7A5P

Human C Complex Spliceosome - Medium-resolution PERIPHERY

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

  • Deposited: 2020-08-21 Released: 2020-10-14 
  • Deposition Author(s): Bertram, K., Kastner, B.
  • Funding Organization(s): Max Planck Society, German Research Foundation (DFG)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Insights into the Roles of Metazoan-Specific Splicing Factors in the Human Step 1 Spliceosome.

Bertram, K.El Ayoubi, L.Dybkov, O.Agafonov, D.E.Will, C.L.Hartmuth, K.Urlaub, H.Kastner, B.Stark, H.Luhrmann, R.

(2020) Mol Cell 80: 127-139.e6

  • DOI: https://doi.org/10.1016/j.molcel.2020.09.012
  • Primary Citation of Related Structures:  
    6ZYM, 7A5P

  • PubMed Abstract: 

    Human spliceosomes contain numerous proteins absent in yeast, whose functions remain largely unknown. Here we report a 3D cryo-EM structure of the human spliceosomal C complex at 3.4 Å core resolution and 4.5-5.7 Å at its periphery, and aided by protein crosslinking we determine its molecular architecture. Our structure provides additional insights into the spliceosome's architecture between the catalytic steps of splicing, and how proteins aid formation of the spliceosome's catalytically active RNP (ribonucleoprotein) conformation. It reveals the spatial organization of the metazoan-specific proteins PPWD1, WDR70, FRG1, and CIR1 in human C complexes, indicating they stabilize functionally important protein domains and RNA structures rearranged/repositioned during the B act to C transition. Structural comparisons with human B act , C , and P complexes reveal an intricate cascade of RNP rearrangements during splicing catalysis, with intermediate RNP conformations not found in yeast, and additionally elucidate the structural basis for the sequential recruitment of metazoan-specific spliceosomal proteins.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
UNKNOWND [auth 8]204Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 8E [auth A]2,335Homo sapiensMutation(s): 0 
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PHAROS:  Q6P2Q9
GTEx:  ENSG00000174231 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
SNW domain-containing protein 1F [auth C]536Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100603 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17G [auth E]579Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168438 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19H [auth G],
I [auth H],
J [auth I],
K [auth J]
504Homo sapiensMutation(s): 0 
EC: 2.3.2.27
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GTEx:  ENSG00000110107 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SPF27L [auth K]225Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116752 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division cycle 5-like proteinM [auth L]802Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000096401 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF1N [auth M]855Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000076924 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF2O [auth N]243Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000117614 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Crooked neck-like protein 1P [auth O]848Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000101343 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RBM22Q [auth P]420Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000086589 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/arginine repetitive matrix protein 2R [auth S]2,752Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167978 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC22 homologS [auth T]908Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163510 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Intron-binding protein aquariusT [auth U]1,485Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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GTEx:  ENSG00000021776 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'U [auth W]255Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131876 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''V [auth X]225Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125870 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3IA [auth l],
X [auth a]
126Homo sapiensMutation(s): 0 
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Find proteins for P62318 (Homo sapiens)
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GTEx:  ENSG00000100028 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'JA [auth m],
Y [auth b]
240Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125835 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1KA [auth n],
Z [auth c]
119Homo sapiensMutation(s): 0 
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Find proteins for P62314 (Homo sapiens)
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GTEx:  ENSG00000167088 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2AA [auth d],
EA [auth h]
118Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125743 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EBA [auth e],
GA [auth j]
92Homo sapiensMutation(s): 0 
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Find proteins for P62304 (Homo sapiens)
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PHAROS:  P62304
GTEx:  ENSG00000182004 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FCA [auth f],
FA [auth i]
86Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000139343 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GDA [auth g],
HA [auth k]
76Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143977 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase ELA [auth o]301Homo sapiensMutation(s): 0 
EC: 5.2.1.8
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Find proteins for Q9UNP9 (Homo sapiens)
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GTEx:  ENSG00000084072 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
WD repeat-containing protein 70MA [auth p]654Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000082068 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 200 kDa helicaseNA [auth q]2,136Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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Find proteins for O75643 (Homo sapiens)
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GTEx:  ENSG00000144028 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16OA [auth r]1,227Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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Find proteins for Q92620 (Homo sapiens)
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GTEx:  ENSG00000140829 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ISY1 homologPA [auth s]285Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000240682 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor YJU2QA [auth u]323Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105248 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Protein mago nashi homologRA [auth v]146Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000162385 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-binding protein 8ASA [auth w]174Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000265241 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Protein FRG1TA [auth x]258Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000109536 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic initiation factor 4A-IIIUA [auth y]411Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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Find proteins for P38919 (Homo sapiens)
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GTEx:  ENSG00000141543 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidylprolyl isomerase domain and WD repeat-containing protein 1VA [auth z]646Homo sapiensMutation(s): 0 
EC: 5.2.1.8
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Find proteins for Q96BP3 (Homo sapiens)
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GTEx:  ENSG00000113593 
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Entity ID: 1
MoleculeChains LengthOrganismImage
U2 snRNAA [auth 2]975Homo sapiens
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Entity ID: 2
MoleculeChains LengthOrganismImage
U5 snRNAB [auth 5]116Homo sapiens
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Entity ID: 3
MoleculeChains LengthOrganismImage
U6 snRNAC [auth 6]106Homo sapiens
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Entity ID: 20
MoleculeChains LengthOrganismImage
pre-mRNAW [auth Y]324Homo sapiens
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Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
T [auth U]L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
German Research Foundation (DFG)GermanySFB 860

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-14
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Data collection, Database references, Structure summary