5O9Z

Cryo-EM structure of a pre-catalytic human spliceosome primed for activation (B complex)

  • Classification: SPLICING
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2017-06-20 Released: 2017-08-16 
  • Deposition Author(s): Bertram, K., Kastner, B.
  • Funding Organization(s): Max Planck Society, German Research Foundation

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 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

Cryo-EM Structure of a Pre-catalytic Human Spliceosome Primed for Activation.

Bertram, K.Agafonov, D.E.Dybkov, O.Haselbach, D.Leelaram, M.N.Will, C.L.Urlaub, H.Kastner, B.Luhrmann, R.Stark, H.

(2017) Cell 170: 701-713.e11

  • DOI: https://doi.org/10.1016/j.cell.2017.07.011
  • Primary Citation of Related Structures:  
    5O9Z

  • PubMed Abstract: 

    Little is known about the spliceosome's structure before its extensive remodeling into a catalytically active complex. Here, we report a 3D cryo-EM structure of a pre-catalytic human spliceosomal B complex. The U2 snRNP-containing head domain is connected to the B complex main body via three main bridges. U4/U6.U5 tri-snRNP proteins, which are located in the main body, undergo significant rearrangements during tri-snRNP integration into the B complex. These include formation of a partially closed Prp8 conformation that creates, together with Dim1, a 5' splice site (ss) binding pocket, displacement of Sad1, and rearrangement of Brr2 such that it contacts its U4/U6 substrate and is poised for the subsequent spliceosome activation step. The molecular organization of several B-specific proteins suggests that they are involved in negatively regulating Brr2, positioning the U6/5'ss helix, and stabilizing the B complex structure. Our results indicate significant differences between the early activation phase of human and yeast spliceosomes.


  • Organizational Affiliation

    Department of Structural Dynamics, MPI for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 82,335Homo sapiensMutation(s): 0 
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PHAROS:  Q6P2Q9
GTEx:  ENSG00000174231 
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UniProt GroupQ6P2Q9
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein component972Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108883 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 200 kDa helicase2,136Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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GTEx:  ENSG00000144028 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 40 kDa protein357Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000060688 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein Prp3683Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000117360 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein Prp4521Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136875 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 6941Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000101161 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein Prp31499Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105618 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 38A312Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134748 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Thioredoxin-like protein 4A142Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000141759 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Microfibrillar-associated protein 1439Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000140259 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
WD40 repeat-containing protein SMU1513Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122692 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase H177Homo sapiensMutation(s): 0 
EC: 5.2.1.8
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GTEx:  ENSG00000171960 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger matrin-type protein 2199Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000146007 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NHP2-like protein 1128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100138 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
U4/U6.U5 tri-snRNP-associated protein 1800Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175467 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
WW domain-binding protein 4376Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000120688 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Protein Red557Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000113141 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2S [auth a],
TA [auth S],
Z [auth h]
118Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125743 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FAA [auth i],
T [auth b],
UA [auth T]
86Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000139343 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EBA [auth j],
U [auth c],
VA [auth U]
92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182004 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GCA [auth k],
V [auth d],
WA [auth V]
76Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143977 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3DA [auth l],
W [auth e],
XA [auth W]
126Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100028 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'EA [auth m],
X [auth f],
YA [auth X]
240Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125835 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1FA [auth n],
Y [auth g],
ZA [auth Z]
119Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167088 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm2GA [auth o]95Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204392 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm3HA [auth p]102Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170860 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm4IA [auth q]139Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130520 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm5JA [auth r]91Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106355 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm6KA [auth s]80Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164167 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm7LA [auth t]103Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130332 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm8MA [auth u]96Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000128534 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 1NA [auth v]1,304Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115524 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 3 (SF3B3)OA [auth w]1,217Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000189091 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 5PA [auth x]86Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000169976 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
PHD finger-like domain-containing protein 5AQA [auth y]110Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100410 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'RA [auth z]256Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131876 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''SA [auth 1]225Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125870 
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Entity ID: 39
MoleculeChains LengthOrganismImage
MINX pre-mRNAAB [auth Y]324Homo sapiens
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Entity ID: 40
MoleculeChains LengthOrganismImage
Human gene for small nuclear RNA U2 (snRNA U2)BB [auth 2]188Homo sapiens
Sequence Annotations
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Entity ID: 41
MoleculeChains LengthOrganismImage
Homo sapiens U4A snRNACB [auth 4]145Homo sapiens
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Entity ID: 42
MoleculeChains LengthOrganismImage
Homo sapiens U5 A small nuclear RNADB [auth 5]116Homo sapiens
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Entity ID: 43
MoleculeChains LengthOrganismImage
Homo sapiens RNA, U6 small nuclear 1 (RNU6-1), small nuclear RNAEB [auth 6]106Homo sapiens
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
German Research FoundationGermanySFB 860
German Research FoundationGermanyLU294/15-1

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-16
    Type: Initial release
  • Version 1.1: 2017-08-23
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Author supporting evidence
  • Version 1.3: 2018-10-24
    Changes: Advisory, Data collection, Derived calculations