6ZYM

Human C Complex Spliceosome - High-resolution CORE

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

  • Deposited: 2020-08-02 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: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



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: 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 prot ...

    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

    Cellular Biochemistry, MPI for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany. Electronic address: reinhard.luehrmann@mpibpc.mpg.de.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Corepressor interacting with RBPJ 19450Homo sapiensMutation(s): 0 
Gene Names: CIR1CIR
Find proteins for Q86X95 (Homo sapiens)
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PHAROS  Q86X95
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 8A1755Homo sapiensMutation(s): 0 
Gene Names: PRPF8PRPC8
Find proteins for Q6P2Q9 (Homo sapiens)
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PHAROS  Q6P2Q9
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein componentB952Homo sapiensMutation(s): 0 
Gene Names: EFTUD2KIAA0031SNRP116
Find proteins for Q15029 (Homo sapiens)
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PHAROS  Q15029
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
SNW domain-containing protein 1C536Homo sapiensMutation(s): 0 
Gene Names: SNW1SKIIPSKIP
Find proteins for Q13573 (Homo sapiens)
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PHAROS  Q13573
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Pleiotropic regulator 1D514Homo sapiensMutation(s): 0 
Gene Names: PLRG1
Find proteins for O43660 (Homo sapiens)
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PHAROS  O43660
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17E579Homo sapiensMutation(s): 0 
Gene Names: CDC40EHB3PRP17PRPF17
Find proteins for O60508 (Homo sapiens)
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PHAROS  O60508
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 40 kDa proteinF357Homo sapiensMutation(s): 0 
Gene Names: SNRNP40PRP8BPSFP38WDR57
Find proteins for Q96DI7 (Homo sapiens)
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PHAROS  Q96DI7
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division cycle 5-like proteinL802Homo sapiensMutation(s): 0 
Gene Names: CDC5LKIAA0432PCDC5RP
Find proteins for Q99459 (Homo sapiens)
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PHAROS  Q99459
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Crooked neck-like protein 1O848Homo sapiensMutation(s): 0 
Gene Names: CRNKL1CRNCGI-201MSTP021
Find proteins for Q9BZJ0 (Homo sapiens)
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PHAROS  Q9BZJ0
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RBM22P218Homo sapiensMutation(s): 0 
Gene Names: RBM22ZC3H16199G4
Find proteins for Q9NW64 (Homo sapiens)
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PHAROS  Q9NW64
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Protein BUD31 homologQ144Homo sapiensMutation(s): 0 
Gene Names: BUD31EDG2
Find proteins for P41223 (Homo sapiens)
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PHAROS  P41223
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homologR229Homo sapiensMutation(s): 0 
Gene Names: CWC15C11orf5AD-002HSPC148
Find proteins for Q9P013 (Homo sapiens)
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PHAROS  Q9P013
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/arginine repetitive matrix protein 2S2752Homo sapiensMutation(s): 0 
Gene Names: SRRM2KIAA0324SRL300SRM300HSPC075
Find proteins for Q9UQ35 (Homo sapiens)
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PHAROS  Q9UQ35
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC22 homologT908Homo sapiensMutation(s): 0 
Gene Names: CWC22KIAA1604NCM
Find proteins for Q9HCG8 (Homo sapiens)
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PHAROS  Q9HCG8
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase-like 1V166Homo sapiensMutation(s): 0 
Gene Names: PPIL1CYPL1CGI-124UNQ2425/PRO4984
EC: 5.2.1.8
Find proteins for Q9Y3C6 (Homo sapiens)
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PHAROS  Q9Y3C6
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
WD repeat-containing protein 70p654Homo sapiensMutation(s): 0 
Gene Names: WDR70
Find proteins for Q9NW82 (Homo sapiens)
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PHAROS  Q9NW82
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16r1227Homo sapiensMutation(s): 0 
Gene Names: DHX38DDX38KIAA0224PRP16
EC: 3.6.4.13
Find proteins for Q92620 (Homo sapiens)
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PHAROS  Q92620
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ISY1 homologs285Homo sapiensMutation(s): 0 
Gene Names: ISY1KIAA1160
Find proteins for Q9ULR0 (Homo sapiens)
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PHAROS  Q9ULR0
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC25 homologt425Homo sapiensMutation(s): 0 
Gene Names: CWC25CCDC49
Find proteins for Q9NXE8 (Homo sapiens)
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PHAROS  Q9NXE8
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor YJU2u178Homo sapiensMutation(s): 0 
Gene Names: YJU2CCDC94
Find proteins for Q9BW85 (Homo sapiens)
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PHAROS  Q9BW85
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Protein FRG1x258Homo sapiensMutation(s): 0 
Gene Names: FRG1
Find proteins for Q14331 (Homo sapiens)
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PHAROS  Q14331
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
U2 snRNA2188Homo sapiens
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Entity ID: 2
MoleculeChainsLengthOrganismImage
U5 snRNA5116Homo sapiens
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Entity ID: 3
MoleculeChainsLengthOrganismImage
U6 snRNA679Homo sapiens
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Entity ID: 19
MoleculeChainsLengthOrganismImage
pre-mRNAY, Z324Homo sapiens
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP

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A
INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
 Ligand Interaction
GTP
Query on GTP

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B
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
ZN
Query on ZN

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P, Q, u
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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6
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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 Foundation (DFG)GermanySFB 860

Revision History 

  • Version 1.0: 2020-10-14
    Type: Initial release