQTKPKLTIHGDLYYEGKEFETR
LKEKKPGDLSDELRISLGMPVGPNAHKVPPPWLIAMQRYGPPPSYPNLKIPGLNSPIPES
CSFGYHAGGWGKPPVDETGKPLYGDVFGTNAAEFQTKTEEEEIDRTPWGELEPSDEESSE
EEEEEESDEDKPDETGFITPADSGLITPGGFSSVPAGMETPELIELRKKKIEEAMDGSET
PQLFTVLPEKRTATVGGAMMGSTHIYDMSTVMSRKGPAPELQGVEVALAPEELELDPMAM
TQKYEEHVREQQAQVEKEDFSDMVAEHAAKQKQKKRKAQPQDSRGGSKKYKEFKF
Sequence of entity 9 (M), FASTA
>7ONB_9 Splicing factor 3A subunit 2 (chains M)
MDFQHRPGGKTGSGGVASSSESNRDRRERLRQLALETIDINKDPYFMKNHLGSYECKLCL
TLHNNEGSYLAHTQGKKHQTNLARRAAKEAKEAPAQPAPEKVKVEVKKFVKIGRPGYKVT
KQRDSEMGQQSLLFQIDYPEIAEGIMPRHRFMSAYEQRIEPPDRRWQYLLMAAEPYETIA
FKVPSREIDKAEGKFWTHWNRETKQFFLQFHFKMEKPPAPPSLPAGPPGVKRPPPPLMNG
LPPRPPLPESLPPPPPGGLPLPPMPPTGPAPSGPPGPPQLPPPAPGVHPPAPVVHPPASG
VHPPAPGVHPPAPGVHPPAPGVHPPTSGVHPPAPGVHPPAPGVHPPAPGVHPPAPGVHPP
APGVHPPPSAGVHPQAPGVHPAAPAVHPQAPGVHPPAPGMHPQAPGVHPQPPGVHPSAPG
VHPQPPGVHPSNPGVHPPTPMPPMLRPPLPSEGPGNIPPPPPTN
Sequence of entity 10 (N), FASTA
>7ONB_10 Splicing factor 3A subunit 3 (chains N)
METILEQQRRYHEEKERLMDVMAKEMLTKKSTLRDQINSDHRTRAMQDRYMEVSGNLRDL
YDDKDGLRKEELNAISGPNEFAEFYNRLKQIKEFHRKHPNEICVPMSVEFEELLKARENP
SEEAQNLVEFTDEEGYGRYLDLHDCYLKYINLKASEKLDYITYLSIFDQLFDIPKERKNA
EYKRYLEMLLEYLQDYTDRVKPLQDQNELFGKIQAEFEKKWENGTFPGWPKETSSALTHA
GAHLDLSAFSSWEELASLGLDRLKSALLALGLKCGGTLEERAQRLFSTKGKSLESLDTSL
FAKNPKSKGTKRDTERNKDIAFLEAQIYEYVEILGEQRHLTHENVQRKQARTGEEREEEE
EEQISESESEDEENEIIYNPKNLPLGWDGKPIPYWLYKLHGLNINYNCEICGNYTYRGPK
AFQRHFAEWRHAHGMRCLGIPNTAHFANVTQIEDAVSLWAKLKLQKASERWQPDTEEEYE
DSSGNVVNKKTYEDLKRQGLL
Sequence of entity 11 (K), FASTA
>7ONB_11 Splicing factor 3B subunit 4 (chains K)
MAAGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVE
FLSEEDADYAIKIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTF
SAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKK
DSKGERHGSAAERLLAAQNPLSQADRPHQLFADAPPPPSAPNPVVSSLGSGLPPPGMPPP
GSFPPPVPPPGALPPGIPPAMPPPPMPPGAAGHGPPSAGTPGAGHPGHGHSHPHPFPPGG
MPHPGMSQMQLAHHGPHGLGHPHAGPPGSGGQPPPRPPPGMPHPGPPPMGMPPRGPPFGS
PMGHPGPMPPHGMRGPPPLMPPHGYTGPPRPPPYGYQRGPLPPPRPTPRPPVPPRGPLRG
PLPQ

Ligands and cofactors

IDNameFormulaCopies
SJTspliceostatin A (form II)C28 H45 N O81
ZNZinc ionZn5

Primary citation

Structural basis of intron selection by U2 snRNP in the presence of covalent inhibitors. Cretu, C., Gee, P., Liu, X. et al. Nat Commun (2021) 12:4491-4491. DOI 10.1038/s41467-021-24741-1 · PubMed

Other PDB entries of the same protein (UniProt Q15393 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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