6Y50: 5'domain of human 17S U2 snRNP

5'domain of human 17S U2 snRNP. Determined by electron microscopy at 4.1 Å resolution. Released 1 Jul 2020.

Method
Electron microscopy
Resolution
4.1 Å
Organism
Homo sapiens
Chains
9
Atoms
14,916
Mol. weight
727.56 kDa
Ligands
ZN
Released
1 Jul 2020

Explore 6Y50 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Y50 contains 101 α-helices and 124 β-strands across 8 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 8: 8 helices, 0 β-strands

ElementResiduesLengthSheet
α-helix464-4674
α-helix472-4743
α-helix478-4814
α-helix485-4928
α-helix523-5253
α-helix526-5294
α-helix572-5754
α-helix579-5824
Chain 9: 5 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix394-4007
β-strand406-40831
β-strand414-41631
α-helix419-4246
α-helix429-43810
α-helix453-4619
α-helix491-4977
Chain p: 2 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix149-17830
α-helix190-1934
Chain q: 2 helices, 5 β-strands
ElementResiduesLengthSheet
β-strand134-138538
α-helix146-1549
β-strand183-187538
α-helix191-20010
β-strand204-205239
β-strand210-211239
β-strand212-214338
Chain u: 62 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix469-4713
α-helix493-50513
α-helix509-52012
α-helix523-5253
α-helix528-54013
α-helix546-56217
α-helix565-5673
α-helix571-58212
α-helix587-60317
α-helix606-6138
α-helix615-6184
α-helix622-63817
α-helix641-65212
α-helix658-67518
α-helix677-6793
α-helix682-6909
α-helix691-6933
α-helix699-71517
α-helix723-7264
α-helix728-7336
α-helix734-7363
α-helix741-75616
α-helix760-77314
α-helix782-79716
α-helix803-8053
α-helix806-8105
α-helix811-8133
α-helix814-8185
α-helix821-8233
α-helix827-84418
α-helix846-8505
α-helix862-87918
α-helix886-90116
α-helix908-92114
α-helix922-9254
α-helix929-94012
α-helix945-95713
α-helix959-9624
α-helix970-9789
α-helix987-100317
α-helix1013-102412
α-helix1029-104214
α-helix1052-106211
α-helix1063-10653
α-helix1071-108818
α-helix1090-110213
α-helix1109-112214
α-helix1125-11273
α-helix1129-11335
α-helix1134-11363
α-helix1141-115717
α-helix1159-11613
α-helix1170-11778
α-helix1186-119611
α-helix1205-121511
α-helix1217-12193
α-helix1224-124118
α-helix1243-12508
α-helix1262-127413
α-helix1281-12833
α-helix1288-12903
α-helix1298-13003
Chain v: 14 helices, 109 β-strands
ElementResiduesLengthSheet
β-strand3-646
β-strand18-2037
β-strand29-3357
β-strand37-4377
β-strand50-5787
β-strand65-6628
β-strand77-8048
β-strand8419
β-strand87-9158
β-strand93110
β-strand98110
β-strand101-10558
β-strand11019
β-strand120-122311
β-strand130-133411
β-strand136112
β-strand139-142411
β-strand144-146313
β-strand152-154313
β-strand165-173912
α-helix1801
β-strand181-188812
α-helix199-2013
β-strand207-212612
β-strand221-227712
β-strand234114
β-strand237-238214
α-helix2391
β-strand247-252614
β-strand255-259514
β-strand267-270414
α-helix2731
β-strand274115
β-strand302-304316
β-strand310-312316
β-strand316-317217
β-strand322-324317
β-strand327118
β-strand329116
β-strand336-342719
β-strand346-351619
β-strand356-360519
β-strand373118
β-strand387115
β-strand396-401619
β-strand407-413720
β-strand422-427620
β-strand434-440720
β-strand442-443221
β-strand448-450322
β-strand458-463623
β-strand471-477723
β-strand482-486523
β-strand493123
β-strand507-509324
β-strand516-520524
β-strand523-527524
β-strand533-537524
β-strand546-548325
β-strand553-558625
α-helix559-5613
β-strand562-567625
β-strand576125
β-strand589-592426
α-helix593-5964
β-strand605-608426
β-strand613-618626
β-strand626-632726
β-strand637-643727
β-strand664-669627
β-strand673-678627
β-strand686-690527
β-strand700-706728
β-strand709-715728
β-strand720-725628
β-strand728-733628
β-strand734-735221
β-strand741-745522
β-strand753-758622
β-strand761-765522
β-strand774-780720
β-strand784-787429
β-strand790-791229
β-strand796-804929
α-helix809-82315
α-helix836-8449
α-helix849-8524
β-strand862-869829
β-strand876-881629
β-strand886130
β-strand891-894430
β-strand904-911830
β-strand914131
β-strand919131
β-strand922-928730
α-helix931-9333
β-strand939-945730
β-strand949132
β-strand954132
β-strand959-963532
β-strand966-971632
β-strand978-983632
β-strand990133
β-strand999-1003534
β-strand1004133
β-strand1009-1015734
β-strand1020-1022334
β-strand1025-1026235
β-strand1036-1037236
β-strand1043-1047536
β-strand1052-1057636
β-strand1087-1088235
β-strand1090-1096736
β-strand1104-110746
β-strand1111137
β-strand1113137
β-strand1116-111946
β-strand1127-113156
α-helix1135-115117
β-strand1173-117426
α-helix1176-11794
α-helix1187-119610
α-helix1201-121515
Chain x: 5 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix28-3912
α-helix41-444
α-helix48-514
α-helix53-564
α-helix61-7111
Chain y: 3 helices, 8 β-strands
ElementResiduesLengthSheet
β-strand18-1922
β-strand2213
β-strand39-4244
β-strand44-4522
α-helix47-493
α-helix52-543
β-strand5715
β-strand6415
β-strand6713
β-strand70-7234
α-helix73-764

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Splicing factor 3A subunit 39protein501Homo sapiensQ12874 (AlphaFold model)
PHD finger-like domain-containing protein 5Ayprotein110Homo sapiensQ7RTV0 (AlphaFold model)
Splicing factor 3B subunit 5xprotein86Homo sapiensQ9BWJ5 (AlphaFold model)
Splicing factor 3B subunit 28protein895Homo sapiensQ13435 (AlphaFold model)
Splicing factor 3B subunit 3vprotein1217Homo sapiensQ15393
Splicing factor 3B subunit 1uprotein1304Homo sapiensO75533
U2 snRNA2RNA188Homo sapiens
HIV Tat-specific factor 1qprotein755Homo sapiensO43719
Probable ATP-dependent RNA helicase DDX46pprotein1031Homo sapiensQ7L014
Sequence of entity 1 (9), FASTA
>6Y50_1 Splicing factor 3A subunit 3 (chains 9)
METILEQQRRYHEEKERLMDVMAKEMLTKKSTLRDQINSDHRTRAMQDRYMEVSGNLRDL
YDDKDGLRKEELNAISGPNEFAEFYNRLKQIKEFHRKHPNEICVPMSVEFEELLKARENP
SEEAQNLVEFTDEEGYGRYLDLHDCYLKYINLKASEKLDYITYLSIFDQLFDIPKERKNA
EYKRYLEMLLEYLQDYTDRVKPLQDQNELFGKIQAEFEKKWENGTFPGWPKETSSALTHA
GAHLDLSAFSSWEELASLGLDRLKSALLALGLKCGGTLEERAQRLFSTKGKSLESLDTSL
FAKNPKSKGTKRDTERNKDIAFLEAQIYEYVEILGEQRHLTHENVQRKQARTGEEREEEE
EEQISESESEDEENEIIYNPKNLPLGWDGKPIPYWLYKLHGLNINYNCEICGNYTYRGPK
AFQRHFAEWRHAHGMRCLGIPNTAHFANVTQIEDAVSLWAKLKLQKASERWQPDTEEEYE
DSSGNVVNKKTYEDLKRQGLL
Sequence of entity 2 (y), FASTA
>6Y50_2 PHD finger-like domain-containing protein 5A (chains y)
MAKHHPDLIFCRKQAGVAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVI
CGGPGVSDAYYCKECTIQEKDRDGCPKIVNLGSSKTDLFYERKKYGFKKR
Sequence of entity 3 (x), FASTA
>6Y50_3 Splicing factor 3B subunit 5 (chains x)
MTDRYTIHSQLEHLQSKYIGTGHADTTKWEWLVNQHRDSYCSYMGHFDLLNYFAIAENES
KARVRFNLMEKMLQPCGPPADKPEEN
Sequence of entity 4 (8), FASTA
>6Y50_4 Splicing factor 3B subunit 2 (chains 8)
MATEHPEPPKAELQLPPPPPPGHYGAWAAQELQAKLAEIGAPIQGNREELVERLQSYTRQ
TGIVLNRPVLRGEDGDKAAPPPMSAQLPGIPMPPPPLGLPPLQPPPPPPPPPPGLGLGFP
MAHPPNLGPPPPLRVGEPVALSEEERLKLAQQQAALLMQQEERAKQQGDHSLKEHELLEQ
QKRAAVLLEQERQQEIAKMGTPVPRPPQDMGQIGVRTPLGPRVAAPVGPVGPTPTVLPMG
APVPRPRGPPPPPGDENREMDDPSVGPKIPQALEKILQLKESRQEEMNSQQEEEEMETDA
RSSLGQSASETEEDTVSVSKKEKNRKRRNRKKKKKPQRVRGVSSESSGDREKDSTRSRGS
DSPAADVEIEYVTEEPEIYEPNFIFFKRIFEAFKLTDDVKKEKEKEPEKLDKLENSAAPK
KKGFEEEHKDSDDDSSDDEQEKKPEAPKLSKKKLRRMNRFTVAELKQLVARPDVVEMHDV
TAQDPKLLVHLKATRNSVPVPRHWCFKRKYLQGKRGIEKPPFELPDFIKRTGIQEMREAL
QEKEEQKTMKSKMREKVRPKMGKIDIDYQKLHDAFFKWQTKPKLTIHGDLYYEGKEFETR
LKEKKPGDLSDELRISLGMPVGPNAHKVPPPWLIAMQRYGPPPSYPNLKIPGLNSPIPES
CSFGYHAGGWGKPPVDETGKPLYGDVFGTNAAEFQTKTEEEEIDRTPWGELEPSDEESSE
EEEEEESDEDKPDETGFITPADSGLITPGGFSSVPAGMETPELIELRKKKIEEAMDGSET
PQLFTVLPEKRTATVGGAMMGSTHIYDMSTVMSRKGPAPELQGVEVALAPEELELDPMAM
TQKYEEHVREQQAQVEKEDFSDMVAEHAAKQKQKKRKAQPQDSRGGSKKYKEFKF
Sequence of entity 5 (v), FASTA
>6Y50_5 Splicing factor 3B subunit 3 (chains v)
MFLYNLTLQRATGISFAIHGNFSGTKQQEIVVSRGKILELLRPDPNTGKVHTLLTVEVFG
VIRSLMAFRLTGGTKDYIVVGSDSGRIVILEYQPSKNMFEKIHQETFGKSGCRRIVPGQF
LAVDPKGRAVMISAIEKQKLVYILNRDAAARLTISSPLEAHKANTLVYHVVGVDVGFENP
MFACLEMDYEEADNDPTGEAAANTQQTLTFYELDLGLNHVVRKYSEPLEEHGNFLITVPG
GSDGPSGVLICSENYITYKNFGDQPDIRCPIPRRRNDLDDPERGMIFVCSATHKTKSMFF
FLAQTEQGDIFKITLETDEDMVTEIRLKYFDTVPVAAAMCVLKTGFLFVASEFGNHYLYQ
IAHLGDDDEEPEFSSAMPLEEGDTFFFQPRPLKNLVLVDELDSLSPILFCQIADLANEDT
PQLYVACGRGPRSSLRVLRHGLEVSEMAVSELPGNPNAVWTVRRHIEDEFDAYIIVSFVN
ATLVLSIGETVEEVTDSGFLGTTPTLSCSLLGDDALVQVYPDGIRHIRADKRVNEWKTPG
KKTIVKCAVNQRQVVIALTGGELVYFEMDPSGQLNEYTERKEMSADVVCMSLANVPPGEQ
RSRFLAVGLVDNTVRIISLDPSDCLQPLSMQALPAQPESLCIVEMGGTEKQDELGERGSI
GFLYLNIGLQNGVLLRTVLDPVTGDLSDTRTRYLGSRPVKLFRVRMQGQEAVLAMSSRSW
LSYSYQSRFHLTPLSYETLEFASGFASEQCPEGIVAISTNTLRILALEKLGAVFNQVAFP
LQYTPRKFVIHPESNNLIIIETDHNAYTEATKAQRKQQMAEEMVEAAGEDERELAAEMAA
AFLNENLPESIFGAPKAGNGQWASVIRVMNPIQGNTLDLVQLEQNEAAFSVAVCRFSNTG
EDWYVLVGVAKDLILNPRSVAGGFVYTYKLVNNGEKLEFLHKTPVEEVPAAIAPFQGRVL
IGVGKLLRVYDLGKKKLLRKCENKHIANYISGIQTIGHRVIVSDVQESFIWVRYKRNENQ
LIIFADDTYPRWVTTASLLDYDTVAGADKFGNICVVRLPPNTNDEVDEDPTGNKALWDRG
LLNGASQKAEVIMNYHVGETVLSLQKTTLIPGGSESLVYTTLSGGIGILVPFTSHEDHDF
FQHVEMHLRSEHPPLCGRDHLSFRSYYFPVKNVIDGDLCEQFNSMEPNKQKNVSEELDRT
PPEVSKKLEDIRTRYAF
Sequence of entity 6 (u), FASTA
>6Y50_6 Splicing factor 3B subunit 1 (chains u)
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 7 (2), FASTA
>6Y50_7 U2 snRNA (chains 2)
AUCGCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGUAUCUGUUCUUAUCAGUUUAAUAU
CUGAUACGUCCUCUAUCCGAGGACAAUAUAUUAAAUGGAUUUUUGGAGCAGGGAGAUGGA
AUAGGAGCUUGCUCCGUCCACUCCACGCAUCGACCUGGUAUUGCAGUACCUCCAGGAACG
GUGCACCC
Sequence of entity 8 (q), FASTA
>6Y50_8 HIV Tat-specific factor 1 (chains q)
MSGTNLDGNDEFDEQLRMQELYGDGKDGDTQTDAGGEPDSLGQQPTDTPYEWDLDKKAWF
PKITEDFIATYQANYGFSNDGASSSTANVEDVHARTAEEPPQEKAPEPTDARKKGEKRKA
ESGWFHVEEDRNTNVYVSGLPPDITVDEFIQLMSKFGIIMRDPQTEEFKVKLYKDNQGNL
KGDGLCCYLKRESVELALKLLDEDEIRGYKLHVEVAKFQLKGEYDASKKKKKCKDYKKKL
SMQQKQLDWRPERRAGPSRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQ
IRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTDYQVEETSR
EREERLRGWEAFLNAPEANRGLRRSDSVSASERAGPSRARHFSEHPSTSKMNAQETATGM
AFEEPIDEKKFEKTEDGGEFEEGASENNAKESSPEKEAEEGCPEKESEEGCPKRGFEGSC
SQKESEEGNPVRGSEEDSPKKESKKKTLKNDCEENGLAKESEDDLNKESEEEVGPTKESE
EDDSEKESDEDCSEKQSEDGSEREFEENGLEKDLDEEGSEKELHENVLDKELEENDSENS
EFEDDGSEKVLDEEGSEREFDEDSDEKEEEEDTYEKVFDDESDEKEDEEYADEKGLEAAD
KKAEEGDADEKLFEESDDKEDEDADGKEVEDADEKLFEDDDSNEKLFDEEEDSSEKLFDD
SDERGTLGGFGSVEEGPLSTGSSFILSSDDDDDDI
Sequence of entity 9 (p), FASTA
>6Y50_9 Probable ATP-dependent RNA helicase DDX46 (chains p)
MGRESRHYRKRSASRGRSGSRSRSRSPSDKRSKRGDDRRSRSRDRDRRRERSRSRDKRRS
RSRDRKRLRRSRSRERDRSRERRRSRSRDRRRSRSRSRGRRSRSSSPGNKSKKTENRSRS
KEKTDGGESSKEKKKDKDDKEDEKEKDAGNFDQNKLEEEMRKRKERVEKWREEQRKKAME
NIGELKKEIEEMKQGKKWSLEDDDDDEDDPAEAEKEGNEMEGEELDPLDAYMEEVKEEVK
KFNMRSVKGGGGNEKKSGPTVTKVVTVVTTKKAVVDSDKKKGELMENDQDAMEYSSEEEE
VDLQTALTGYQTKQRKLLEPVDHGKIEYEPFRKNFYVEVPELAKMSQEEVNVFRLEMEGI
TVKGKGCPKPIKSWVQCGISMKILNSLKKHGYEKPTPIQTQAIPAIMSGRDLIGIAKTGS
GKTIAFLLPMFRHIMDQRSLEEGEGPIAVIMTPTRELALQITKECKKFSKTLGLRVVCVY
GGTGISEQIAELKRGAEIIVCTPGRMIDMLAANSGRVTNLRRVTYVVLDEADRMFDMGFE
PQVMRIVDNVRPDRQTVMFSATFPRAMEALARRILSKPIEVQVGGRSVVCSDVEQQVIVI
EEEKKFLKLLELLGHYQESGSVIIFVDKQEHADGLLKDLMRASYPCMSLHGGIDQYDRDS
IINDFKNGTCKLLVATSVAARGLDVKHLILVVNYSCPNHYEDYVHRAGRTGRAGNKGYAY
TFITEDQARYAGDIIKALELSGTAVPPDLEKLWSDFKDQQKAEGKIIKKSSGFSGKGFKF
DETEQALANERKKLQKAALGLQDSDDEDAAVDIDEQIESMFNSKKRVKDMAAPGTSSVPA
PTAGNAEKLEIAKRLALRINAQKNLGIESQDVMQQATNAILRGGTILAPTVSAKTIAEQL
AEKINAKLNYVPLEKQEEERQDGGQNESFKRYEEELEINDFPQTARWKVTSKEALQRISE
YSEAAITIRGTYFPPGKEPKEGERKIYLAIESANELAVQKAKAEITRLIKEELIRLQNSY
QPTNKGRYKVL

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn3

Primary citation

Molecular architecture of the human 17S U2 snRNP. Zhang, Z., Will, C.L., Bertram, K. et al. Nature (2020) 583:310-313. DOI 10.1038/s41586-020-2344-3 · PubMed

Other PDB entries of the same protein (UniProt Q12874 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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