6QX9: PDB entry 6QX9

Structure of a human fully-assembled precatalytic spliceosome (pre-B complex). Determined by electron microscopy at 3.28 Å resolution. Released 17 Apr 2019.

Method: Electron microscopy
Resolution: 3.28 Å
Organisms: Homo sapiens, Human adenovirus 2
Chains: 71
Atoms: 137,494
Mol. weight: 2871.62 kDa
Ligands: ZN, MG, GTP, IHP
Released: 17 Apr 2019

Explore 6QX9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6QX9 contains 697 α-helices and 707 β-strands across 65 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 11: 4 helices, 5 β-strands

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

Chain 12: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	19-26	8
α-helix	30-38	9
β-strand	41-46	6	6
β-strand	51-59	9	6
β-strand	65-76	12	6
α-helix	89	1
β-strand	90-101	12	6
α-helix	103-105	3
β-strand	106-111	6	6

Chain 13: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	5-12	8
β-strand	17-22	6	6
β-strand	27-35	9	6
β-strand	41-49	9	6
β-strand	55-63	9	6
α-helix	65-67	3
β-strand	68-73	6	6
α-helix	75-79	5

Chain 1A: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	11-15	5	34
α-helix	23-35	13
β-strand	40-45	6	34
β-strand	55-59	5	34
α-helix	62-72	11
β-strand	76	1	35
β-strand	81	1	35
β-strand	83-86	4	34
α-helix	92-98	7

Chain 1b: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
β-strand	16-21	6	6
β-strand	26-34	9	6
β-strand	40-48	9	6
β-strand	50-51	2	20
α-helix	59-60	2
β-strand	61-62	2	20
β-strand	65-72	8	6
α-helix	74-76	3
β-strand	77-84	8	6
α-helix	85-88	4

Chain 1C: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	44
β-strand	11-13	3	44
α-helix	18-25	8
α-helix	28-50	23

Chain 1e: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	17-27	11
β-strand	30-35	6	6
β-strand	41-50	10	6
β-strand	56-65	10	6
β-strand	71-79	9	6
α-helix	81-83	3
β-strand	84-89	6	6

Chain 1f: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-14	8
β-strand	18-23	6	6
β-strand	28-36	9	6
β-strand	42-51	10	6
β-strand	54-58	5	6
β-strand	62-64	3	6
α-helix	66-68	3
β-strand	69-74	6	6

55 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
U1 snRNA	1	RNA	164	Homo sapiens
U6 snRNA	6	RNA	106	Homo sapiens
U5 small nuclear ribonucleoprotein 40 kDa protein	5O	protein	357	Homo sapiens	Q96DI7 (AlphaFold model)
Splicing factor 3B subunit 4	B4	protein	424	Homo sapiens	Q15427 (AlphaFold model)
Small nuclear ribonucleoprotein Sm D3	13, 23, 43, 53	protein	126	Homo sapiens	P62318 (AlphaFold model)
U4/U6 small nuclear ribonucleoprotein Prp4	4B	protein	522	Homo sapiens	O43172 (AlphaFold model)
Small nuclear ribonucleoprotein E	1e, 2e, 4e, 5e	protein	92	Homo sapiens	P62304
AdML pre-mRNA	I	RNA	62	Human adenovirus 2
U1 small nuclear ribonucleoprotein 70 kDa	1K	protein	437	Homo sapiens	P08621
U4/U6 small nuclear ribonucleoprotein Prp31	4C	protein	499	Homo sapiens	Q8WWY3
Small nuclear ribonucleoprotein Sm D1	11, 21, 41, 51	protein	119	Homo sapiens	P62314
RNA-binding protein 42	R	protein	480	Homo sapiens	Q9BTD8

38 more molecules are not listed.

Sequence of entity 1 (1), FASTA

>6QX9_1 U1 snRNA (chains 1)
AUACUUACCUGGCAGGGGAGAUACCAUGAUCACGAAGGUGGUUUUCCCAGGGCGAGGCUU
AUCCAUUGCACUCCGGAUGUGCUGACCCCUGCGAUUUCCCCAAAUGUGGGAAACUCGACU
GCAUAAUUUGUGGUAGUGGGGGACUGCGUUCGCGCUUUCCCCUG

Sequence of entity 2 (6), FASTA

>6QX9_2 U6 snRNA (chains 6)
GUGCUCGCUUCGGCAGCACAUAUACUAAAAUUGGAACGAUACAGAGAAGAUUAGCAUGGC
CCCUGCGCAAGGAUGACACGCAAAUUCGUGAAGCGUUCCAUAUUUU

Sequence of entity 3 (5O), FASTA

>6QX9_3 U5 small nuclear ribonucleoprotein 40 kDa protein (chains 5O)
MIEQQKRKGPELPLVPVKRQRHELLLGAGSGPGAGQQQATPGALLQAGPPRCSSLQAPIM
LLSGHEGEVYCCKFHPNGSTLASAGFDRLILLWNVYGDCDNYATLKGHSGAVMELHYNTD
GSMLFSASTDKTVAVWDSETGERVKRLKGHTSFVNSCYPARRGPQLVCTGSDDGTVKLWD
IRKKAAIQTFQNTYQVLAVTFNDTSDQIISGGIDNDIKVWDLRQNKLTYTMRGHADSVTG
LSLSSEGSYLLSNAMDNTVRVWDVRPFAPKERCVKIFQGNVHNFEKNLLRCSWSPDGSKI
AAGSADRFVYVWDTTSRRILYKLPGHAGSINEVAFHPDEPIIISASSDKRLYMGEIQ

Sequence of entity 4 (B4), FASTA

>6QX9_4 Splicing factor 3B subunit 4 (chains B4)
MAAGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVE
FLSEEDADYAIKIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTF
SAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKK
DSKGERHGSAAERLLAAQNPLSQADRPHQLFADAPPPPSAPNPVVSSLGSGLPPPGMPPP
GSFPPPVPPPGALPPGIPPAMPPPPMPPGAAGHGPPSAGTPGAGHPGHGHSHPHPFPPGG
MPHPGMSQMQLAHHGPHGLGHPHAGPPGSGGQPPPRPPPGMPHPGPPPMGMPPRGPPFGS
PMGHPGPMPPHGMRGPPPLMPPHGYTGPPRPPPYGYQRGPLPPPRPTPRPPVPPRGPLRG
PLPQ

Sequence of entity 5 (13, 23, 43, 53), FASTA

>6QX9_5 Small nuclear ribonucleoprotein Sm D3 (chains 13, 23, 43, 53)
MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQ
VYIRGSKIRFLILPDMLKNAPMLKSMKNKNQGSGAGRGKAAILKAQVAARGRGRGMGRGN
IFQKRR

Sequence of entity 6 (4B), FASTA

>6QX9_6 U4/U6 small nuclear ribonucleoprotein Prp4 (chains 4B)
MASSRASSTQATKTKAPDDLVAPVVKKPHIYYGSLEEKERERLAKGESGILGKDGLKAGI
EAGNINITSGEVFEIEEHISERQAEVLAEFERRKRARQINVSTDDSEVKACLRALGEPIT
LFGEGPAERRERLRNILSVVGTDALKKTKKDDEKSKKSKEEYQQTWYHEGPNSLKVARLW
IANYSLPRAMKRLEEARLHKEIPETTRTSQMQELHKSLRSLNNFCSQIGDDRPISYCHFS
PNSKMLATACWSGLCKLWSVPDCNLLHTLRGHNTNVGAIVFHPKSTVSLDPKDVNLASCA
ADGSVKLWSLDSDEPVADIEGHTVRVARVMWHPSGRFLGTTCYDRSWRLWDLEAQEEILH
QEGHSMGVYDIAFHQDGSLAGTGGLDAFGRVWDLRTGRCIMFLEGHLKEIYGINFSPNGY
HIATGSGDNTCKVWDLRQRRCVYTIPAHQNLVTGVKFEPIHGNFLLTGAYDNTAKIWTHP
GWSPLKTLAGHEGKVMGLDISSDGQLIATCSYDRTFKLWMAE

Sequence of entity 7 (1e, 2e, 4e, 5e), FASTA

>6QX9_7 Small nuclear ribonucleoprotein E (chains 1e, 2e, 4e, 5e)
MAYRGQGQKVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDD
AEEIHSKTKSRKQLGRIMLKGDNITLLQSVSN

Sequence of entity 8 (I), FASTA

>6QX9_8 AdML pre-mRNA (chains I)
GGGUGAGUACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGCUUUCGUGCUGA
CC

Sequence of entity 9 (1K), FASTA

>6QX9_9 U1 small nuclear ribonucleoprotein 70 kDa (chains 1K)
MTQFLPPNLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRA
ETREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLR
REFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER
GRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDERPGPSPLPHRDRDRDRERE
RRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERAR
RERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRS
ERERRRDRDRDRDRDREHKRGERGSERGRDEARGGGGGQDNGLEGLGNDSRDMYMESEGG
DGYLAPENGYLMEAAPE

Sequence of entity 10 (4C), FASTA

>6QX9_10 U4/U6 small nuclear ribonucleoprotein Prp31 (chains 4C)
MSLADELLADLEEAAEEEEGGSYGEEEEEPAIEDVQEETQLDLSGDSVKTIAKLWDSKMF
AEIMMKIEEYISKQAKASEVMGPVEAAPEYRVIVDANNLTVEIENELNIIHKFIRDKYSK
RFPELESLVPNALDYIRTVKELGNSLDKCKNNENLQQILTNATIMVVSVTASTTQGQQLS
EEELERLEEACDMALELNASKHRIYEYVESRMSFIAPNLSIIIGASTAAKIMGVAGGLTN
LSKMPACNIMLLGAQRKTLSGFSSTSVLPHTGYIYHSDIVQSLPPDLRRKAARLVAAKCT
LAARVDSFHESTEGKVGYELKDEIERKFDKWQEPPPVKQVKPLPAPLDGQRKKRGGRRYR
KMKERLGLTEIRKQANRMSFGEIEEDAYQEDLGFSLGHLGKSGSGRVRQTQVNEATKARI
SKTLQRTLQKQSVVYGGKSTIRDRSSGTASSVAFTPLQGLEIVNPQAAEKKVAEANQKYF
SSMAEFLKVKGEKSGLMST

Sequence of entity 11 (11, 21, 41, 51), FASTA

>6QX9_11 Small nuclear ribonucleoprotein Sm D1 (chains 11, 21, 41, 51)
MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSI
RGNNIRYFILPDSLPLDTLLVDVEPKVKSKKREAVAGRGRGRGRGRGRGRGRGRGGPRR

Sequence of entity 12 (R), FASTA

>6QX9_12 RNA-binding protein 42 (chains R)
MAGAGPAPGLPGAGGPVVPGPGAGIPGKSGEERLKEMEAEMALFEQEVLGAPVPGIPTAV
PAVPTVPTVPTVEAMQVPAAPVIRPIIATNTYQQVQQTLEARAAAAATVVPPMVGGPPFV
GPVGFGPGDRSHLDSPEAREAMFLRRAAVAPQRAPILRPAFVPHVLQRADSALSSAAAGP
RPMALRPPHQALVGPPLPGPPGPPMMLPPMARAPGPPLGSMAALRPPLEEPAAPRELGLG
LGLGLKEKEEAVVAAAAGLEEASAAVAVGAGGAPAGPAVIGPSLPLALAMPLPEPEPLPL
PLEVVRGLLPPLRIPELLSLRPRPRPPRPEPPPGLMALEVPEPLGEDKKKGKPEKLKRCI
RTAAGSSWEDPSLLEWDADDFRIFCGDLGNEVNDDILARAFSRFPSFLKAKVIRDKRTGK
TKGYGFVSFKDPSDYVRAMREMNGKYVGSRPIKLRKSMWKDRNLDVVRKKQKEKKKLGLR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6
MG	Magnesium ion	Mg	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
IHP	Inositol hexakisphosphate	C6 H18 O24 P6	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 Q96DI7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9S2E 2.4 Å, Human intron-lariat spliceosome-Aquarius (ILSaqr)
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.
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)…
7DVQ 2.89 Å, Cryo-EM Structure of the Activated Human Minor Spliceosome (minor Bact Complex)
6ID0 2.9 Å, Cryo-EM structure of a human intron lariat spliceosome prior to Prp43 loaded (ILS1…
6QW6 2.92 Å, Structure of the human U5.U4/U6 tri-snRNP at 2.9A resolution.
9XTT 2.92 Å, Human minor spliceosome branching-completed C complex (after step-I)
6ICZ 3.0 Å, Cryo-EM structure of a human post-catalytic spliceosome (P complex) at 3.0 angstrom
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

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