6Y53: Human 17S U2 snRNP low resolution part
human 17S U2 snRNP low resolution part. Determined by electron microscopy at 7.1 Å resolution. Released 17 Jun 2020.
- Method
- Electron microscopy
- Resolution
- 7.1 Å
- Organism
- Homo sapiens
- Chains
- 19
- Atoms
- 11,306
- Mol. weight
- 914.91 kDa
- Released
- 17 Jun 2020
Explore 6Y53 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6Y53 contains 77 α-helices and 115 β-strands across 18 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 6: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 161-174 | 14 | |
| α-helix | 186-189 | 4 | |
| α-helix | 205-217 | 13 | |
| α-helix | 221-225 | 5 | |
| α-helix | 236-271 | 36 | |
Chain 7: 2 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 105-108 | 4 | |
| α-helix | 115-117 | 3 | |
| β-strand | 118-121 | 4 | 10 |
| β-strand | 134-137 | 4 | 10 |
| β-strand | 148-153 | 6 | 11 |
| β-strand | 167-172 | 6 | 11 |
| β-strand | 179-183 | 5 | 11 |
| β-strand | 197-200 | 4 | 10 |
| β-strand | 205-208 | 4 | 10 |
Chain 8: 3 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 608 | 1 | 22 |
| α-helix | 611-617 | 7 | |
| α-helix | 619-622 | 4 | |
| α-helix | 633-639 | 7 | |
| β-strand | 648-649 | 2 | 23 |
| β-strand | 651 | 1 | 24 |
| β-strand | 655 | 1 | 24 |
| β-strand | 683 | 1 | 22 |
| β-strand | 686 | 1 | 22 |
| β-strand | 689-690 | 2 | 23 |
Chain 9: 16 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-27 | 22 | |
| α-helix | 33-58 | 26 | |
| α-helix | 64-71 | 8 | |
| α-helix | 78-87 | 10 | |
| α-helix | 103-108 | 6 | |
| α-helix | 126-128 | 3 | |
| α-helix | 143-153 | 11 | |
| α-helix | 160-167 | 8 | |
| α-helix | 182-200 | 19 | |
| α-helix | 206-219 | 14 | |
| α-helix | 221-223 | 3 | |
| β-strand | 227 | 1 | 12 |
| β-strand | 282-283 | 2 | 12 |
| β-strand | 290-291 | 2 | 12 |
| α-helix | 294-301 | 8 | |
| α-helix | 304-307 | 4 | |
| α-helix | 318-333 | 16 | |
| α-helix | 335-350 | 16 | |
| α-helix | 353-361 | 9 | |
Chain a: 7 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-10 | 5 | |
| β-strand | 13-16 | 4 | 1 |
| β-strand | 22-25 | 4 | 1 |
| α-helix | 37-39 | 3 | |
| β-strand | 46-48 | 3 | 1 |
| β-strand | 56-57 | 2 | 2 |
| β-strand | 68-70 | 3 | 1 |
| β-strand | 78-79 | 2 | 2 |
| α-helix | 83-86 | 4 | |
| β-strand | 92-94 | 3 | 1 |
| α-helix | 103-106 | 4 | |
| α-helix | 108-111 | 4 | |
| β-strand | 117-119 | 3 | 1 |
| α-helix | 131-138 | 8 | |
| β-strand | 144-145 | 2 | 1 |
| β-strand | 149 | 1 | 1 |
| α-helix | 152-160 | 9 | |
Chain b: 5 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 11-15 | 5 | 3 |
| α-helix | 23-34 | 12 | |
| β-strand | 40-45 | 6 | 3 |
| β-strand | 55-59 | 5 | 3 |
| α-helix | 62-71 | 10 | |
| β-strand | 76-77 | 2 | 4 |
| β-strand | 80-81 | 2 | 4 |
| β-strand | 83-86 | 4 | 3 |
| α-helix | 92-98 | 7 | |
| β-strand | 152-156 | 5 | 5 |
| α-helix | 164-171 | 8 | |
| β-strand | 177-181 | 5 | 5 |
| β-strand | 189-194 | 6 | 5 |
| α-helix | 197-206 | 10 | |
| β-strand | 219-222 | 4 | 5 |
Chain h: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 20-26 | 7 | |
| α-helix | 29-37 | 9 | |
| β-strand | 41-46 | 6 | 19 |
| β-strand | 51-58 | 8 | 19 |
| β-strand | 65-76 | 12 | 19 |
| β-strand | 90-101 | 12 | 19 |
| β-strand | 106-111 | 6 | 19 |
Chain i: 1 helix, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-13 | 7 | |
| β-strand | 18-23 | 6 | 19 |
| β-strand | 27-36 | 10 | 19 |
| β-strand | 42-51 | 10 | 19 |
| β-strand | 54-64 | 11 | 19 |
| β-strand | 69-74 | 6 | 19 |
10 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| U2 small nuclear ribonucleoprotein A' | a | protein | 255 | Homo sapiens | P09661 (AlphaFold model) |
| U2 small nuclear ribonucleoprotein B'' | b | protein | 225 | Homo sapiens | P08579 (AlphaFold model) |
| Splicing factor 3B subunit 6 | z | protein | 125 | Homo sapiens | Q9Y3B4 (AlphaFold model) |
| Probable ATP-dependent RNA helicase DDX46 | p | protein | 1031 | Homo sapiens | Q7L014 (AlphaFold model) |
| Splicing factor 3A subunit 1 | 6 | protein | 793 | Homo sapiens | Q15459 |
| Splicing factor 3A subunit 2 | 7 | protein | 464 | Homo sapiens | Q15428 |
| Splicing factor 3A subunit 3 | 9 | protein | 501 | Homo sapiens | Q12874 |
| Splicing factor 3B subunit 4 | o | protein | 424 | Homo sapiens | Q15427 |
| Small nuclear ribonucleoprotein-associated proteins B and B' | m | protein | 240 | Homo sapiens | P14678 |
| Small nuclear ribonucleoprotein G | k | protein | 76 | Homo sapiens | P62308 |
| Small nuclear ribonucleoprotein Sm D1 | n | protein | 119 | Homo sapiens | P62314 |
| Small nuclear ribonucleoprotein Sm D2 | h | protein | 118 | Homo sapiens | P62316 |
7 more molecules are not listed.
Sequence of entity 1 (a), FASTA
>6Y53_1 U2 small nuclear ribonucleoprotein A' (chains a)
MVKLTAELIEQAAQYTNAVRDRELDLRGYKIPVIENLGATLDQFDAIDFSDNEIRKLDGF
PLLRRLKTLLVNNNRICRIGEGLDQALPCLTELILTNNSLVELGDLDPLASLKSLTYLSI
LRNPVTNKKHYRLYVIYKVPQVRVLDFQKVKLKERQEAEKMFKGKRGAQLAKDIARRSKT
FNPGAGLPTDKKKGGPSPGDVEAIKNAIANASTLAEVERLKGLLQSGQIPGRERRSGPTD
DGEEEMEEDTVTNGS
Sequence of entity 2 (b), FASTA
>6Y53_2 U2 small nuclear ribonucleoprotein B'' (chains b)
MDIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELG
SSTNALRQLQGFPFYGKPMRIQYAKTDSDIISKMRGTFADKEKKKEKKKAKTVEQTATTT
NKKPGQGTPNSANTQGNSTPNPQVPDYPPNYILFLNNLPEETNEMMLSMLFNQFPGFKEV
RLVPGRHDIAFVEFENDGQAGAARDALQGFKITPSHAMKITYAKK
Sequence of entity 3 (z), FASTA
>6Y53_3 Splicing factor 3B subunit 6 (chains z)
MAMQAAKRANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTA
YVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGIN
TDPPK
Sequence of entity 4 (p), FASTA
>6Y53_4 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
Sequence of entity 5 (6), FASTA
>6Y53_5 Splicing factor 3A subunit 1 (chains 6)
MPAGPVQAVPPPPPVPTEPKQPTEEEASSKEDSAPSKPVVGIIYPPPEVRNIVDKTASFV
ARNGPEFEARIRQNEINNPKFNFLNPNDPYHAYYRHKVSEFKEGKAQEPSAAIPKVMQQQ
QQTTQQQLPQKVQAQVIQETIVPKEPPPEFEFIADPPSISAFDLDVVKLTAQFVARNGRQ
FLTQLMQKEQRNYQFDFLRPQHSLFNYFTKLVEQYTKILIPPKGLFSKLKKEAENPREVL
DQVCYRVEWAKFQERERKKEEEEKEKERVAYAQIDWHDFVVVETVDFQPNEQGNFPPPTT
PEELGARILIQERYEKFGESEEVEMEVESDEEDDKQEKAEEPPSQLDQDTQVQDMDEGSD
DEEEGQKVPPPPETPMPPPLPPTPDQVIVRKDYDPKASKPLPPAPAPDEYLVSPITGEKI
PASKMQEHMRIGLLDPRWLEQRDRSIREKQSDDEVYAPGLDIESSLKQLAERRTDIFGVE
ETAIGKKIGEEEIQKPEEKVTWDGHSGSMARTQQAAQANITLQEQIEAIHKAKGLVPEDD
TKEKIGPSKPNEIPQQPPPPSSATNIPSSAPPITSVPRPPTMPPPVRTTVVSAVPVMPRP
PMASVVRLPPGSVIAPMPPIIHAPRINVVPMPPSAPPIMAPRPPPMIVPTAFVPAPPVAP
VPAPAPMPPVHPPPPMEDEPTSKKLKTEDSLMPEEEFLRRNKGPVSIKVQVPNMQDKTEW
KLNGQVLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMANGAV
IHLALKERGGRKK
Sequence of entity 6 (7), FASTA
>6Y53_6 Splicing factor 3A subunit 2 (chains 7)
MDFQHRPGGKTGSGGVASSSESNRDRRERLRQLALETIDINKDPYFMKNHLGSYECKLCL
TLHNNEGSYLAHTQGKKHQTNLARRAAKEAKEAPAQPAPEKVKVEVKKFVKIGRPGYKVT
KQRDSEMGQQSLLFQIDYPEIAEGIMPRHRFMSAYEQRIEPPDRRWQYLLMAAEPYETIA
FKVPSREIDKAEGKFWTHWNRETKQFFLQFHFKMEKPPAPPSLPAGPPGVKRPPPPLMNG
LPPRPPLPESLPPPPPGGLPLPPMPPTGPAPSGPPGPPQLPPPAPGVHPPAPVVHPPASG
VHPPAPGVHPPAPGVHPPAPGVHPPTSGVHPPAPGVHPPAPGVHPPAPGVHPPAPGVHPP
APGVHPPPSAGVHPQAPGVHPAAPAVHPQAPGVHPPAPGMHPQAPGVHPQPPGVHPSAPG
VHPQPPGVHPSNPGVHPPTPMPPMLRPPLPSEGPGNIPPPPPTN
Sequence of entity 7 (9), FASTA
>6Y53_7 Splicing factor 3A subunit 3 (chains 9)
METILEQQRRYHEEKERLMDVMAKEMLTKKSTLRDQINSDHRTRAMQDRYMEVSGNLRDL
YDDKDGLRKEELNAISGPNEFAEFYNRLKQIKEFHRKHPNEICVPMSVEFEELLKARENP
SEEAQNLVEFTDEEGYGRYLDLHDCYLKYINLKASEKLDYITYLSIFDQLFDIPKERKNA
EYKRYLEMLLEYLQDYTDRVKPLQDQNELFGKIQAEFEKKWENGTFPGWPKETSSALTHA
GAHLDLSAFSSWEELASLGLDRLKSALLALGLKCGGTLEERAQRLFSTKGKSLESLDTSL
FAKNPKSKGTKRDTERNKDIAFLEAQIYEYVEILGEQRHLTHENVQRKQARTGEEREEEE
EEQISESESEDEENEIIYNPKNLPLGWDGKPIPYWLYKLHGLNINYNCEICGNYTYRGPK
AFQRHFAEWRHAHGMRCLGIPNTAHFANVTQIEDAVSLWAKLKLQKASERWQPDTEEEYE
DSSGNVVNKKTYEDLKRQGLL
Sequence of entity 8 (o), FASTA
>6Y53_8 Splicing factor 3B subunit 4 (chains o)
MAAGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVE
FLSEEDADYAIKIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTF
SAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKK
DSKGERHGSAAERLLAAQNPLSQADRPHQLFADAPPPPSAPNPVVSSLGSGLPPPGMPPP
GSFPPPVPPPGALPPGIPPAMPPPPMPPGAAGHGPPSAGTPGAGHPGHGHSHPHPFPPGG
MPHPGMSQMQLAHHGPHGLGHPHAGPPGSGGQPPPRPPPGMPHPGPPPMGMPPRGPPFGS
PMGHPGPMPPHGMRGPPPLMPPHGYTGPPRPPPYGYQRGPLPPPRPTPRPPVPPRGPLRG
PLPQ
Sequence of entity 9 (m), FASTA
>6Y53_9 Small nuclear ribonucleoprotein-associated proteins B and B' (chains m)
MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAE
REEKRVLGLVLLRGENLVSMTVEGPPPKDTGIARVPLAGAAGGPGIGRAAGRGIPAGVPM
PQAPAGLAGPVRGVGGPSQQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMG
RGAPPPGMMGPPPGMRPPMGPPMGIPPGRGTPMGMPPPGMRPPPPGMRGPPPPGMRPPRP
Sequence of entity 10 (k), FASTA
>6Y53_10 Small nuclear ribonucleoprotein G (chains k)
MSKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMV
VIRGNSIIMLEALERV
Sequence of entity 11 (n), FASTA
>6Y53_11 Small nuclear ribonucleoprotein Sm D1 (chains n)
MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSI
RGNNIRYFILPDSLPLDTLLVDVEPKVKSKKREAVAGRGRGRGRGRGRGRGRGRGGPRR
Sequence of entity 12 (h), FASTA
>6Y53_12 Small nuclear ribonucleoprotein Sm D2 (chains h)
MSLLNKPKSEMTPEELQKREEEEFNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFD
RHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVIVVLRNPLIAGK
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 P09661 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 1A9N 2.38 Å, Crystal structure of the spliceosomal U2B''-U2A' protein complex bound to a fragment of…
- 7EVO 2.5 Å, The cryo-EM structure of the human 17S U2 snRNP
- 8H6L 2.6 Å, Cryo-EM structure of human exon-defined spliceosome in the early B state.
- 8H6K 2.7 Å, Cryo-EM structure of human exon-defined spliceosome in the mature B state.
- 8HK1 2.7 Å, The cryo-EM structure of human pre-17S U2 snRNP
- 8C6J 2.8 Å, Human spliceosomal PM5 C* complex
- 6ID1 2.86 Å, Cryo-EM structure of a human intron lariat spliceosome after Prp43 loaded (ILS2 complex)…
- 6ID0 2.9 Å, Cryo-EM structure of a human intron lariat spliceosome prior to Prp43 loaded (ILS1…
- 6ICZ 3.0 Å, Cryo-EM structure of a human post-catalytic spliceosome (P complex) at 3.0 angstrom
- 7VPX 3.0 Å, The cryo-EM structure of the human pre-A complex
- 8I0R 3.0 Å, The cryo-EM structure of human Bact-I complex
- 8I0T 3.0 Å, The cryo-EM structure of human Bact-III complex
Browse structure collections
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