8XI2

Cryo-EM structure of the Chlamydomonas C* complex

  • Classification: SPLICING
  • Organism(s): Chlamydomonas reinhardtii
  • Mutation(s): No 

  • Deposited: 2023-12-19 Released: 2024-10-09 
  • Deposition Author(s): Lu, Y., Zhan, X.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a step II catalytically activated spliceosome from Chlamydomonas reinhardtii.

Lu, Y.Liang, K.Zhan, X.

(2024) EMBO J 

  • DOI: https://doi.org/10.1038/s44318-024-00274-3
  • Primary Citation of Related Structures:  
    8XI2

  • PubMed Abstract: 

    Pre-mRNA splicing, a fundamental step in eukaryotic gene expression, is executed by the spliceosomes. While there is extensive knowledge of the composition and structure of spliceosomes in yeasts and humans, the structural diversity of spliceosomes in non-canonical organisms remains unclear. Here, we present a cryo-EM structure of a step II catalytically activated spliceosome (C * complex) derived from the unicellular green alga Chlamydomonas reinhardtii at 2.6 Å resolution. This Chlamydomonas C * complex comprises 29 proteins and four RNA elements, creating a dynamic assembly that shares a similar overall architecture with yeast and human counterparts but also has unique features of its own. Distinctive structural characteristics include variations in protein compositions as well as some noteworthy RNA features. The splicing factor Prp17, with four fragments and a WD40 domain, is engaged in intricate interactions with multiple protein and RNA components. The structural elucidation of Chlamydomonas C * complex provides insights into the molecular mechanism of RNA splicing in plants and understanding splicing evolution in eukaryotes.


  • Organizational Affiliation

    College of Life Sciences, Fudan University, Shanghai, 200433, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MPN domain-containing protein2,398Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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UniProt GroupA0A2K3E5Q8
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor Tu, chloroplastic989Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
U5-40KD [auth E]362Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19F [auth q],
G [auth r],
H [auth s],
I [auth t]
503Chlamydomonas reinhardtiiMutation(s): 0 
EC: 2.3.2.27
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3J [auth a]127Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GK [auth g]77Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EL [auth e]87Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Sm protein FM [auth f]85Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2N [auth d]110Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1O [auth c]114Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Sm domain-containing proteinP [auth b]265Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3CX88 (Chlamydomonas reinhardtii)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Syf1Q [auth I]925Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Crooked neck proteinR [auth J]835Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Cwf15/Cwc15 cell cycle control proteinS [auth P]235Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
PPIase cyclophilin-type domain-containing proteinT [auth M]563Chlamydomonas reinhardtiiMutation(s): 0 
EC: 5.2.1.8
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
PLRG1U [auth T]518Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Rbm22V [auth O]417Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3E050 (Chlamydomonas reinhardtii)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
G10 proteinW [auth N]233Chlamydomonas reinhardtiiMutation(s): 0 
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Find proteins for A0A2K3DAL7 (Chlamydomonas reinhardtii)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
SKI-interacting protein SKIP SNW domain-containing proteinX [auth R]684Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3E831 (Chlamydomonas reinhardtii)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomeraseZ [auth S]157Chlamydomonas reinhardtiiMutation(s): 0 
EC: 5.2.1.8
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Prp17AA [auth W]576Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3DUN6 (Chlamydomonas reinhardtii)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Cdc5LBA [auth L]833Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3DYR4 (Chlamydomonas reinhardtii)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SPF27CA [auth K]303Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
CWF21 domain-containing proteinDA [auth U]721Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
MI domain-containing proteinEA [auth V]928Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Intron-binding protein aquariusFA [auth Q]1,844Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

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IA [auth C]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ZN
Query on ZN

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QA [auth O],
RA [auth O],
SA [auth N]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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JA [auth C]
KA [auth F]
LA [auth F]
MA [auth F]
NA [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
X [auth R]L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-09
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-27
    Changes: Data collection