2024-05-15 REL PDBe RCSB PDBe 2015-12-15 2016-01-27 2016-01-27 2024-05-15 Medical Research Council (United Kingdom) United Kingdom Head region of the yeast spliceosomal U4/U6.U5 tri-snRNP Nguyen THD Galej WP Transcription, pre-mRNA splicing, snRNP, GTPase, spliceosome Nguyen TH Galej WP Bai XC Oubridge C Newman AJ Scheres SH Nagai K Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 angstrom resolution. Nature UK 530 298 302 2016 26829225 doi:10.1038/nature16940 1476-4687 0006 NATUAS Nguyen THD Galej W Bai XC Savva CG Newman AJ Scheres SHW Nagai K The architecture of the spliceosomal U4/U6.U5 tri-snRNP. Nature UK 523 47 52 2015 26106855 doi:10.1038/nature14548 1476-4687 0006 NATUAS 5gao FULLOVERLAP Head region of the yeast spliceosomal U4/U6.U5 tri-snRNP Head region of the yeast spliceosomal U4/U6.U5 tri-snRNP 0 1 2 3 4 5 6 7 8 9 10 11 Saccharomyces cerevisiae BCY123 0.40 Small nuclear ribonucleoprotein-associated protein B Saccharomyces cerevisiae BCY123 0.02242699
The SmB protein from the U4 snRNP Sm protein ring. The C-terminus is disordered in this and other previously reported structures.
1 LEVO MSKIQVAHSSRLANLIDYKLRVLTQDGRVYIGQLMAFDKHMNLVLNECIEERVPKTQLDKLRPRKDSKDGTTLNIKVEKR VLGLTILRGEQILSTVVEDKPLLSKKERLVRDKKEKKQAQKQTKLRKEKEKKPGKIAKPNTANAKHTSSNSREIAQPSSS RYNGGNDNIGANRSRFNNEAPPQTRKFQPPPGFKRK P40018 Small nuclear ribonucleoprotein Sm D1 Saccharomyces cerevisiae BCY123 0.016296798
The SmD1 protein from the U4 snRNP Sm protein ring.
1 LEVO MKLVNFLKKLRNEQVTIELKNGTTVWGTLQSVSPQMNAILTDVKLTLPQPRLNKLNSNGIAMASLYLTGGQQPTASDNIA SLQYINIRGNTIRQIILPDSLNLDSLLVDQKQLNSLRRSGQIANDPSKKRRRDFGAPANKRPRRGL Q02260 Small nuclear ribonucleoprotein Sm D2 Saccharomyces cerevisiae BCY123 0.012876066
The SmD2 protein from the U4 snRNP Sm protein ring.
1 LEVO MSSQIIDRPKHELSRAELEELEEFEFKHGPMSLINDAMVTRTPVIISLRNNHKIIARVKAFDRHCNMVLENVKELWTEKK GKNVINRERFISKLFLRGDSVIVVLKTPVE Q06217 Small nuclear ribonucleoprotein Sm D3 Saccharomyces cerevisiae BCY123 0.011240138999999998
The SmD3 protein from the U4 snRNP Sm protein ring.
1 LEVO MTMNGIPVKLLNEAQGHIVSLELTTGATYRGKLVESEDSMNVQLRDVIATEPQGAVTHMDQIFVRGSQIKFIVVPDLLKN APLFKKNSSRPMPPIRGPKRR P43321 Small nuclear ribonucleoprotein E Saccharomyces cerevisiae BCY123 0.010385097999999999
The SmE protein from the U4 snRNP Sm protein ring.
1 LEVO MSNKVKTKAMVPPINCIFNFLQQQTPVTIWLFEQIGIRIKGKIVGFDEFMNVVIDEAVEIPVNSADGKEDVEKGTPLGKI LLKGDNITLITSAD Q12330 Small nuclear ribonucleoprotein F Saccharomyces cerevisiae BCY123 0.009669945
The SmF protein from the U4 snRNP Sm protein ring.
1 LEVO MSESSDISAMQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLY IRELPN P54999 Small nuclear ribonucleoprotein G Saccharomyces cerevisiae BCY123 0.008490808999999998
The SmG protein from the U4 snRNP Sm protein ring.
1 LEVO MVSTPELKKYMDKKILLNINGSRKVAGILRGYDIFLNVVLDDAMEINGEDPANNHQLGLQTVIRGNSIISLEALDAI P40204 Snu66 Saccharomyces cerevisiae BCY123 0.025078721
NB: Snu66 protein has been mostly fitted as poly(Ala) into helices and extended polypeptide within the EM map. The authors do not believe the numbering to be accurate and it is likely incorrect.
1 LEVO AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAARAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTK EAYKKLSQKFHGTKSNKK Pre-mRNA-splicing helicase BRR2 Saccharomyces cerevisiae BCY123 0.246470266
Brr2 RNA helicase loaded onto U4 snRNA strand of the U4/U6 duplex between Stem 1 duplex and the 3' stem loop.
1 LEVO MTEHETKDKAKKIREIYRYDEMSNKVLKVDKRFMNTSQNPQRDAEISQPKSMSGRISAKDMGQGLCNNINKGLKENDVAV EKTGKSASLKKIQQHNTILNSSSDFRLHYYPKDPSNVETYEQILQWVTEVLGNDIPHDLIIGTADIFIRQLKENEENEDG NIEERKEKIQHELGINIDSLKFNELVKLMKNITDYETHPDNSNKQAVAILADDEKSDEEEVTEMSNNANVLGGEINDNED DDEEYDYNDVEVNSKKKNKRALPNIENDIIKLSDSKTSNIESVPIYSIDEFFLQRKLRSELGYKDTSVIQDLSEKILNDI ETLEHNPVALEQKLVDLLKFENISLAEFILKNRSTIFWGIRLAKSTENEIPNLIEKMVAKGLNDLVEQYKFRETTHSKRE LDSGDDQPQSSEAKRTKFSNPAIPPVIDLEKIKFDESSKLMTVTKVSLPEGSFKRVKPQYDEIHIPAPSKPVIDYELKEI TSLPDWCQEAFPSSETTSLNPIQSKVFHAAFEGDSNMLICAPTGSGKTNIALLTVLKALSHHYNPKTKKLNLSAFKIVYI APLKALVQEQVREFQRRLAFLGIKVAELTGDSRLSRKQIDETQVLVSTPEKWDITTRNSNNLAIVELVRLLIIDEIHLLH DDRGPVLESIVARTFWASKYGQEYPRIIGLSATLPNYEDVGRFLRVPKEGLFYFDSSFRPCPLSQQFCGIKERNSLKKLK AMNDACYEKVLESINEGNQIIVFVHSRKETSRTATWLKNKFAEENITHKLTKNDAGSKQILKTEAANVLDPSLRKLIESG IGTHHAGLTRSDRSLSEDLFADGLLQVLVCTATLAWGVNLPAHTVIIKGTDVYSPEKGSWEQLSPQDVLQMLGRAGRPRY DTFGEGIIITDQSNVQYYLSVLNQQLPIESQFVSKLVDNLNAEVVAGNIKCRNDAVNWLAYTYLYVRMLASPMLYKVPDI SSDGQLKKFRESLVHSALCILKEQELVLYDAENDVIEATDLGNIASSFYINHASMDVYNRELDEHTTQIDLFRIFSMSEE FKYVSVRYEEKRELKQLLEKAPIPIREDIDDPLAKVNVLLQSYFSQLKFEGFALNSDIVFIHQNAGRLLRAMFEICLKRG WGHPTRMLLNLCKSATTKMWPTNCPLRQFKTCPVEVIKRLEASTVPWGDYLQLETPAEVGRAIRSEKYGKQVYDLLKRFP KMSVTCNAQPITRSVMRFNIEIIADWIWDMNVHGSLEPFLLMLEDTDGDSILYYDVLFITPDIVGHEFTLSFTYELKQHN QNNLPPNFFLTLISENWWHSEFEIPVSFNGFKLPKKFPPPTPLLENISISTSELGNDDFSEVFEFKTFNKIQSQVFESLY NSNDSVFVGSGKGTGKTAMAELALLNHWRQNKGRAVYINPSGEKIDFLLSDWNKRFSHLAGGKIINKLGNDPSLNLKLLA KSHVLLATPVQFELLSRRWRQRKNIQSLELMIYDDAHEISQGVYGAVYETLISRMIFIATQLEKKIRFVCLSNCLANARD FGEWAGMTKSNIYNFSPSERIEPLEINIQSFKDVEHISFNFSMLQMAFEASAAAAGNRNSSSVFLPSRKDCMEVASAFMK FSKAIEWDMLNVEEEQIVPYIEKLTDGHLRAPLKHGVGILYKGMASNDERIVKRLYEYGAVSVLLISKDCSAFACKTDEV IILGTNLYDGAEHKYMPYTINELLEMVGLASGNDSMAGKVLILTSHNMKAYYKKFLIEPLPTESYLQYIIHDTLNNEIAN SIIQSKQDCVDWFTYSYFYRRIHVNPSYYGVRDTSPHGISVFLSNLVETCLNDLVESSFIEIDDTEAEVTAEVNGGDDEA TEIISTLSNGLIASHYGVSFFTIQSFVSSLSNTSTLKNMLYVLSTAVEFESVPLRKGDRALLVKLSKRLPLRFPEHTSSG SVSFKVFLLLQAYFSRLELPVDFQNDLKDILEKVVPLINVVVDILSANGYLNATTAMDLAQMLIQGVWDVDNPLRQIPHF NNKILEKCKEINVETVYDIMALEDEERDEILTLTDSQLAQVAAFVNNYPNVELTYSLNNSDSLISGVKQKITIQLTRDVE PENLQVTSEKYPFDKLESWWLVLGEVSKKELYAIKKVTLNKETQQYELEFDTPTSGKHNLTIWCVCDSYLDADKELSFEI NVK P32639 3.6.4.13 Saccharomyces cerevisiae strain UOA_M2 chromosome 5 sequence Saccharomyces cerevisiae BCY123 0.030615993999999997
This U4 snRNA region has a disordered region between stem 1 of the U4/U6 snRNA duplex and where the RNA is loaded into Brr2 protein. The apical part of the 3' stem loop and the region following the Sm site are also disordered.
1 GAAAUUUAAUUAUAAACCAGACCGUCUCCUCAUGGUCAAUUCGGUGUUCGCUUUUGAAUACUUCAAGACUAUGUAGGGAA UUUUUGGAAUACCUUU CP011083.1 Pre-mRNA-splicing factor 8 Saccharomyces cerevisiae BCY123 0.030231008
Prp8 Jab1/MPN domain is connected to the rest of the Prp8 protein by a flexible linker peptide.
1 LEVO SSKNEWRKSAIANTLLYLRLKNIYVSADDFVEEQNVYVLPKNLLKKFIEISDVKIQVAAFIYGMSAKDHPKVKEIKTVVL VPQLGHVGSVQISNIPDIGDLPDTEGLELLGWIHTQTEELKFMAASEVATHSKLFADKKRDCIDISIFSTPGSVSLSAYN LTDEGYQWGEENKDIMNVLSEGFEPTFSTHAQLLLSDRITGNFIIPSGNVWNYTFMGTAFNQEGDYNFKYGIPLEFYNEM HRPVHFLQFSELAGDEELEAEQIDVFS P33334 singleParticle particle 0.2 7.9 1.0 DTT Quantifoil R1.2/1.3 COPPER 400 CARBON CONTINUOUS 6.0 GLOW DISCHARGE OTHER
Grids are made of holey carbon, carbon-coated and glow discharged in N-amylamine.
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.0 0.5 3.5 81000.0 35714.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Quantum GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 1-20 2477 16.0 38.0 1 473827 EMD-2966
Startup model was 60 Angstrom low-pass filtered.
 1 4.2 FSC 0.143 CUT-OFF RELION 140155 OTHER RELION OTHER RELION emd_8013.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 380 380 380 0 0 0 380 380 380 543.39996 543.39996 543.39996 90.0 90.0 90.0 X Y Z -0.07287737 0.15714578 -0.00023307164 0.003403494 1.43 1.43 1.43 0.02 AUTHOR Head Region of yeast spliceosomal U4/U6.U5 tri-snRNP. 4BGD B 442-2163 PDB experimental model 4BGD A 2143-2396 PDB experimental model OTHER RECIPROCAL