6QX9 image
Deposition Date 2019-03-07
Release Date 2019-04-17
Last Version Date 2024-11-13
Entry Detail
PDB ID:
6QX9
Keywords:
SPLICING
Title:
Structure of a human fully-assembled precatalytic spliceosome (pre-B complex).
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Human adenovirus 2 (Taxon ID: 10515)
Host Organism:
Saccharomyces cerevisiae
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.28 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
6QX9 validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:U1 snRNA
Chain IDs:A (auth: 1)
Chain Length:164
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein Sm D3
Gene (Uniprot):SNRPD3
Chain IDs:E (auth: 13), V (auth: 53), RA (auth: 23), UA (auth: 43)
Chain Length:126
Number of Molecules:4
Biological Source:Homo sapiens
UniProt ID:P62318 Pfam ID:PF01423
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U1 small nuclear ribonucleoprotein A
Gene (Uniprot):SNRPA
Chain IDs:FA (auth: 1A)
Chain Length:282
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P09012 Pfam ID:PF00076
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U1 small nuclear ribonucleoprotein C
Gene (Uniprot):SNRPC
Chain IDs:GB (auth: 1C)
Chain Length:159
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P09234 Pfam ID:PF06220
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U1 small nuclear ribonucleoprotein 70 kDa
Gene (Uniprot):SNRNP70
Chain IDs:I (auth: 1K)
Chain Length:437
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P08621 Pfam ID:PF12220, PF00076
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein-associated proteins B and B'
Gene (Uniprot):SNRPB
Chain IDs:DA (auth: 1b), MA (auth: 2b), SA (auth: 5b), JB (auth: 4b)
Chain Length:240
Number of Molecules:4
Biological Source:Homo sapiens
UniProt ID:P14678 Pfam ID:PF01423
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein F
Gene (Uniprot):SNRPF
Chain IDs:M (auth: 1f), Y (auth: 2f), HA (auth: 5f), OA (auth: 4f)
Chain Length:86
Number of Molecules:4
Biological Source:Homo sapiens
UniProt ID:P62306 Pfam ID:PF01423
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein G
Gene (Uniprot):SNRPG
Chain IDs:QA (auth: 1g), ZA (auth: 2g), HB (auth: 5g), MB (auth: 4g)
Chain Length:76
Number of Molecules:4
Biological Source:Homo sapiens
UniProt ID:P62308 Pfam ID:PF01423
Polymer Type:polyribonucleotide
Molecule:U2 snRNA
Chain IDs:NA (auth: 2)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein Sm D2
Gene (Uniprot):SNRPD2
Chain IDs:Q (auth: 22), CA (auth: 42), BB (auth: 52), CB (auth: 12)
Chain Length:118
Number of Molecules:4
Biological Source:Homo sapiens
UniProt ID:P62316 Pfam ID:PF01423
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U2 small nuclear ribonucleoprotein A'
Gene (Uniprot):SNRPA1
Chain IDs:OB (auth: 2A)
Chain Length:255
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P09661 Pfam ID:PF14580
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U2 small nuclear ribonucleoprotein B''
Gene (Uniprot):SNRPB2
Chain IDs:U (auth: 2B)
Chain Length:225
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P08579 Pfam ID:PF00076
Polymer Type:polyribonucleotide
Molecule:U4 snRNA
Chain IDs:NB (auth: 4)
Chain Length:146
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein Sm D1
Gene (Uniprot):SNRPD1
Chain IDs:K (auth: 41), BA (auth: 11), JA (auth: 51), LB (auth: 21)
Chain Length:119
Number of Molecules:4
Biological Source:Homo sapiens
UniProt ID:P62314 Pfam ID:PF01423
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U4/U6 small nuclear ribonucleoprotein Prp3
Gene (Uniprot):PRPF3
Chain IDs:KB (auth: 4A)
Chain Length:683
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O43395 Pfam ID:PF01480, PF08572, PF06544
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U4/U6 small nuclear ribonucleoprotein Prp4
Gene (Uniprot):PRPF4
Chain IDs:F (auth: 4B)
Chain Length:240
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O43172 Pfam ID:PF08799, PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U4/U6 small nuclear ribonucleoprotein Prp31
Gene (Uniprot):PRPF31
Chain IDs:J (auth: 4C)
Chain Length:499
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8WWY3 Pfam ID:PF01798, PF09785
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NHP2-like protein 1
Gene (Uniprot):SNU13
Chain IDs:KA (auth: 4D)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P55769 Pfam ID:PF01248
Polymer Type:polyribonucleotide
Molecule:U5 snRNA
Chain IDs:R (auth: 5)
Chain Length:117
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-processing-splicing factor 8
Gene (Uniprot):PRPF8
Chain IDs:WA (auth: 5A)
Chain Length:2311
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q6P2Q9 Pfam ID:PF08082, PF08083, PF10598, PF10597, PF10596, PF12134, PF01398, PF08084
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U5 small nuclear ribonucleoprotein 200 kDa helicase
Gene (Uniprot):SNRNP200
Chain IDs:RB (auth: 5B)
Chain Length:2136
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O75643 Pfam ID:PF21188, PF18149, PF00270, PF00271, PF02889 EC:3.6.4.13
Protein Blast
Polymer Type:polypeptide(L)
Molecule:116 kDa U5 small nuclear ribonucleoprotein component
Gene (Uniprot):EFTUD2
Chain IDs:Z (auth: 5C)
Chain Length:854
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q15029 Pfam ID:PF00009, PF03144, PF14492, PF03764, PF00679
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Thioredoxin-like protein 4A
Gene (Uniprot):TXNL4A
Chain IDs:AB (auth: 5D)
Chain Length:142
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P83876 Pfam ID:PF02966
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-processing factor 6
Chain IDs:IA (auth: 5J)
Chain Length:850
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q91YR7,O94906 Pfam ID:PF06424, PF14559, PF13432
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U5 small nuclear ribonucleoprotein 40 kDa protein
Gene (Uniprot):SNRNP40
Chain IDs:C (auth: 5O)
Chain Length:357
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96DI7 Pfam ID:PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Probable ATP-dependent RNA helicase DDX23
Gene (Uniprot):DDX23
Chain IDs:AA (auth: 5X)
Chain Length:820
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BUQ8 Pfam ID:PF00270, PF00271
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein E
Gene (Uniprot):SNRPE
Chain IDs:G (auth: 5e), N (auth: 4e), VA (auth: 1e), EB (auth: 2e)
Chain Length:92
Number of Molecules:4
Biological Source:Homo sapiens
UniProt ID:P62304 Pfam ID:PF01423
Polymer Type:polyribonucleotide
Molecule:U6 snRNA
Chain IDs:B (auth: 6)
Chain Length:106
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U6 snRNA-associated Sm-like protein LSm2
Gene (Uniprot):LSM2
Chain IDs:T (auth: 62)
Chain Length:95
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y333 Pfam ID:PF01423
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U6 snRNA-associated Sm-like protein LSm3
Gene (Uniprot):LSM3
Chain IDs:LA (auth: 63)
Chain Length:102
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62310 Pfam ID:PF01423
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U6 snRNA-associated Sm-like protein LSm4
Gene (Uniprot):LSM4
Chain IDs:DB (auth: 64)
Chain Length:139
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y4Z0 Pfam ID:PF01423
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U6 snRNA-associated Sm-like protein LSm5
Gene (Uniprot):LSM5
Chain IDs:QB (auth: 65)
Chain Length:91
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y4Y9 Pfam ID:PF01423
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U6 snRNA-associated Sm-like protein LSm6
Gene (Uniprot):LSM6
Chain IDs:O (auth: 66)
Chain Length:80
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62312 Pfam ID:PF01423
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U6 snRNA-associated Sm-like protein LSm7
Gene (Uniprot):LSM7
Chain IDs:S (auth: 67)
Chain Length:103
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9UK45 Pfam ID:PF01423
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U6 snRNA-associated Sm-like protein LSm8
Gene (Uniprot):LSM8
Chain IDs:TA (auth: 68)
Chain Length:96
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O95777 Pfam ID:PF01423
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Splicing factor 3A subunit 1,Splicing factor 3A subunit 1,Splicing factor 3A subunit 1
Gene (Uniprot):SF3A1
Chain IDs:PB (auth: A1)
Chain Length:647
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q15459 Pfam ID:PF01805, PF12230, PF00240
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Splicing factor 3A subunit 2
Gene (Uniprot):SF3A2
Chain IDs:W (auth: A2)
Chain Length:209
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q15428 Pfam ID:PF12874, PF16835
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Splicing factor 3A subunit 3
Gene (Uniprot):SF3A3
Chain IDs:XA (auth: A3)
Chain Length:501
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q12874 Pfam ID:PF12108, PF16837, PF13297, PF11931
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Splicing factor 3B subunit 1
Gene (Uniprot):SF3B1
Chain IDs:SB (auth: B1)
Chain Length:1304
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O75533 Pfam ID:PF08920, PF22646
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Splicing factor 3B subunit 2
Gene (Uniprot):SF3B2
Chain IDs:X (auth: B2)
Chain Length:895
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q13435 Pfam ID:PF02037, PF04037, PF04046
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Splicing factor 3B subunit 3
Gene (Uniprot):SF3B3
Chain IDs:PA (auth: B3)
Chain Length:1217
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q15393 Pfam ID:PF10433, PF03178
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Splicing factor 3B subunit 4
Gene (Uniprot):SF3B4
Chain IDs:D (auth: B4)
Chain Length:424
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q15427 Pfam ID:PF00076
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Splicing factor 3B subunit 5
Gene (Uniprot):SF3B5
Chain IDs:EA (auth: B5)
Chain Length:86
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BWJ5 Pfam ID:PF07189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:PHD finger-like domain-containing protein 5A
Gene (Uniprot):PHF5A
Chain IDs:FB (auth: BP)
Chain Length:104
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q7RTV0 Pfam ID:PF03660
Polymer Type:polyribonucleotide
Molecule:AdML pre-mRNA
Chain IDs:H (auth: I)
Chain Length:62
Number of Molecules:1
Biological Source:Human adenovirus 2
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Serine/threonine-protein kinase PRP4 homolog
Gene (Uniprot):PRP4K
Chain IDs:IB (auth: K)
Chain Length:1007
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q13523 Pfam ID:PF00069 EC:2.7.11.1
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA-binding protein 42
Gene (Uniprot):RBM42
Chain IDs:L (auth: R)
Chain Length:480
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BTD8 Pfam ID:PF00076
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U4/U6.U5 tri-snRNP-associated protein 1
Gene (Uniprot):SART1
Chain IDs:GA (auth: S)
Chain Length:800
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O43290 Pfam ID:PF19252, PF03343
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U4/U6.U5 tri-snRNP-associated protein 2
Gene (Uniprot):USP39
Chain IDs:YA (auth: U)
Chain Length:555
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q53GS9 Pfam ID:PF02148, PF00443
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein
Gene (Uniprot):SNRNP27
Chain IDs:P (auth: X)
Chain Length:155
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8WVK2 Pfam ID:PF08648
Ligand Molecules
GTP
IHP
MG
ZN
Primary Citation
Mechanism of 5' splice site transfer for human spliceosome activation.
Science 364 362 367 (2019)
PMID: 30975767 DOI: 10.1126/science.aax3289

Abstact

The prespliceosome, comprising U1 and U2 small nuclear ribonucleoproteins (snRNPs) bound to the precursor messenger RNA 5' splice site (5'SS) and branch point sequence, associates with the U4/U6.U5 tri-snRNP to form the fully assembled precatalytic pre-B spliceosome. Here, we report cryo-electron microscopy structures of the human pre-B complex captured before U1 snRNP dissociation at 3.3-angstrom core resolution and the human tri-snRNP at 2.9-angstrom resolution. U1 snRNP inserts the 5'SS-U1 snRNA helix between the two RecA domains of the Prp28 DEAD-box helicase. Adenosine 5'-triphosphate-dependent closure of the Prp28 RecA domains releases the 5'SS to pair with the nearby U6 ACAGAGA-box sequence presented as a mobile loop. The structures suggest that formation of the 5'SS-ACAGAGA helix triggers remodeling of an intricate protein-RNA network to induce Brr2 helicase relocation to its loading sequence in U4 snRNA, enabling Brr2 to unwind the U4/U6 snRNA duplex to allow U6 snRNA to form the catalytic center of the spliceosome.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
6QW6