5MQF

Cryo-EM structure of a human spliceosome activated for step 2 of splicing (C* complex)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.90 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 human spliceosome activated for step 2 of splicing.

Bertram, K.Agafonov, D.E.Liu, W.T.Dybkov, O.Will, C.L.Hartmuth, K.Urlaub, H.Kastner, B.Stark, H.Lu Hrmann, R.

(2017) Nature 542: 318-323

  • DOI: https://doi.org/10.1038/nature21079
  • Primary Citation of Related Structures:  
    5MQF

  • PubMed Abstract: 

    Spliceosome rearrangements facilitated by RNA helicase PRP16 before catalytic step two of splicing are poorly understood. Here we report a 3D cryo-electron microscopy structure of the human spliceosomal C complex stalled directly after PRP16 action (C*). The architecture of the catalytic U2-U6 ribonucleoprotein (RNP) core of the human C* spliceosome is very similar to that of the yeast pre-Prp16 C complex. However, in C* the branched intron region is separated from the catalytic centre by approximately 20 Å, and its position close to the U6 small nuclear RNA ACAGA box is stabilized by interactions with the PRP8 RNase H-like and PRP17 WD40 domains. RNA helicase PRP22 is located about 100 Å from the catalytic centre, suggesting that it destabilizes the spliced mRNA after step two from a distance. Comparison of the structure of the yeast C and human C* complexes reveals numerous RNP rearrangements that are likely to be facilitated by PRP16, including a large-scale movement of the U2 small nuclear RNP.


  • Organizational Affiliation

    Bioanalytics Group, Institute for Clinical Chemistry, University Medical Centre Göttingen, Robert-Koch-Straße 40, D-37075 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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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
SNW domain-containing protein 1536Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100603 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Pleiotropic regulator 1515Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171566 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17579Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168438 
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UniProt GroupO60508
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 40 kDa protein357Homo sapiensMutation(s): 0 
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PHAROS:  Q96DI7
GTEx:  ENSG00000060688 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19
G, H, I, J
504Homo sapiensMutation(s): 0 
EC: 6.3.2
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GTEx:  ENSG00000110107 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SPF27225Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116752 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division cycle 5-like protein802Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000096401 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF1855Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000076924 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF2243Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000117614 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Crooked neck-like protein 1848Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000101343 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RBM22420Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000086589 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Protein BUD31 homolog144Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106245 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homolog229Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000150316 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/arginine repetitive matrix protein 22,752Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167978 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC22 homolog908Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163510 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Intron-binding protein aquarius1,485Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000021776 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase-like 1166Homo sapiensMutation(s): 0 
EC: 5.2.1.8
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GTEx:  ENSG00000137168 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'255Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131876 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''225Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125870 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2FA [auth h],
Y [auth a]
118Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125743 
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UniProt GroupP62316
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FGA [auth i],
Z [auth b]
86Homo sapiensMutation(s): 0 
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PHAROS:  P62306
GTEx:  ENSG00000139343 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EAA [auth c],
HA [auth j]
92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182004 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GBA [auth d],
IA [auth k]
76Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143977 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3CA [auth e],
JA [auth l]
126Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100028 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'DA [auth f],
KA [auth m]
240Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125835 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1EA [auth g],
LA [auth n]
119Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167088 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase EMA [auth o]301Homo sapiensMutation(s): 0 
EC: 5.2.1.8
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GTEx:  ENSG00000084072 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic initiation factor 4A-IIINA [auth p]411Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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GTEx:  ENSG00000141543 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent RNA helicase DHX8OA [auth q]1,218Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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GTEx:  ENSG00000067596 
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Entity ID: 32
MoleculeChains LengthOrganismImage
MINX pre-mRNA (intron)PA [auth Y],
QA [auth Z]
324Homo sapiens
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Entity ID: 33
MoleculeChains LengthOrganismImage
Human gene for small nuclear RNA U2 (snRNA U2)RA [auth 2]188Homo sapiens
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Entity ID: 34
MoleculeChains LengthOrganismImage
Homo sapiens U5 A small nuclear RNASA [auth 5]116Homo sapiens
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Entity ID: 35
MoleculeChains LengthOrganismImage
Homo sapiens RNA, U6 small nuclear 1 (RNU6-1), small nuclear RNATA [auth 6]106Homo sapiens
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Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
U
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB 860

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Author supporting evidence
  • Version 1.2: 2018-10-24
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.3: 2018-11-21
    Changes: Advisory, Data collection, Derived calculations