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
  • Structures With Same Primary Citation

  • 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

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
U5 small nuclear ribonucleoprotein 40 kDa protein
5O
357Homo sapiensMutation(s): 0 
Gene Names: SNRNP40PRP8BPSFP38WDR57
Find proteins for Q96DI7 (Homo sapiens)
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PHAROS  Q96DI7

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3B subunit 4
B4
424Homo sapiensMutation(s): 0 
Gene Names: SF3B4SAP49
Find proteins for Q15427 (Homo sapiens)
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PHAROS  Q15427

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3
13, 23, 43, 53
126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
Find proteins for P62318 (Homo sapiens)
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PHAROS  P62318

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
U4/U6 small nuclear ribonucleoprotein Prp4
4B
522Homo sapiensMutation(s): 0 
Gene Names: PRPF4PRP4
Find proteins for O43172 (Homo sapiens)
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PHAROS  O43172

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein E
1e, 2e, 4e, 5e
92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
Find proteins for P62304 (Homo sapiens)
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PHAROS  P62304

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein 70 kDa
1K
437Homo sapiensMutation(s): 0 
Gene Names: SNRNP70RNPU1ZRPU1SNRP70U1AP1
Find proteins for P08621 (Homo sapiens)
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PHAROS  P08621

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
U4/U6 small nuclear ribonucleoprotein Prp31
4C
499Homo sapiensMutation(s): 0 
Gene Names: PRPF31PRP31
Find proteins for Q8WWY3 (Homo sapiens)
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PHAROS  Q8WWY3

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1
11, 21, 41, 51
119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
Find proteins for P62314 (Homo sapiens)
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PHAROS  P62314

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
RNA-binding protein 42
R
480Homo sapiensMutation(s): 0 
Gene Names: RBM42
Find proteins for Q9BTD8 (Homo sapiens)
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PHAROS  Q9BTD8

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F
1f, 2f, 4f, 5f
86Homo sapiensMutation(s): 0 
Gene Names: SNRPFPBSCF
Find proteins for P62306 (Homo sapiens)
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PHAROS  P62306

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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)
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PHAROS  P62312

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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)
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PHAROS  Q8WVK2

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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2
12, 22, 42, 52
118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2SNRPD1
Find proteins for P62316 (Homo sapiens)
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PHAROS  P62316

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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)
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PHAROS  Q9UK45

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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm2
62
95Homo sapiensMutation(s): 0 
Gene Names: LSM2C6orf28G7B
Find proteins for Q9Y333 (Homo sapiens)
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PHAROS  Q9Y333

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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3A subunit 2
A2
209Homo sapiensMutation(s): 0 
Gene Names: SF3A2SAP62
Find proteins for Q15428 (Homo sapiens)
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PHAROS  Q15428

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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3B subunit 2
B2
895Homo sapiensMutation(s): 0 
Gene Names: SF3B2SAP145
Find proteins for Q13435 (Homo sapiens)
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PHAROS  Q13435

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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
116 kDa U5 small nuclear ribonucleoprotein component
5C
854Homo sapiensMutation(s): 0 
Gene Names: EFTUD2KIAA0031SNRP116
Find proteins for Q15029 (Homo sapiens)
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PHAROS  Q15029

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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)
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PHAROS  Q9BUQ8

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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated proteins B and B'
1b, 2b, 4b, 5b
240Homo sapiensMutation(s): 0 
Gene Names: SNRPBCODSNRPB1
Find proteins for P14678 (Homo sapiens)
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PHAROS  P14678

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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3B subunit 5
B5
86Homo sapiensMutation(s): 0 
Gene Names: SF3B5SF3B10
Find proteins for Q9BWJ5 (Homo sapiens)
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PHAROS  Q9BWJ5

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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein A
1A
282Homo sapiensMutation(s): 0 
Gene Names: SNRPA
Find proteins for P09012 (Homo sapiens)
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PHAROS  P09012

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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)
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PHAROS  O43290

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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 6
5J
850Homo sapiensMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
NHP2-like protein 1
4D
128Homo sapiensMutation(s): 0 
Gene Names: SNU13NHP2L1
Find proteins for P55769 (Homo sapiens)
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PHAROS  P55769

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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm3
63
102Homo sapiensMutation(s): 0 
Gene Names: LSM3MDS017
Find proteins for P62310 (Homo sapiens)
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PHAROS  P62310

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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3B subunit 3
B3
1217Homo sapiensMutation(s): 0 
Gene Names: SF3B3KIAA0017SAP130
Find proteins for Q15393 (Homo sapiens)
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PHAROS  Q15393

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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G
1g, 2g, 4g, 5g
76Homo sapiensMutation(s): 0 
Gene Names: SNRPGPBSCG
Find proteins for P62308 (Homo sapiens)
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PHAROS  P62308

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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)
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PHAROS  O95777

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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing-splicing factor 8
5A
2311Homo sapiensMutation(s): 0 
Gene Names: PRPF8PRPC8
Find proteins for Q6P2Q9 (Homo sapiens)
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PHAROS  Q6P2Q9

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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3A subunit 3
A3
501Homo sapiensMutation(s): 0 
Gene Names: SF3A3SAP61
Find proteins for Q12874 (Homo sapiens)
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PHAROS  Q12874

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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
U4/U6.U5 tri-snRNP-associated protein 2
U
555Homo sapiensMutation(s): 0 
Gene Names: USP39CGI-21HSPC332PRO2855
Find proteins for Q53GS9 (Homo sapiens)
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PHAROS  Q53GS9

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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
Thioredoxin-like protein 4A
5D
142Homo sapiensMutation(s): 0 
Gene Names: TXNL4ADIM1TXNL4
Find proteins for P83876 (Homo sapiens)
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PHAROS  P83876

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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)
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PHAROS  Q9Y4Z0

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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)
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PHAROS  Q7RTV0

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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein C
1C
159Homo sapiensMutation(s): 0 
Gene Names: SNRPC
Find proteins for P09234 (Homo sapiens)
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PHAROS  P09234

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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase PRP4 homolog
K
1007Homo sapiensMutation(s): 0 
Gene Names: PRPF4BKIAA0536PRP4PRP4HPRP4K
EC: 2.7.11.1
Find proteins for Q13523 (Homo sapiens)
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PHAROS  Q13523

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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
U4/U6 small nuclear ribonucleoprotein Prp3
4A
683Homo sapiensMutation(s): 0 
Gene Names: PRPF3HPRP3PRP3
Find proteins for O43395 (Homo sapiens)
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PHAROS  O43395

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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
U2 small nuclear ribonucleoprotein A'
2A
255Homo sapiensMutation(s): 0 
Gene Names: SNRPA1
Find proteins for P09661 (Homo sapiens)
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PHAROS  P09661

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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
Find proteins for Q15459 (Homo sapiens)
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PHAROS  Q15459

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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)
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PHAROS  Q9Y4Y9

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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
U5 small nuclear ribonucleoprotein 200 kDa helicase
5B
2136Homo sapiensMutation(s): 0 
Gene Names: SNRNP200ASCC3L1HELIC2KIAA0788
EC: 3.6.4.13
Find proteins for O75643 (Homo sapiens)
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PHAROS  O75643

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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3B subunit 1
B1
1304Homo sapiensMutation(s): 0 
Gene Names: SF3B1SAP155
Find proteins for O75533 (Homo sapiens)
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PHAROS  O75533

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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
U2 small nuclear ribonucleoprotein B''
2B
225Homo sapiensMutation(s): 0 
Gene Names: SNRPB2
Find proteins for P08579 (Homo sapiens)
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PHAROS  P08579

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Entity ID: 1
MoleculeChainsLengthOrganism
U1 snRNA1164Homo sapiens

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Entity ID: 2
MoleculeChainsLengthOrganism
U6 snRNA6106Homo sapiens

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Entity ID: 8
MoleculeChainsLengthOrganism
AdML pre-mRNAI62Human adenovirus 2

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Entity ID: 17
MoleculeChainsLengthOrganism
U5 snRNA5117Homo sapiens

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Entity ID: 32
MoleculeChainsLengthOrganism
U2 snRNA2188Homo sapiens

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Entity ID: 45
MoleculeChainsLengthOrganism
U4 snRNA4146Homo sapiens
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP

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5A
INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-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
ZN
Query on ZN

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

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5C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

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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
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-08
    Changes: Data collection, Database references