6QW6

Structure of the human U5.U4/U6 tri-snRNP at 2.9A resolution.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 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:  
    6QW6, 6QX9

  • 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 pre-B spliceosome ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
U4/U6.U5 small nuclear ribonucleoprotein 27 kDa proteinA [auth X]155Homo sapiensMutation(s): 0 
Gene Names: SNRNP27
Find proteins for Q8WVK2 (Homo sapiens)
Explore Q8WVK2 
Go to UniProtKB:  Q8WVK2
NIH Common Fund Data Resources
PHAROS:  Q8WVK2
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1C [auth 41], O [auth 51]119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
Find proteins for P62314 (Homo sapiens)
Explore P62314 
Go to UniProtKB:  P62314
NIH Common Fund Data Resources
PHAROS:  P62314
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2D [auth 42], P [auth 52]118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2SNRPD1
Find proteins for P62316 (Homo sapiens)
Explore P62316 
Go to UniProtKB:  P62316
NIH Common Fund Data Resources
PHAROS:  P62316
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3E [auth 43], Q [auth 53]126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
Find proteins for P62318 (Homo sapiens)
Explore P62318 
Go to UniProtKB:  P62318
NIH Common Fund Data Resources
PHAROS:  P62318
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein Prp3F [auth 4A]683Homo sapiensMutation(s): 0 
Gene Names: PRPF3HPRP3PRP3
Find proteins for O43395 (Homo sapiens)
Explore O43395 
Go to UniProtKB:  O43395
NIH Common Fund Data Resources
PHAROS:  O43395
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein Prp4G [auth 4B]522Homo sapiensMutation(s): 0 
Gene Names: PRPF4PRP4
Find proteins for O43172 (Homo sapiens)
Explore O43172 
Go to UniProtKB:  O43172
NIH Common Fund Data Resources
PHAROS:  O43172
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein Prp31H [auth 4C]499Homo sapiensMutation(s): 0 
Gene Names: PRPF31PRP31
Find proteins for Q8WWY3 (Homo sapiens)
Explore Q8WWY3 
Go to UniProtKB:  Q8WWY3
NIH Common Fund Data Resources
PHAROS:  Q8WWY3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
NHP2-like protein 1I [auth 4D]128Homo sapiensMutation(s): 0 
Gene Names: SNU13NHP2L1
Find proteins for P55769 (Homo sapiens)
Explore P55769 
Go to UniProtKB:  P55769
NIH Common Fund Data Resources
PHAROS:  P55769
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'J [auth 4b], Y [auth 5b]240Homo sapiensMutation(s): 0 
Gene Names: SNRPBCODSNRPB1
Find proteins for P14678 (Homo sapiens)
Explore P14678 
Go to UniProtKB:  P14678
NIH Common Fund Data Resources
PHAROS:  P14678
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EK [auth 4e], Z [auth 5e]92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
Find proteins for P62304 (Homo sapiens)
Explore P62304 
Go to UniProtKB:  P62304
NIH Common Fund Data Resources
PHAROS:  P62304
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FL [auth 4f], AA [auth 5f]86Homo sapiensMutation(s): 0 
Gene Names: SNRPFPBSCF
Find proteins for P62306 (Homo sapiens)
Explore P62306 
Go to UniProtKB:  P62306
NIH Common Fund Data Resources
PHAROS:  P62306
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GM [auth 4g], BA [auth 5g]76Homo sapiensMutation(s): 0 
Gene Names: SNRPGPBSCG
Find proteins for P62308 (Homo sapiens)
Explore P62308 
Go to UniProtKB:  P62308
NIH Common Fund Data Resources
PHAROS:  P62308
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 8R [auth 5A]2311Homo sapiensMutation(s): 0 
Gene Names: PRPF8PRPC8
Find proteins for Q6P2Q9 (Homo sapiens)
Explore Q6P2Q9 
Go to UniProtKB:  Q6P2Q9
NIH Common Fund Data Resources
PHAROS:  Q6P2Q9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 200 kDa helicaseS [auth 5B]2136Homo sapiensMutation(s): 0 
Gene Names: SNRNP200ASCC3L1HELIC2KIAA0788
EC: 3.6.4.13
Find proteins for O75643 (Homo sapiens)
Explore O75643 
Go to UniProtKB:  O75643
NIH Common Fund Data Resources
PHAROS:  O75643
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein componentT [auth 5C]853Homo sapiensMutation(s): 0 
Gene Names: EFTUD2KIAA0031SNRP116
Find proteins for Q15029 (Homo sapiens)
Explore Q15029 
Go to UniProtKB:  Q15029
NIH Common Fund Data Resources
PHAROS:  Q15029
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Thioredoxin-like protein 4AU [auth 5D]142Homo sapiensMutation(s): 0 
Gene Names: TXNL4ADIM1TXNL4
Find proteins for P83876 (Homo sapiens)
Explore P83876 
Go to UniProtKB:  P83876
NIH Common Fund Data Resources
PHAROS:  P83876
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 6V [auth 5J]941Homo sapiensMutation(s): 0 
Gene Names: PRPF6C20orf14
Find proteins for O94906 (Homo sapiens)
Explore O94906 
Go to UniProtKB:  O94906
NIH Common Fund Data Resources
PHAROS:  O94906
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 40 kDa proteinW [auth 5O]357Homo sapiensMutation(s): 0 
Gene Names: SNRNP40PRP8BPSFP38WDR57
Find proteins for Q96DI7 (Homo sapiens)
Explore Q96DI7 
Go to UniProtKB:  Q96DI7
NIH Common Fund Data Resources
PHAROS:  Q96DI7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Probable ATP-dependent RNA helicase DDX23X [auth 5X]820Homo sapiensMutation(s): 0 
Gene Names: DDX23
EC: 3.6.4.13
Find proteins for Q9BUQ8 (Homo sapiens)
Explore Q9BUQ8 
Go to UniProtKB:  Q9BUQ8
NIH Common Fund Data Resources
PHAROS:  Q9BUQ8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm2DA [auth 62]95Homo sapiensMutation(s): 0 
Gene Names: LSM2C6orf28G7B
Find proteins for Q9Y333 (Homo sapiens)
Explore Q9Y333 
Go to UniProtKB:  Q9Y333
NIH Common Fund Data Resources
PHAROS:  Q9Y333
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm3EA [auth 63]102Homo sapiensMutation(s): 0 
Gene Names: LSM3MDS017
Find proteins for P62310 (Homo sapiens)
Explore P62310 
Go to UniProtKB:  P62310
NIH Common Fund Data Resources
PHAROS:  P62310
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm4FA [auth 64]139Homo sapiensMutation(s): 0 
Gene Names: LSM4
Find proteins for Q9Y4Z0 (Homo sapiens)
Explore Q9Y4Z0 
Go to UniProtKB:  Q9Y4Z0
NIH Common Fund Data Resources
PHAROS:  Q9Y4Z0
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm5GA [auth 65]91Homo sapiensMutation(s): 0 
Gene Names: LSM5
Find proteins for Q9Y4Y9 (Homo sapiens)
Explore Q9Y4Y9 
Go to UniProtKB:  Q9Y4Y9
NIH Common Fund Data Resources
PHAROS:  Q9Y4Y9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm6HA [auth 66]80Homo sapiensMutation(s): 0 
Gene Names: LSM6
Find proteins for P62312 (Homo sapiens)
Explore P62312 
Go to UniProtKB:  P62312
NIH Common Fund Data Resources
PHAROS:  P62312
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm7IA [auth 67]103Homo sapiensMutation(s): 0 
Gene Names: LSM7
Find proteins for Q9UK45 (Homo sapiens)
Explore Q9UK45 
Go to UniProtKB:  Q9UK45
NIH Common Fund Data Resources
PHAROS:  Q9UK45
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm8JA [auth 68]96Homo sapiensMutation(s): 0 
Gene Names: LSM8
Find proteins for O95777 (Homo sapiens)
Explore O95777 
Go to UniProtKB:  O95777
NIH Common Fund Data Resources
PHAROS:  O95777
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-binding protein 42KA [auth R]480Homo sapiensMutation(s): 0 
Gene Names: RBM42
Find proteins for Q9BTD8 (Homo sapiens)
Explore Q9BTD8 
Go to UniProtKB:  Q9BTD8
NIH Common Fund Data Resources
PHAROS:  Q9BTD8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
U4/U6.U5 tri-snRNP-associated protein 1LA [auth S]800Homo sapiensMutation(s): 0 
Gene Names: SART1
Find proteins for O43290 (Homo sapiens)
Explore O43290 
Go to UniProtKB:  O43290
NIH Common Fund Data Resources
PHAROS:  O43290
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
U4/U6.U5 tri-snRNP-associated protein 2MA [auth U]555Homo sapiensMutation(s): 0 
Gene Names: USP39CGI-21HSPC332PRO2855
Find proteins for Q53GS9 (Homo sapiens)
Explore Q53GS9 
Go to UniProtKB:  Q53GS9
NIH Common Fund Data Resources
PHAROS:  Q53GS9
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
U4 snRNAB [auth 4]146Homo sapiens
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 14
MoleculeChainsLengthOrganismImage
U5 snRNAN [auth 5]117Homo sapiens
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 22
MoleculeChainsLengthOrganismImage
U6 snRNACA [auth 6]88Homo sapiens
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP

Download Ideal Coordinates CCD File 
NA [auth 5A]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
 Ligand Interaction
GTP
Query on GTP

Download Ideal Coordinates CCD File 
PA [auth 5C]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
QA [auth U]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
OA [auth 5C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



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  (Full details and data files)

  • 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
  • Version 1.3: 2020-10-07
    Changes: Derived calculations, Structure summary