8R09: Cross-exon pre-B+5'ss+ATPgammaS complex

Cryo-EM structure of the cross-exon pre-B+5'ss+ATPgammaS complex. Determined by electron microscopy at 4.3 Å resolution. Released 22 May 2024.

Method: Electron microscopy
Resolution: 4.3 Å
Organism: Homo sapiens
Chains: 60
Atoms: 82,094
Mol. weight: 2638.72 kDa
Released: 22 May 2024

Explore 8R09 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8R09 contains 597 α-helices and 617 β-strands across 54 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 21: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
β-strand	13-19	7	2
β-strand	24-32	9	2
β-strand	38-46	9	2
β-strand	53-60	8	2
β-strand	65-70	6	2

Chain 22: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	14-26	13
α-helix	30-35	6
β-strand	42-45	4	2
β-strand	51-58	8	2
β-strand	65-73	9	2
β-strand	76	1	121
β-strand	90	1	121
β-strand	93-101	9	2
β-strand	108-110	3	2

Chain 23: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	5-12	8
β-strand	17-21	5	2
β-strand	27-35	9	2
β-strand	41-48	8	2
β-strand	56-58	3	2
β-strand	61-63	3	2
β-strand	70-73	4	2
α-helix	75-79	5

Chain 2A: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	6-10	5
β-strand	13-16	4	3
β-strand	22-25	4	3
α-helix	37-40	4
β-strand	46-48	3	3
β-strand	56-57	2	4
β-strand	68-70	3	3
β-strand	78-79	2	4
β-strand	92-94	3	3
α-helix	103-106	4
α-helix	108-111	4
β-strand	117-119	3	3
α-helix	124-126	3
α-helix	131-138	8
β-strand	144-145	2	3
β-strand	149	1	3
α-helix	152-160	9

Chain 2b: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	8-11	4
β-strand	16-21	6	2
β-strand	26-34	9	2
β-strand	40-50	11	2
α-helix	58-60	3
β-strand	62-72	11	2
β-strand	77-84	8	2

Chain 2B: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	129
α-helix	20-30	11
β-strand	37-42	6	129
β-strand	52-56	5	129
α-helix	59-68	10
β-strand	72-74	3	130
β-strand	77-79	3	130
β-strand	80-83	4	129
α-helix	89-93	5

Chain 2e: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
α-helix	17-27	11
β-strand	30-35	6	2
β-strand	38-49	12	2
β-strand	56-65	10	2
β-strand	71-79	9	2
β-strand	84-89	6	2

Chain 2f: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-13	7
β-strand	18-23	6	2
β-strand	27-36	10	2
β-strand	42-51	10	2
β-strand	54-64	11	2
β-strand	69-74	6	2

46 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
U6 snRNA-associated Sm-like protein LSm6	66	protein	80	Homo sapiens	P62312 (AlphaFold model)
U6 snRNA-associated Sm-like protein LSm7	67	protein	103	Homo sapiens	Q9UK45 (AlphaFold model)
U6 snRNA-associated Sm-like protein LSm2	62	protein	95	Homo sapiens	Q9Y333 (AlphaFold model)
U6 snRNA-associated Sm-like protein LSm3	63	protein	102	Homo sapiens	P62310 (AlphaFold model)
U6 snRNA-associated Sm-like protein LSm8	68	protein	96	Homo sapiens	O95777
U6 snRNA-associated Sm-like protein LSm4	64	protein	139	Homo sapiens	Q9Y4Z0
U6 snRNA-associated Sm-like protein LSm5	65	protein	91	Homo sapiens	Q9Y4Y9
U5 small nuclear ribonucleoprotein 40 kDa protein	E	protein	357	Homo sapiens	Q96DI7
Splicing factor 3B subunit 4	B4	protein	424	Homo sapiens	Q15427
pre-mRNA	Z	RNA	347	Homo sapiens
Splicing factor 3A subunit 2	8	protein	464	Homo sapiens	Q15428
Splicing factor 3A subunit 3	9	protein	501	Homo sapiens	Q12874

34 more molecules are not listed.

Sequence of entity 1 (66), FASTA

>8R09_1 U6 snRNA-associated Sm-like protein LSm6 (chains 66)
MSLRKQTPSDFLKQIIGRPVVVKLNSGVDYRGVLACLDGYMNIALEQTEEYVNGQLKNKY
GDAFIRGNNVLYISTQKRRM

Sequence of entity 2 (67), FASTA

>8R09_2 U6 snRNA-associated Sm-like protein LSm7 (chains 67)
MADKEKKKKESILDLSKYIDKTIRVKFQGGREASGILKGFDPLLNLVLDGTIEYMRDPDD
QYKLTEDTRQLGLVVCRGTSVVLICPQDGMEAIPNPFIQQQDA

Sequence of entity 3 (62), FASTA

>8R09_3 U6 snRNA-associated Sm-like protein LSm2 (chains 62)
MLFYSFFKSLVGKDVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPEKYPHMLSVKNC
FIRGSVVRYVQLPADEVDTQLLQDAARKEALQQKQ

Sequence of entity 4 (63), FASTA

>8R09_4 U6 snRNA-associated Sm-like protein LSm3 (chains 63)
MADDVDQQQTTNTVEEPLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEET
VTTIEIDEETYEEIYKSTKRNIPMLFVRGDGVVLVAPPLRVG

Sequence of entity 5 (68), FASTA

>8R09_5 U6 snRNA-associated Sm-like protein LSm8 (chains 68)
MTSALENYINRTVAVITSDGRMIVGTLKGFDQTINLILDESHERVFSSSQGVEQVVLGLY
IVRGDNVAVIGEIDEETDSALDLGNIRAEPLNSVAH

Sequence of entity 6 (64), FASTA

>8R09_6 U6 snRNA-associated Sm-like protein LSm4 (chains 64)
MLPLSLLKTAQNHPMLVELKNGETYNGHLVSCDNWMNINLREVICTSRDGDKFWRMPECY
IRGSTIKYLRIPDEIIDMVKEEVVAKGRGRGGLQQQKQQKGRGMGGAGRGVFGGRGRGGI
PGTGRGQPEKKPGRQAGKQ

Sequence of entity 7 (65), FASTA

>8R09_7 U6 snRNA-associated Sm-like protein LSm5 (chains 65)
MAANATTNPSQLLPLELVDKCIGSRIHIVMKSDKEIVGTLLGFDDFVNMVLEDVTEFEIT
PEGRRITKLDQILLNGNNITMLVPGGEGPEV

Sequence of entity 8 (E), FASTA

>8R09_8 U5 small nuclear ribonucleoprotein 40 kDa protein (chains E)
MIEQQKRKGPELPLVPVKRQRHELLLGAGSGPGAGQQQATPGALLQAGPPRCSSLQAPIM
LLSGHEGEVYCCKFHPNGSTLASAGFDRLILLWNVYGDCDNYATLKGHSGAVMELHYNTD
GSMLFSASTDKTVAVWDSETGERVKRLKGHTSFVNSCYPARRGPQLVCTGSDDGTVKLWD
IRKKAAIQTFQNTYQVLAVTFNDTSDQIISGGIDNDIKVWDLRQNKLTYTMRGHADSVTG
LSLSSEGSYLLSNAMDNTVRVWDVRPFAPKERCVKIFQGNVHNFEKNLLRCSWSPDGSKI
AAGSADRFVYVWDTTSRRILYKLPGHAGSINEVAFHPDEPIIISASSDKRLYMGEIQ

Sequence of entity 9 (B4), FASTA

>8R09_9 Splicing factor 3B subunit 4 (chains B4)
MAAGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVE
FLSEEDADYAIKIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTF
SAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKK
DSKGERHGSAAERLLAAQNPLSQADRPHQLFADAPPPPSAPNPVVSSLGSGLPPPGMPPP
GSFPPPVPPPGALPPGIPPAMPPPPMPPGAAGHGPPSAGTPGAGHPGHGHSHPHPFPPGG
MPHPGMSQMQLAHHGPHGLGHPHAGPPGSGGQPPPRPPPGMPHPGPPPMGMPPRGPPFGS
PMGHPGPMPPHGMRGPPPLMPPHGYTGPPRPPPYGYQRGPLPPPRPTPRPPVPPRGPLRG
PLPQ

Sequence of entity 10 (Z), FASTA

>8R09_10 pre-mRNA (chains Z)
GGUACCUAAUACGACUCACUAUAGGGAGACGGAAUUCGAGCUCGCCCACUCUUGGAUCGG
AAACCCGUCGGCCUCCGAACGGUAAGAGCCUAGCAUGUAGAACUGGUUACCUGCAGCCCA
AGCUUGCUGCACGUCUAGGGCGCAGUAGUCCAGGGUUUCCUUGAUGAUGUCAUACUUAUC
CUGUCCCUUUUUUUUCCACAGCUCGCGGUUGAGGACAAACUCUUCGCGGUCUUUCCAGUG
GGGAUCCAAUAUCCGUACACCAUCAGGGUACGAGCUAGCCCAUGGCGUACACCAUCAGGG
UACGACUAGUAGAUCUCGUACACCAUCAGGGUACGGAAUUCUCUAGA

Sequence of entity 11 (8), FASTA

>8R09_11 Splicing factor 3A subunit 2 (chains 8)
MDFQHRPGGKTGSGGVASSSESNRDRRERLRQLALETIDINKDPYFMKNHLGSYECKLCL
TLHNNEGSYLAHTQGKKHQTNLARRAAKEAKEAPAQPAPEKVKVEVKKFVKIGRPGYKVT
KQRDSEMGQQSLLFQIDYPEIAEGIMPRHRFMSAYEQRIEPPDRRWQYLLMAAEPYETIA
FKVPSREIDKAEGKFWTHWNRETKQFFLQFHFKMEKPPAPPSLPAGPPGVKRPPPPLMNG
LPPRPPLPESLPPPPPGGLPLPPMPPTGPAPSGPPGPPQLPPPAPGVHPPAPVVHPPASG
VHPPAPGVHPPAPGVHPPAPGVHPPTSGVHPPAPGVHPPAPGVHPPAPGVHPPAPGVHPP
APGVHPPPSAGVHPQAPGVHPAAPAVHPQAPGVHPPAPGMHPQAPGVHPQPPGVHPSAPG
VHPQPPGVHPSNPGVHPPTPMPPMLRPPLPSEGPGNIPPPPPTN

Sequence of entity 12 (9), FASTA

>8R09_12 Splicing factor 3A subunit 3 (chains 9)
METILEQQRRYHEEKERLMDVMAKEMLTKKSTLRDQINSDHRTRAMQDRYMEVSGNLRDL
YDDKDGLRKEELNAISGPNEFAEFYNRLKQIKEFHRKHPNEICVPMSVEFEELLKARENP
SEEAQNLVEFTDEEGYGRYLDLHDCYLKYINLKASEKLDYITYLSIFDQLFDIPKERKNA
EYKRYLEMLLEYLQDYTDRVKPLQDQNELFGKIQAEFEKKWENGTFPGWPKETSSALTHA
GAHLDLSAFSSWEELASLGLDRLKSALLALGLKCGGTLEERAQRLFSTKGKSLESLDTSL
FAKNPKSKGTKRDTERNKDIAFLEAQIYEYVEILGEQRHLTHENVQRKQARTGEEREEEE
EEQISESESEDEENEIIYNPKNLPLGWDGKPIPYWLYKLHGLNINYNCEICGNYTYRGPK
AFQRHFAEWRHAHGMRCLGIPNTAHFANVTQIEDAVSLWAKLKLQKASERWQPDTEEEYE
DSSGNVVNKKTYEDLKRQGLL

Primary citation

Structural insights into the cross-exon to cross-intron spliceosome switch. Zhang, Z., Kumar, V., Dybkov, O. et al. Nature (2024) 630:1012-1019. DOI 10.1038/s41586-024-07458-1 · PubMed

Other PDB entries of the same protein (UniProt P62312 (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.
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).
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
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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