8H6J: U6 snRNA-associated Sm-like protein LSm2

Cryo-EM structure of human exon-defined spliceosome in the mature pre-B state. Determined by electron microscopy at 3.25 Å resolution. Released 1 May 2024.

Method: Electron microscopy
Resolution: 3.25 Å
Organism: Homo sapiens
Chains: 61
Atoms: 96,473
Mol. weight: 2735.96 kDa
Ligands: IHP, MG, GTP, ZN
Released: 1 May 2024

Explore 8H6J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8H6J contains 652 α-helices and 637 β-strands across 55 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 2a and 5a: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
β-strand	16-21	6	13
β-strand	26-33	8	13
β-strand	40-48	9	13
β-strand	64-72	9	13
α-helix	74-76	3
β-strand	77-84	8	13
α-helix	85-87	3

Chains 2b and 5b: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	3-8	6
β-strand	14-19	6	13
β-strand	24-32	9	13
β-strand	38-46	9	13
β-strand	53-60	8	13
α-helix	62-64	3
β-strand	65-69	5	13
α-helix	70-71	2
α-helix	76-79	4

Chain 2B: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	6-10	5
β-strand	14-16	3	90
β-strand	22-25	4	90
α-helix	37-40	4
β-strand	46-48	3	90
β-strand	56-57	2	91
β-strand	68-70	3	90
β-strand	78-79	2	91
α-helix	83-86	4
β-strand	92-94	3	90
α-helix	103-111	9
β-strand	117-119	3	90
α-helix	124-127	4
α-helix	131-138	8
β-strand	144-145	2	90
β-strand	148-149	2	90
α-helix	150-151	2
α-helix	152-160	9

Chain 2c: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	21-26	6
α-helix	30-38	9
β-strand	41-46	6	13
β-strand	51-59	9	13
β-strand	65-75	11	13
β-strand	91-101	11	13
α-helix	103-105	3
β-strand	106-111	6	13

Chain 2C: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	92
α-helix	20-32	13
β-strand	37-41	5	92
β-strand	52-56	5	92
α-helix	59-68	10
β-strand	73-74	2	93
β-strand	77-78	2	93
β-strand	80-83	4	92
α-helix	89-95	7

Chains 2d and 5d: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-14	8
β-strand	18-23	6	13
β-strand	28-36	9	13
β-strand	42-51	10	13
β-strand	54-64	11	13
α-helix	66-68	3
β-strand	69-74	6	13

Chain 2D: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	161-174	14
α-helix	179-189	11
α-helix	192-198	7
α-helix	205-218	14
α-helix	241-272	32
β-strand	281-284	4	94

Chains 2e and 5e: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	17-27	11
β-strand	30-35	6	13
β-strand	38-50	13	13
β-strand	56-65	10	13
β-strand	70-79	10	13
α-helix	81-83	3
β-strand	84-90	7	13

42 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
pre-mRNA	A	RNA	144	Homo sapiens
U6 snRNA	6A	RNA	107	Homo sapiens
U6 snRNA-associated Sm-like protein LSm2	6a	protein	95	Homo sapiens	Q9Y333 (AlphaFold model)
U6 snRNA-associated Sm-like protein LSm3	6b	protein	102	Homo sapiens	P62310 (AlphaFold model)
U6 snRNA-associated Sm-like protein LSm4	6c	protein	139	Homo sapiens	Q9Y4Z0 (AlphaFold model)
U6 snRNA-associated Sm-like protein LSm5	6d	protein	91	Homo sapiens	Q9Y4Y9 (AlphaFold model)
U6 snRNA-associated Sm-like protein LSm6	6e	protein	80	Homo sapiens	P62312
U6 snRNA-associated Sm-like protein LSm7	6f	protein	103	Homo sapiens	Q9UK45
U6 snRNA-associated Sm-like protein LSm8	6g	protein	96	Homo sapiens	O95777
U5 snRNA	5A	RNA	117	Homo sapiens
Pre-mRNA-processing-splicing factor 8	5B	protein	2335	Homo sapiens	Q6P2Q9
116 kDa U5 small nuclear ribonucleoprotein component	5C	protein	972	Homo sapiens	Q15029

35 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>8H6J_1 pre-mRNA (chains A)
GGGAGGUUUCCUUGAAGCUUUCGUGCUGACCCUGUCCCUUUUUUUUCCACAGGGGCGAAU
UCGAGCUCACUCUCUUCCGCAUCGCUGUCUGCGAGGUACCCUACCAGGUGAGUAUGGAUC
CCUCUAAAAGCGGGCAUGACUUCU

Sequence of entity 2 (6A), FASTA

>8H6J_2 U6 snRNA (chains 6A)
GUGCUCGCUUCGGCAGCACAUAUACUAAAAUUGGAACGAUACAGAGAAGAUUAGCAUGGC
CCCUGCGCAAGGAUGACACGCAAAUUCGUGAAGCGUUCCAUAUUUUU

Sequence of entity 3 (6a), FASTA

>8H6J_3 U6 snRNA-associated Sm-like protein LSm2 (chains 6a)
MLFYSFFKSLVGKDVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPEKYPHMLSVKNC
FIRGSVVRYVQLPADEVDTQLLQDAARKEALQQKQ

Sequence of entity 4 (6b), FASTA

>8H6J_4 U6 snRNA-associated Sm-like protein LSm3 (chains 6b)
MADDVDQQQTTNTVEEPLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEET
VTTIEIDEETYEEIYKSTKRNIPMLFVRGDGVVLVAPPLRVG

Sequence of entity 5 (6c), FASTA

>8H6J_5 U6 snRNA-associated Sm-like protein LSm4 (chains 6c)
MLPLSLLKTAQNHPMLVELKNGETYNGHLVSCDNWMNINLREVICTSRDGDKFWRMPECY
IRGSTIKYLRIPDEIIDMVKEEVVAKGRGRGGLQQQKQQKGRGMGGAGRGVFGGRGRGGI
PGTGRGQPEKKPGRQAGKQ

Sequence of entity 6 (6d), FASTA

>8H6J_6 U6 snRNA-associated Sm-like protein LSm5 (chains 6d)
MAANATTNPSQLLPLELVDKCIGSRIHIVMKSDKEIVGTLLGFDDFVNMVLEDVTEFEIT
PEGRRITKLDQILLNGNNITMLVPGGEGPEV

Sequence of entity 7 (6e), FASTA

>8H6J_7 U6 snRNA-associated Sm-like protein LSm6 (chains 6e)
MSLRKQTPSDFLKQIIGRPVVVKLNSGVDYRGVLACLDGYMNIALEQTEEYVNGQLKNKY
GDAFIRGNNVLYISTQKRRM

Sequence of entity 8 (6f), FASTA

>8H6J_8 U6 snRNA-associated Sm-like protein LSm7 (chains 6f)
MADKEKKKKESILDLSKYIDKTIRVKFQGGREASGILKGFDPLLNLVLDGTIEYMRDPDD
QYKLTEDTRQLGLVVCRGTSVVLICPQDGMEAIPNPFIQQQDA

Sequence of entity 9 (6g), FASTA

>8H6J_9 U6 snRNA-associated Sm-like protein LSm8 (chains 6g)
MTSALENYINRTVAVITSDGRMIVGTLKGFDQTINLILDESHERVFSSSQGVEQVVLGLY
IVRGDNVAVIGEIDEETDSALDLGNIRAEPLNSVAH

Sequence of entity 10 (5A), FASTA

>8H6J_10 U5 snRNA (chains 5A)
AUACUCUGGUUUCUCUUCAGAUCGCAUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGG
AGAGGAACAACUCUGAGUCUUAACCCAAUUUUUUGAGGCCUUGCUUUGGCAAGGCUA

Sequence of entity 11 (5B), FASTA

>8H6J_11 Pre-mRNA-processing-splicing factor 8 (chains 5B)
MAGVFPYRGPGNPVPGPLAPLPDYMSEEKLQEKARKWQQLQAKRYAEKRKFGFVDAQKED
MPPEHVRKIIRDHGDMTNRKFRHDKRVYLGALKYMPHAVLKLLENMPMPWEQIRDVPVLY
HITGAISFVNEIPWVIEPVYISQWGSMWIMMRREKRDRRHFKRMRFPPFDDEEPPLDYAD
NILDVEPLEAIQLELDPEEDAPVLDWFYDHQPLRDSRKYVNGSTYQRWQFTLPMMSTLYR
LANQLLTDLVDDNYFYLFDLKAFFTSKALNMAIPGGPKFEPLVRDINLQDEDWNEFNDIN
KIIIRQPIRTEYKIAFPYLYNNLPHHVHLTWYHTPNVVFIKTEDPDLPAFYFDPLINPIS
HRHSVKSQEPLPDDDEEFELPEFVEPFLKDTPLYTDNTANGIALLWAPRPFNLRSGRTRR
ALDIPLVKNWYREHCPAGQPVKVRVSYQKLLKYYVLNALKHRPPKAQKKRYLFRSFKATK
FFQSTKLDWVEVGLQVCRQGYNMLNLLIHRKNLNYLHLDYNFNLKPVKTLTTKERKKSRF
GNAFHLCREVLRLTKLVVDSHVQYRLGNVDAFQLADGLQYIFAHVGQLTGMYRYKYKLMR
QIRMCKDLKHLIYYRFNTGPVGKGPGCGFWAAGWRVWLFFMRGITPLLERWLGNLLARQF
EGRHSKGVAKTVTKQRVESHFDLELRAAVMHDILDMMPEGIKQNKARTILQHLSEAWRCW
KANIPWKVPGLPTPIENMILRYVKAKADWWTNTAHYNRERIRRGATVDKTVCKKNLGRLT
RLYLKAEQERQHNYLKDGPYITAEEAVAVYTTTVHWLESRRFSPIPFPPLSYKHDTKLLI
LALERLKEAYSVKSRLNQSQREELGLIEQAYDNPHEALSRIKRHLLTQRAFKEVGIEFMD
LYSHLVPVYDVEPLEKITDAYLDQYLWYEADKRRLFPPWIKPADTEPPPLLVYKWCQGIN
NLQDVWETSEGECNVMLESRFEKMYEKIDLTLLNRLLRLIVDHNIADYMTAKNNVVINYK
DMNHTNSYGIIRGLQFASFIVQYYGLVMDLLVLGLHRASEMAGPPQMPNDFLSFQDIATE
AAHPIRLFCRYIDRIHIFFRFTADEARDLIQRYLTEHPDPNNENIVGYNNKKCWPRDARM
RLMKHDVNLGRAVFWDIKNRLPRSVTTVQWENSFVSVYSKDNPNLLFNMCGFECRILPKC
RTSYEEFTHKDGVWNLQNEVTKERTAQCFLRVDDESMQRFHNRVRQILMASGSTTFTKIV
NKWNTALIGLMTYFREAVVNTQELLDLLVKCENKIQTRIKIGLNSKMPSRFPPVVFYTPK
ELGGLGMLSMGHVLIPQSDLRWSKQTDVGITHFRSGMSHEEDQLIPNLYRYIQPWESEFI
DSQRVWAEYALKRQEAIAQNRRLTLEDLEDSWDRGIPRINTLFQKDRHTLAYDKGWRVRT
DFKQYQVLKQNPFWWTHQRHDGKLWNLNNYRTDMIQALGGVEGILEHTLFKGTYFPTWEG
LFWEKASGFEESMKWKKLTNAQRSGLNQIPNRRFTLWWSPTINRANVYVGFQVQLDLTGI
FMHGKIPTLKISLIQIFRAHLWQKIHESIVMDLCQVFDQELDALEIETVQKETIHPRKSY
KMNSSCADILLFASYKWNVSRPSLLADSKDVMDSTTTQKYWIDIQLRWGDYDSHDIERYA
RAKFLDYTTDNMSIYPSPTGVLIAIDLAYNLHSAYGNWFPGSKPLIQQAMAKIMKANPAL
YVLRERIRKGLQLYSSEPTEPYLSSQNYGELFSNQIIWFVDDTNVYRVTIHKTFEGNLTT
KPINGAIFIFNPRTGQLFLKIIHTSVWAGQKRLGQLAKWKTAEEVAALIRSLPVEEQPKQ
IIVTRKGMLDPLEVHLLDFPNIVIKGSELQLPFQACLKVEKFGDLILKATEPQMVLFNLY
DDWLKTISSYTAFSRLILILRALHVNNDRAKVILKPDKTTITEPHHIWPTLTDEEWIKVE
VQLKDLILADYGKKNNVNVASLTQSEIRDIILGMEISAPSQQRQQIAEIEKQTKEQSQLT
ATQTRTVNKHGDEIITSTTSNYETQTFSSKTEWRVRAISAANLHLRTNHIYVSSDDIKET
GYTYILPKNVLKKFICISDLRAQIAGYLYGVSPPDNPQVKEIRCIVMVPQWGTHQTVHLP
GQLPQHEYLKEMEPLGWIHTQPNESPQLSPQDVTTHAKIMADNPSWDGEKTIIITCSFTP
GSCTLTAYKLTPSGYEWGRQNTDKGNNPKGYLPSHYERVQMLLSDRFLGFFMVPAQSSWN
YNFMGVRHDPNMKYELQLANPKEFYHEVHRPSHFLNFALLQEGEVYSADREDLYA

Sequence of entity 12 (5C), FASTA

>8H6J_12 116 kDa U5 small nuclear ribonucleoprotein component (chains 5C)
MDTDLYDEFGNYIGPELDSDEDDDELGRETKDLDEMDDDDDDDDVGDHDDDHPGMEVVLH
EDKKYYPTAEEVYGPEVETIVQEEDTQPLTEPIIKPVKTKKFTLMEQTLPVTVYEMDFLA
DLMDNSELIRNVTLCGHLHHGKTCFVDCLIEQTHPEIRKRYDQDLCYTDILFTEQERGVG
IKSTPVTVVLPDTKGKSYLFNIMDTPGHVNFSDEVTAGLRISDGVVLFIDAAEGVMLNTE
RLIKHAVQERLAVTVCINKIDRLILELKLPPTDAYYKLRHIVDEVNGLISMYSTDENLIL
SPLLGNVCFSSSQYSICFTLGSFAKIYADTFGDINYQEFAKRLWGDIYFNPKTRKFTKKA
PTSSSQRSFVEFILEPLYKILAQVVGDVDTSLPRTLDELGIHLTKEELKLNIRPLLRLVC
KKFFGEFTGFVDMCVQHIPSPKVGAKPKIEHTYTGGVDSDLGEAMSDCDPDGPLMCHTTK
MYSTDDGVQFHAFGRVLSGTIHAGQPVKVLGENYTLEDEEDSQICTVGRLWISVARYHIE
VNRVPAGNWVLIEGVDQPIVKTATITEPRGNEEAQIFRPLKFNTTSVIKIAVEPVNPSEL
PKMLDGLRKVNKSYPSLTTKVEESGEHVILGTGELYLDCVMHDLRKMYSEIDIKVADPVV
TFCETVVETSSLKCFAETPNKKNKITMIAEPLEKGLAEDIENEVVQITWNRKKLGEFFQT
KYDWDLLAARSIWAFGPDATGPNILVDDTLPSEVDKALLGSVKDSIVQGFQWGTREGPLC
DELIRNVKFKILDAVVAQEPLHRGGGQIIPTARRVVYSAFLMATPRLMEPYYFVEVQAPA
DCVSAVYTVLARRRGHVTQDAPIPGSPLYTIKAFIPAIDSFGFETDLRTHTQGQAFSLSV
FHHWQIVPGDPLDKSIVIRPLEPQPAPHLAREFMIKTRRRKGLSEDVSISKFFDDPMLLE
LAKQDVVLNYPM

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

Structural insights into human exon-defined spliceosome prior to activation. Zhang, W., Zhang, X., Zhan, X. et al. Cell Res (2024) 34:428-439. DOI 10.1038/s41422-024-00949-w · PubMed

Other PDB entries of the same protein (UniProt Q9Y333 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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.
6QW6 2.92 Å, Structure of the human U5.U4/U6 tri-snRNP at 2.9A resolution.
9XU3 3.0 Å, Human minor spliceosome exon-ligation-ready C* complex (prior to step-II)
8H6E 3.2 Å, Cryo-EM structure of human exon-defined spliceosome in the late pre-B state.
6QX9 3.28 Å, Structure of a human fully-assembled precatalytic spliceosome (pre-B complex).
6AHD 3.8 Å, The Cryo-EM Structure of Human Pre-catalytic Spliceosome (B complex) at 3.8 angstrom…
8QZS 4.1 Å, Cryo-EM structure of the cross-exon B-like complex
8R09 4.3 Å, Cryo-EM structure of the cross-exon pre-B+5'ss+ATPgammaS complex
8R0B 4.4 Å, Cryo-EM structure of the cross-exon pre-B+ATP complex
5O9Z 4.5 Å, Cryo-EM structure of a pre-catalytic human spliceosome primed for activation (B complex)
8QO9 5.29 Å, Cryo-EM structure of a human spliceosomal B complex protomer

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