6QX9

Structure of a human fully-assembled precatalytic spliceosome (pre-B complex).


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanism of 5' splice site transfer for human spliceosome activation.

Charenton, C.Wilkinson, M.E.Nagai, K.

(2019) Science 364: 362-367

  • DOI: 10.1126/science.aax3289
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 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 p ...

    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.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK. ccharent@mrc-lmb.cam.ac.uk mwilkin@mrc-lmb.cam.ac.uk kn@mrc-lmb.cam.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
U5 small nuclear ribonucleoprotein 40 kDa protein
5O
357Homo sapiensMutation(s): 0 
Gene Names: SNRNP40 (PRP8BP, SFP38, WDR57)
Find proteins for Q96DI7 (Homo sapiens)
Go to Gene View: SNRNP40
Go to UniProtKB:  Q96DI7
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3B subunit 4
B4
424Homo sapiensMutation(s): 0 
Gene Names: SF3B4 (SAP49)
Find proteins for Q15427 (Homo sapiens)
Go to Gene View: SF3B4
Go to UniProtKB:  Q15427
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3
13, 53, 23, 43
126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
Find proteins for P62318 (Homo sapiens)
Go to Gene View: SNRPD3
Go to UniProtKB:  P62318
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
U4/U6 small nuclear ribonucleoprotein Prp4
4B
522Homo sapiensMutation(s): 0 
Gene Names: PRPF4 (PRP4)
Find proteins for O43172 (Homo sapiens)
Go to Gene View: PRPF4
Go to UniProtKB:  O43172
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein E
5e, 4e, 1e, 2e
92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
Find proteins for P62304 (Homo sapiens)
Go to Gene View: SNRPE
Go to UniProtKB:  P62304
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein 70 kDa
1K
437Homo sapiensMutation(s): 0 
Gene Names: SNRNP70 (RNPU1Z, RPU1, SNRP70, U1AP1)
Find proteins for P08621 (Homo sapiens)
Go to Gene View: SNRNP70
Go to UniProtKB:  P08621
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
U4/U6 small nuclear ribonucleoprotein Prp31
4C
499Homo sapiensMutation(s): 0 
Gene Names: PRPF31 (PRP31)
Find proteins for Q8WWY3 (Homo sapiens)
Go to Gene View: PRPF31
Go to UniProtKB:  Q8WWY3
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1
41, 11, 51, 21
119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
Find proteins for P62314 (Homo sapiens)
Go to Gene View: SNRPD1
Go to UniProtKB:  P62314
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
RNA-binding protein 42
R
480Homo sapiensMutation(s): 0 
Gene Names: RBM42
Find proteins for Q9BTD8 (Homo sapiens)
Go to Gene View: RBM42
Go to UniProtKB:  Q9BTD8
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F
1f, 2f, 5f, 4f
86Homo sapiensMutation(s): 0 
Gene Names: SNRPF (PBSCF)
Find proteins for P62306 (Homo sapiens)
Go to Gene View: SNRPF
Go to UniProtKB:  P62306
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm6
66
80Homo sapiensMutation(s): 0 
Gene Names: LSM6
Find proteins for P62312 (Homo sapiens)
Go to Gene View: LSM6
Go to UniProtKB:  P62312
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein
X
155Homo sapiensMutation(s): 0 
Gene Names: SNRNP27
Find proteins for Q8WVK2 (Homo sapiens)
Go to Gene View: SNRNP27
Go to UniProtKB:  Q8WVK2
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2
22, 42, 52, 12
118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2 (SNRPD1)
Find proteins for P62316 (Homo sapiens)
Go to Gene View: SNRPD2
Go to UniProtKB:  P62316
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm7
67
103Homo sapiensMutation(s): 0 
Gene Names: LSM7
Find proteins for Q9UK45 (Homo sapiens)
Go to Gene View: LSM7
Go to UniProtKB:  Q9UK45
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm2
62
95Homo sapiensMutation(s): 0 
Gene Names: LSM2 (C6orf28, G7B)
Find proteins for Q9Y333 (Homo sapiens)
Go to Gene View: LSM2
Go to UniProtKB:  Q9Y333
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
U2 small nuclear ribonucleoprotein B''
2B
225Homo sapiensMutation(s): 0 
Gene Names: SNRPB2
Find proteins for P08579 (Homo sapiens)
Go to Gene View: SNRPB2
Go to UniProtKB:  P08579
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3A subunit 2
A2
209Homo sapiensMutation(s): 0 
Gene Names: SF3A2 (SAP62)
Find proteins for Q15428 (Homo sapiens)
Go to Gene View: SF3A2
Go to UniProtKB:  Q15428
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3B subunit 2
B2
895Homo sapiensMutation(s): 0 
Gene Names: SF3B2 (SAP145)
Find proteins for Q13435 (Homo sapiens)
Go to Gene View: SF3B2
Go to UniProtKB:  Q13435
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
116 kDa U5 small nuclear ribonucleoprotein component
5C
854Homo sapiensMutation(s): 0 
Gene Names: EFTUD2 (KIAA0031, SNRP116)
Find proteins for Q15029 (Homo sapiens)
Go to Gene View: EFTUD2
Go to UniProtKB:  Q15029
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Probable ATP-dependent RNA helicase DDX23
5X
820Homo sapiensMutation(s): 0 
Gene Names: DDX23
EC: 3.6.4.13
Find proteins for Q9BUQ8 (Homo sapiens)
Go to Gene View: DDX23
Go to UniProtKB:  Q9BUQ8
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated proteins B and B'
1b, 2b, 5b, 4b
240Homo sapiensMutation(s): 0 
Gene Names: SNRPB (COD, SNRPB1)
Find proteins for P14678 (Homo sapiens)
Go to Gene View: SNRPB
Go to UniProtKB:  P14678
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3B subunit 5
B5
86Homo sapiensMutation(s): 0 
Gene Names: SF3B5 (SF3B10)
Find proteins for Q9BWJ5 (Homo sapiens)
Go to Gene View: SF3B5
Go to UniProtKB:  Q9BWJ5
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein A
1A
282Homo sapiensMutation(s): 0 
Gene Names: SNRPA
Find proteins for P09012 (Homo sapiens)
Go to Gene View: SNRPA
Go to UniProtKB:  P09012
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
U4/U6.U5 tri-snRNP-associated protein 1
S
800Homo sapiensMutation(s): 0 
Gene Names: SART1
Find proteins for O43290 (Homo sapiens)
Go to Gene View: SART1
Go to UniProtKB:  O43290
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 6
5J
850Homo sapiensMus musculus
This entity is chimeric
Mutation(s): 0 
Gene Names: PRPF6 (C20orf14), Prpf6
Find proteins for O94906 (Homo sapiens)
Go to Gene View: PRPF6
Go to UniProtKB:  O94906
Find proteins for Q91YR7 (Mus musculus)
Go to UniProtKB:  Q91YR7
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
NHP2-like protein 1
4D
128Homo sapiensMutation(s): 0 
Gene Names: SNU13 (NHP2L1)
Find proteins for P55769 (Homo sapiens)
Go to Gene View: SNU13
Go to UniProtKB:  P55769
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm3
63
102Homo sapiensMutation(s): 0 
Gene Names: LSM3
Find proteins for P62310 (Homo sapiens)
Go to Gene View: LSM3
Go to UniProtKB:  P62310
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3B subunit 3
B3
1217Homo sapiensMutation(s): 0 
Gene Names: SF3B3 (KIAA0017, SAP130)
Find proteins for Q15393 (Homo sapiens)
Go to Gene View: SF3B3
Go to UniProtKB:  Q15393
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G
1g, 2g, 5g, 4g
76Homo sapiensMutation(s): 0 
Gene Names: SNRPG (PBSCG)
Find proteins for P62308 (Homo sapiens)
Go to Gene View: SNRPG
Go to UniProtKB:  P62308
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm8
68
96Homo sapiensMutation(s): 0 
Gene Names: LSM8
Find proteins for O95777 (Homo sapiens)
Go to Gene View: LSM8
Go to UniProtKB:  O95777
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing-splicing factor 8
5A
2311Homo sapiensMutation(s): 0 
Gene Names: PRPF8 (PRPC8)
Find proteins for Q6P2Q9 (Homo sapiens)
Go to Gene View: PRPF8
Go to UniProtKB:  Q6P2Q9
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3A subunit 3
A3
501Homo sapiensMutation(s): 0 
Gene Names: SF3A3 (SAP61)
Find proteins for Q12874 (Homo sapiens)
Go to Gene View: SF3A3
Go to UniProtKB:  Q12874
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
U4/U6.U5 tri-snRNP-associated protein 2
U
555Homo sapiensMutation(s): 0 
Gene Names: USP39
Find proteins for Q53GS9 (Homo sapiens)
Go to Gene View: USP39
Go to UniProtKB:  Q53GS9
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
Thioredoxin-like protein 4A
5D
142Homo sapiensMutation(s): 0 
Gene Names: TXNL4A (DIM1, TXNL4)
Find proteins for P83876 (Homo sapiens)
Go to Gene View: TXNL4A
Go to UniProtKB:  P83876
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm4
64
139Homo sapiensMutation(s): 0 
Gene Names: LSM4
Find proteins for Q9Y4Z0 (Homo sapiens)
Go to Gene View: LSM4
Go to UniProtKB:  Q9Y4Z0
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
PHD finger-like domain-containing protein 5A
BP
104Homo sapiensMutation(s): 0 
Gene Names: PHF5A
Find proteins for Q7RTV0 (Homo sapiens)
Go to Gene View: PHF5A
Go to UniProtKB:  Q7RTV0
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein C
1C
159Homo sapiensMutation(s): 0 
Gene Names: SNRPC
Find proteins for P09234 (Homo sapiens)
Go to Gene View: SNRPC
Go to UniProtKB:  P09234
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase PRP4 homolog
K
1007Homo sapiensMutation(s): 0 
Gene Names: PRPF4B (KIAA0536, PRP4, PRP4H, PRP4K)
EC: 2.7.11.1
Find proteins for Q13523 (Homo sapiens)
Go to Gene View: PRPF4B
Go to UniProtKB:  Q13523
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
U4/U6 small nuclear ribonucleoprotein Prp3
4A
683Homo sapiensMutation(s): 0 
Gene Names: PRPF3 (HPRP3, PRP3)
Find proteins for O43395 (Homo sapiens)
Go to Gene View: PRPF3
Go to UniProtKB:  O43395
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
U2 small nuclear ribonucleoprotein A'
2A
255Homo sapiensMutation(s): 0 
Gene Names: SNRPA1
Find proteins for P09661 (Homo sapiens)
Go to Gene View: SNRPA1
Go to UniProtKB:  P09661
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3A subunit 1,Splicing factor 3A subunit 1,Splicing factor 3A subunit 1
A1
647Homo sapiensMutation(s): 0 
Gene Names: SF3A1 (SAP114)
Find proteins for Q15459 (Homo sapiens)
Go to Gene View: SF3A1
Go to UniProtKB:  Q15459
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm5
65
91Homo sapiensMutation(s): 0 
Gene Names: LSM5
Find proteins for Q9Y4Y9 (Homo sapiens)
Go to Gene View: LSM5
Go to UniProtKB:  Q9Y4Y9
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
U5 small nuclear ribonucleoprotein 200 kDa helicase
5B
2136Homo sapiensMutation(s): 0 
Gene Names: SNRNP200 (ASCC3L1, HELIC2, KIAA0788)
EC: 3.6.4.13
Find proteins for O75643 (Homo sapiens)
Go to Gene View: SNRNP200
Go to UniProtKB:  O75643
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3B subunit 1
B1
1304Homo sapiensMutation(s): 0 
Gene Names: SF3B1 (SAP155)
Find proteins for O75533 (Homo sapiens)
Go to Gene View: SF3B1
Go to UniProtKB:  O75533
Entity ID: 1
MoleculeChainsLengthOrganism
U1 snRNA1164Homo sapiens
Entity ID: 2
MoleculeChainsLengthOrganism
U6 snRNA6106Homo sapiens
Entity ID: 8
MoleculeChainsLengthOrganism
AdML pre-mRNAI62Human adenovirus 2
Entity ID: 17
MoleculeChainsLengthOrganism
U5 snRNA5117Homo sapiens
Entity ID: 32
MoleculeChainsLengthOrganism
U2 snRNA2188Homo sapiens
Entity ID: 45
MoleculeChainsLengthOrganism
U4 snRNA4146Homo sapiens
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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1C, A2, BP, U
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GTP
Query on GTP

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5C
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
5C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
IHP
Query on IHP

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Download CCD File 
5A
INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
A1
L-PEPTIDE LINKINGC4 H9 N O2

--

N
Query on N
I
RNA LINKINGC5 H11 O7 P

--

M7M
Query on M7M
4
NON-POLYMERC13 H23 N5 O11 P2

--

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilUnited KingdomAdG-693087-SPLICE3D
Medical Research Council (United Kingdom)United KingdomMC_U105184330

Revision History 

  • Version 1.0: 2019-04-17
    Type: Initial release
  • Version 1.1: 2019-04-24
    Type: Data collection, Database references
  • Version 1.2: 2019-05-08
    Type: Data collection, Database references