6QW6: Human U5.U4/U6 tri-snRNP
Structure of the human U5.U4/U6 tri-snRNP at 2.9A resolution. Determined by electron microscopy at 2.92 Å resolution. Released 17 Apr 2019.
- Method
- Electron microscopy
- Resolution
- 2.92 Å
- Organism
- Homo sapiens
- Chains
- 39
- Atoms
- 89,236
- Mol. weight
- 1683.43 kDa
- Ligands
- IHP, MG, GTP, ZN
- Released
- 17 Apr 2019
Explore 6QW6 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6QW6 contains 475 α-helices and 448 β-strands across 36 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.
Chains 41 and 51: 3 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-8 | 5 | |
| β-strand | 14-19 | 6 | 1 |
| β-strand | 24-31 | 8 | 1 |
| β-strand | 38-46 | 9 | 1 |
| β-strand | 53-60 | 8 | 1 |
| α-helix | 62-64 | 3 | |
| β-strand | 65-70 | 6 | 1 |
| α-helix | 76-78 | 3 | |
Chain 42: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 23-25 | 3 | |
| α-helix | 30-33 | 4 | |
| β-strand | 41-46 | 6 | 1 |
| β-strand | 51-59 | 9 | 1 |
| β-strand | 65-76 | 12 | 1 |
| β-strand | 90-101 | 12 | 1 |
| β-strand | 106-111 | 6 | 1 |
Chain 43: 1 helix, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-11 | 7 | |
| β-strand | 17-22 | 6 | 1 |
| β-strand | 27-35 | 9 | 1 |
| β-strand | 41-49 | 9 | 1 |
| β-strand | 55-63 | 9 | 1 |
| β-strand | 68-73 | 6 | 1 |
Chain 4A: 9 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 389-394 | 6 | |
| β-strand | 417-420 | 4 | 5 |
| α-helix | 442-466 | 25 | |
| α-helix | 494-516 | 23 | |
| α-helix | 524-533 | 10 | |
| β-strand | 541-548 | 8 | 6 |
| α-helix | 554-566 | 13 | |
| β-strand | 570-574 | 5 | 6 |
| β-strand | 575 | 1 | 7 |
| β-strand | 580-586 | 7 | 6 |
| α-helix | 588-596 | 9 | |
| α-helix | 597-601 | 5 | |
| β-strand | 630-638 | 9 | 6 |
| β-strand | 647 | 1 | 6 |
| β-strand | 650 | 1 | 7 |
| α-helix | 654-663 | 10 | |
| α-helix | 667-682 | 16 | |
Chain 4b: 2 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-12 | 3 | |
| β-strand | 15-21 | 7 | 1 |
| β-strand | 26-33 | 8 | 1 |
| β-strand | 40-48 | 9 | 1 |
| β-strand | 64-72 | 9 | 1 |
| α-helix | 74-76 | 3 | |
| β-strand | 77-79 | 3 | 1 |
| β-strand | 82-84 | 3 | 1 |
Chain 4B: 3 helices, 36 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 166-169 | 4 | 5 |
| α-helix | 172-201 | 30 | |
| α-helix | 204-218 | 15 | |
| β-strand | 221-228 | 8 | 8 |
| β-strand | 234-239 | 6 | 9 |
| α-helix | 240 | 1 | |
| β-strand | 245-250 | 6 | 9 |
| β-strand | 255 | 1 | 10 |
| β-strand | 257-259 | 3 | 9 |
| β-strand | 264-265 | 2 | 9 |
| β-strand | 269 | 1 | 10 |
| β-strand | 276-281 | 6 | 11 |
| β-strand | 296-300 | 5 | 11 |
| β-strand | 305-308 | 4 | 11 |
| β-strand | 318-319 | 2 | 11 |
| β-strand | 328-331 | 4 | 12 |
| β-strand | 337-341 | 5 | 12 |
| β-strand | 346-351 | 6 | 12 |
| β-strand | 356-362 | 7 | 12 |
| β-strand | 368 | 1 | 13 |
| β-strand | 372-373 | 2 | 14 |
| β-strand | 379-381 | 3 | 14 |
| β-strand | 384 | 1 | 13 |
| β-strand | 389 | 1 | 15 |
| β-strand | 391-393 | 3 | 14 |
| β-strand | 397-399 | 3 | 14 |
| β-strand | 403 | 1 | 15 |
| β-strand | 410-412 | 3 | 16 |
| β-strand | 415 | 1 | 16 |
| β-strand | 422-426 | 5 | 16 |
| β-strand | 431-434 | 4 | 16 |
| β-strand | 441-443 | 3 | 16 |
| β-strand | 455-457 | 3 | 17 |
| β-strand | 464-467 | 4 | 17 |
| β-strand | 475-478 | 4 | 17 |
| β-strand | 484-487 | 4 | 17 |
| β-strand | 498-500 | 3 | 8 |
| β-strand | 506-510 | 5 | 8 |
| β-strand | 515-521 | 7 | 8 |
Chain 4C: 18 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 60-72 | 13 | |
| α-helix | 91-118 | 28 | |
| α-helix | 125-128 | 4 | |
| α-helix | 132-141 | 10 | |
| α-helix | 146-149 | 4 | |
| α-helix | 153-156 | 4 | |
| α-helix | 161-172 | 12 | |
| α-helix | 181-215 | 35 | |
| α-helix | 217-222 | 6 | |
| α-helix | 225-235 | 11 | |
| α-helix | 238-241 | 4 | |
| α-helix | 246-249 | 4 | |
| α-helix | 267-268 | 2 | |
| α-helix | 285-287 | 3 | |
| α-helix | 288-305 | 18 | |
| α-helix | 315-331 | 17 | |
| α-helix | 342-345 | 4 | |
| α-helix | 358-366 | 9 | |
| β-strand | 377 | 1 | 18 |
Chain 4D: 5 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 13 | 1 | 19 |
| α-helix | 16-31 | 16 | |
| β-strand | 35-37 | 3 | 19 |
| α-helix | 39-47 | 9 | |
| β-strand | 51-57 | 7 | 19 |
| α-helix | 64-75 | 12 | |
| β-strand | 80-83 | 4 | 19 |
| α-helix | 86-91 | 6 | |
| β-strand | 101-105 | 5 | 19 |
| α-helix | 113-123 | 11 | |
26 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 |
|---|
| U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein | X | protein | 155 | Homo sapiens | Q8WVK2 (AlphaFold model) |
| U4 snRNA | 4 | RNA | 146 | Homo sapiens | |
| Small nuclear ribonucleoprotein Sm D1 | 41, 51 | protein | 119 | Homo sapiens | P62314 (AlphaFold model) |
| Small nuclear ribonucleoprotein Sm D2 | 42, 52 | protein | 118 | Homo sapiens | P62316 (AlphaFold model) |
| Small nuclear ribonucleoprotein Sm D3 | 43, 53 | protein | 126 | Homo sapiens | P62318 (AlphaFold model) |
| U4/U6 small nuclear ribonucleoprotein Prp3 | 4A | protein | 683 | Homo sapiens | O43395 |
| U4/U6 small nuclear ribonucleoprotein Prp4 | 4B | protein | 522 | Homo sapiens | O43172 |
| U4/U6 small nuclear ribonucleoprotein Prp31 | 4C | protein | 499 | Homo sapiens | Q8WWY3 |
| NHP2-like protein 1 | 4D | protein | 128 | Homo sapiens | P55769 |
| Small nuclear ribonucleoprotein-associated proteins B and B' | 4b, 5b | protein | 240 | Homo sapiens | P14678 |
| Small nuclear ribonucleoprotein E | 4e, 5e | protein | 92 | Homo sapiens | P62304 |
| Small nuclear ribonucleoprotein F | 4f, 5f | protein | 86 | Homo sapiens | P62306 |
20 more molecules are not listed.
Sequence of entity 1 (X), FASTA
>6QW6_1 U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein (chains X)
MGRSRSRSPRRERRRSRSTSRERERRRRERSRSRERDRRRSRSRSPHRRRSRSPRRHRST
SPSPSRLKERRDEEKKETKETKSKERQITEEDLEGKTEEEIEMMKLMGFASFDSTKGKKV
DGSVNAYAINVSQKRKYRQYMNRKGGFNRPLDFIA
Sequence of entity 2 (4), FASTA
>6QW6_2 U4 snRNA (chains 4)
XAGCUUUGCGCAGUGGCAGUAUCGUAGCCAAUGAGGUUUAUCCGAGGCGCGAUUAUUGCU
AAUUGAAAACUUUUCCCAAUACCCCGCCGUGACGACUUGCAAUAUAGUCGGCAUUGGCAA
UUUUUGACAGUCUCUACGGAGACUGG
Sequence of entity 3 (41, 51), FASTA
>6QW6_3 Small nuclear ribonucleoprotein Sm D1 (chains 41, 51)
MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSI
RGNNIRYFILPDSLPLDTLLVDVEPKVKSKKREAVAGRGRGRGRGRGRGRGRGRGGPRR
Sequence of entity 4 (42, 52), FASTA
>6QW6_4 Small nuclear ribonucleoprotein Sm D2 (chains 42, 52)
MSLLNKPKSEMTPEELQKREEEEFNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFD
RHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVIVVLRNPLIAGK
Sequence of entity 5 (43, 53), FASTA
>6QW6_5 Small nuclear ribonucleoprotein Sm D3 (chains 43, 53)
MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQ
VYIRGSKIRFLILPDMLKNAPMLKSMKNKNQGSGAGRGKAAILKAQVAARGRGRGMGRGN
IFQKRR
Sequence of entity 6 (4A), FASTA
>6QW6_6 U4/U6 small nuclear ribonucleoprotein Prp3 (chains 4A)
MALSKRELDELKPWIEKTVKRVLGFSEPTVVTAALNCVGKGMDKKKAADHLKPFLDDSTL
RFVDKLFEAVEEGRSSRHSKSSSDRSRKRELKEVFGDDSEISKESSGVKKRRIPRFEEVE
EEPEVIPGPPSESPGMLTKLQIKQMMEAATRQIEERKKQLSFISPPTPQPKTPSSSQPER
LPIGNTIQPSQAATFMNDAIEKARKAAELQARIQAQLALKPGLIGNANMVGLANLHAMGI
APPKVELKDQTKPTPLILDEQGRTVDATGKEIELTHRMPTLKANIRAVKREQFKQQLKEK
PSEDMESNTFFDPRVSIAPSQRQRRTFKFHDKGKFEKIAQRLRTKAQLEKLQAEISQAAR
KTGIHTSTRLALIAPKKELKEGDIPEIEWWDSYIIPNGFDLTEENPKREDYFGITNLVEH
PAQLNPPVDNDTPVTLGVYLTKKEQKKLRRQTRREAQKELQEKVRLGLMPPPEPKVRISN
LMRVLGTEAVQDPTKVEAHVRAQMAKRQKAHEEANAARKLTAEQRKVKKIKKLKEDISQG
VHISVYRVRNLSNPAKKFKIEANAGQLYLTGVVVLHKDVNVVVVEGGPKAQKKFKRLMLH
RIKWDEQTSNTKGDDDEESDEEAVKKTNKCVLVWEGTAKDRSFGEMKFKQCPTENMAREH
FKKHGAEHYWDLALSESVLESTD
Sequence of entity 7 (4B), FASTA
>6QW6_7 U4/U6 small nuclear ribonucleoprotein Prp4 (chains 4B)
MASSRASSTQATKTKAPDDLVAPVVKKPHIYYGSLEEKERERLAKGESGILGKDGLKAGI
EAGNINITSGEVFEIEEHISERQAEVLAEFERRKRARQINVSTDDSEVKACLRALGEPIT
LFGEGPAERRERLRNILSVVGTDALKKTKKDDEKSKKSKEEYQQTWYHEGPNSLKVARLW
IANYSLPRAMKRLEEARLHKEIPETTRTSQMQELHKSLRSLNNFCSQIGDDRPISYCHFS
PNSKMLATACWSGLCKLWSVPDCNLLHTLRGHNTNVGAIVFHPKSTVSLDPKDVNLASCA
ADGSVKLWSLDSDEPVADIEGHTVRVARVMWHPSGRFLGTTCYDRSWRLWDLEAQEEILH
QEGHSMGVYDIAFHQDGSLAGTGGLDAFGRVWDLRTGRCIMFLEGHLKEIYGINFSPNGY
HIATGSGDNTCKVWDLRQRRCVYTIPAHQNLVTGVKFEPIHGNFLLTGAYDNTAKIWTHP
GWSPLKTLAGHEGKVMGLDISSDGQLIATCSYDRTFKLWMAE
Sequence of entity 8 (4C), FASTA
>6QW6_8 U4/U6 small nuclear ribonucleoprotein Prp31 (chains 4C)
MSLADELLADLEEAAEEEEGGSYGEEEEEPAIEDVQEETQLDLSGDSVKTIAKLWDSKMF
AEIMMKIEEYISKQAKASEVMGPVEAAPEYRVIVDANNLTVEIENELNIIHKFIRDKYSK
RFPELESLVPNALDYIRTVKELGNSLDKCKNNENLQQILTNATIMVVSVTASTTQGQQLS
EEELERLEEACDMALELNASKHRIYEYVESRMSFIAPNLSIIIGASTAAKIMGVAGGLTN
LSKMPACNIMLLGAQRKTLSGFSSTSVLPHTGYIYHSDIVQSLPPDLRRKAARLVAAKCT
LAARVDSFHESTEGKVGYELKDEIERKFDKWQEPPPVKQVKPLPAPLDGQRKKRGGRRYR
KMKERLGLTEIRKQANRMSFGEIEEDAYQEDLGFSLGHLGKSGSGRVRQTQVNEATKARI
SKTLQRTLQKQSVVYGGKSTIRDRSSGTASSVAFTPLQGLEIVNPQAAEKKVAEANQKYF
SSMAEFLKVKGEKSGLMST
Sequence of entity 9 (4D), FASTA
>6QW6_9 NHP2-like protein 1 (chains 4D)
MTEADVNPKAYPLADAHLTKKLLDLVQQSCNYKQLRKGANEATKTLNRGISEFIVMAADA
EPLEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSRPVIACSVTIKEGSQLKQQIQSIQ
QSIERLLV
Sequence of entity 10 (4b, 5b), FASTA
>6QW6_10 Small nuclear ribonucleoprotein-associated proteins B and B' (chains 4b, 5b)
MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAE
REEKRVLGLVLLRGENLVSMTVEGPPPKDTGIARVPLAGAAGGPGIGRAAGRGIPAGVPM
PQAPAGLAGPVRGVGGPSQQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMG
RGAPPPGMMGPPPGMRPPMGPPMGIPPGRGTPMGMPPPGMRPPPPGMRGPPPPGMRPPRP
Sequence of entity 11 (4e, 5e), FASTA
>6QW6_11 Small nuclear ribonucleoprotein E (chains 4e, 5e)
MAYRGQGQKVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDD
AEEIHSKTKSRKQLGRIMLKGDNITLLQSVSN
Sequence of entity 12 (4f, 5f), FASTA
>6QW6_12 Small nuclear ribonucleoprotein F (chains 4f, 5f)
MSLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLG
EVLIRCNNVLYIRGVEEEEEDGEMRE
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| IHP | Inositol hexakisphosphate | C6 H18 O24 P6 | 1 |
| MG | Magnesium ion | Mg | 1 |
| GTP | Guanosine-5'-triphosphate | C10 H16 N5 O14 P3 | 1 |
| ZN | Zinc ion | Zn | 1 |
Primary citation
Mechanism of 5' splice site transfer for human spliceosome activation. Charenton, C., Wilkinson, M.E., Nagai, K. Science (2019) 364:362-367. DOI 10.1126/science.aax3289 · PubMed
Other PDB entries of the same protein (UniProt Q8WVK2 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8H6E 3.2 Å, Cryo-EM structure of human exon-defined spliceosome in the late pre-B state.
- 8H6J 3.25 Å, Cryo-EM structure of human exon-defined spliceosome in the mature pre-B state.
- 6QX9 3.28 Å, Structure of a human fully-assembled precatalytic spliceosome (pre-B complex).
- 8QP8 3.5 Å, Cryo-EM Structure of Pre-B Complex (core part)
- 8QP9 4.1 Å, Cryo-EM Structure of Pre-B+AMPPNP Complex (core part)
- 8QPK 4.2 Å, Cryo-EM Structure of Pre-B+5'ss Complex (core part)
- 8R0A 5.8 Å, Cryo-EM structure of the cross-exon pre-B+5'ss complex
- 8R08 6.1 Å, Cryo-EM structure of the cross-exon pre-B+AMPPNP complex
- 8QXD 9.6 Å, Cryo-EM structure of the cross-exon pre-B complex
Browse structure collections
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