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- PDB-8xi2: Cryo-EM structure of the Chlamydomonas C* complex -

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Entry
Database: PDB / ID: 8xi2
TitleCryo-EM structure of the Chlamydomonas C* complex
Components
  • (Small nuclear ribonucleoprotein ...) x 5
  • CWF21 domain-containing protein
  • Cdc5L
  • Crooked neck protein
  • Cwf15/Cwc15 cell cycle control protein
  • Elongation factor Tu, chloroplastic
  • G10 protein
  • Intron-binding protein aquarius
  • MI domain-containing protein
  • MPN domain-containing protein
  • PLRG1
  • PPIase cyclophilin-type domain-containing protein
  • Peptidyl-prolyl cis-trans isomerase
  • Pre-mRNA-processing factor 19
  • Pre-mRNA-splicing factor SPF27
  • Prp17
  • RNA (173-mer)
  • RNA (5'-R(P*CP*CP*GP*AP*AP*CP*G)-3')
  • Rbm22
  • SKI-interacting protein SKIP SNW domain-containing protein
  • Sm domain-containing protein
  • Sm protein F
  • Syf1
  • U2 snRNA
  • U5 snRNA
  • U5-40K
  • U6 snRNA
KeywordsSPLICING / Chlamydomonas spliceosome / C* complex / Cdc5L / RNA splicing
Function / homology
Function and homology information


post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step / U12-type spliceosomal complex / pICln-Sm protein complex / U2-type catalytic step 1 spliceosome / pre-mRNA binding / snRNP binding / SMN-Sm protein complex / P granule / spliceosomal tri-snRNP complex ...post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step / U12-type spliceosomal complex / pICln-Sm protein complex / U2-type catalytic step 1 spliceosome / pre-mRNA binding / snRNP binding / SMN-Sm protein complex / P granule / spliceosomal tri-snRNP complex / commitment complex / mRNA cis splicing, via spliceosome / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / cyclosporin A binding / spliceosomal complex assembly / spliceosomal tri-snRNP complex assembly / Prp19 complex / protein K63-linked ubiquitination / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / spliceosomal snRNP assembly / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / RNA splicing / peptidyl-prolyl cis-trans isomerase activity / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / helicase activity / spliceosomal complex / RING-type E3 ubiquitin transferase / mRNA splicing, via spliceosome / mRNA processing / metallopeptidase activity / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / protein folding / DNA repair / GTPase activity / mRNA binding / GTP binding / DNA binding / RNA binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
HAT (Half-A-TPR) repeat / : / : / Intron-binding protein aquarius, beta-barrel / Intron-binding protein aquarius insert domain / Pre-mRNA-splicing factor SPF27 / Torus domain / Breast carcinoma amplified sequence 2 (BCAS2) / Torus domain / Intron-binding protein aquarius, N-terminal ...HAT (Half-A-TPR) repeat / : / : / Intron-binding protein aquarius, beta-barrel / Intron-binding protein aquarius insert domain / Pre-mRNA-splicing factor SPF27 / Torus domain / Breast carcinoma amplified sequence 2 (BCAS2) / Torus domain / Intron-binding protein aquarius, N-terminal / Intron-binding protein aquarius N-terminal / mRNA splicing factor SYF2 / SYF2 splicing factor / : / : / Pre-mRNA-processing factor 17 / Pre-mRNA-splicing factor 19 / Pre-mRNA-processing factor 19 / Prp19/Pso4-like / Myb-like domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / : / DNA2/NAM7 helicase, helicase domain / : / AAA domain / STL11, N-terminal / SKI-interacting protein SKIP, SNW domain / SKI-interacting protein, SKIP / SKIP/SNW domain / Pre-mRNA-splicing factor Cwf15/Cwc15 / Cwf15/Cwc15 cell cycle control protein / WD repeat Prp46/PLRG1-like / Pre-mRNA-splicing factor Cwc2/Slt11 / : / G10 protein / Pre-mRNA-splicing factor BUD31 / Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminal / : / : / pre-mRNA splicing factor component / DNA2/NAM7-like helicase / : / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / MIF4G domain / Myb-like DNA-binding domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / Small nuclear ribonucleoprotein D1 / U-box domain profile. / Modified RING finger domain / U-box domain / Zinc finger, CCCH-type superfamily / zinc finger / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / Snu114, GTP-binding domain / 116 kDa U5 small nuclear ribonucleoprotein component N-terminus / Pre-mRNA-splicing factor Syf1-like / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Sm-like protein Lsm7/SmG / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Sm-like protein Lsm6/SmF / Myb-type HTH DNA-binding domain profile. / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / Myb domain / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / : / Sm domain profile. / LSM domain superfamily / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / EF-G domain III/V-like / Cyclophilin-like domain superfamily / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain / PRO8NT domain
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / Cwf15/Cwc15 cell cycle control protein / Pre-mRNA-splicing factor SPF27 / Small nuclear ribonucleoprotein Sm D1 / Sm protein B / Crooked neck protein ...GUANOSINE-5'-TRIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / Cwf15/Cwc15 cell cycle control protein / Pre-mRNA-splicing factor SPF27 / Small nuclear ribonucleoprotein Sm D1 / Sm protein B / Crooked neck protein / Uncharacterized protein / G10 protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / MI domain-containing protein / Intron-binding protein aquarius / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / MPN domain-containing protein / peptidylprolyl isomerase / SKI-interacting protein SKIP SNW domain-containing protein / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein Sm D3 / Pre-mRNA-processing factor 19 / Small nuclear ribonucleoprotein E / Sm protein F / Elongation factor Tu, chloroplastic / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsLu, Y. / Zhan, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: EMBO J / Year: 2025
Title: Structure of a step II catalytically activated spliceosome from Chlamydomonas reinhardtii.
Authors: Yichen Lu / Ke Liang / Xiechao Zhan /
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 ...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.
History
DepositionDec 19, 2023Deposition site: PDBJ / Processing site: PDBJ
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MPN domain-containing protein
B: U5 snRNA
C: Elongation factor Tu, chloroplastic
E: U5-40K
F: U6 snRNA
q: Pre-mRNA-processing factor 19
r: Pre-mRNA-processing factor 19
s: Pre-mRNA-processing factor 19
t: Pre-mRNA-processing factor 19
a: Small nuclear ribonucleoprotein Sm D3
g: Small nuclear ribonucleoprotein G
e: Small nuclear ribonucleoprotein E
f: Sm protein F
d: Small nuclear ribonucleoprotein Sm D2
c: Small nuclear ribonucleoprotein Sm D1
b: Sm domain-containing protein
I: Syf1
J: Crooked neck protein
P: Cwf15/Cwc15 cell cycle control protein
M: PPIase cyclophilin-type domain-containing protein
T: PLRG1
O: Rbm22
N: G10 protein
R: SKI-interacting protein SKIP SNW domain-containing protein
H: U2 snRNA
S: Peptidyl-prolyl cis-trans isomerase
W: Prp17
L: Cdc5L
K: Pre-mRNA-splicing factor SPF27
U: CWF21 domain-containing protein
V: MI domain-containing protein
Q: Intron-binding protein aquarius
5: RNA (5'-R(P*CP*CP*GP*AP*AP*CP*G)-3')
3: RNA (173-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,006,13245
Polymers2,005,24334
Non-polymers89011
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 21 types, 24 molecules ACEqrstfbIJPMTONRSWLKUVQ

#1: Protein MPN domain-containing protein


Mass: 278543.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3E5Q8
#3: Protein Elongation factor Tu, chloroplastic / Snu114


Mass: 109366.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JCA8
#4: Protein U5-40K


Mass: 39437.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DMA3
#6: Protein
Pre-mRNA-processing factor 19


Mass: 54015.840 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: A8I9S6, RING-type E3 ubiquitin transferase
#10: Protein Sm protein F


Mass: 9644.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J834
#13: Protein Sm domain-containing protein


Mass: 27745.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3CX88
#14: Protein Syf1


Mass: 104377.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3D3K4
#15: Protein Crooked neck protein


Mass: 96708.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3CXZ4
#16: Protein Cwf15/Cwc15 cell cycle control protein


Mass: 26422.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3CN43
#17: Protein PPIase cyclophilin-type domain-containing protein


Mass: 61094.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3E769
#18: Protein PLRG1


Mass: 56100.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DAW8
#19: Protein Rbm22


Mass: 44413.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3E050
#20: Protein G10 protein / Bud31


Mass: 26355.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DAL7
#21: Protein SKI-interacting protein SKIP SNW domain-containing protein


Mass: 73924.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3E831
#23: Protein Peptidyl-prolyl cis-trans isomerase / PPIase


Mass: 17309.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JGI0, peptidylprolyl isomerase
#24: Protein Prp17


Mass: 63995.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DUN6
#25: Protein Cdc5L


Mass: 91838.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DYR4
#26: Protein Pre-mRNA-splicing factor SPF27


Mass: 32563.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3CNP4
#27: Protein CWF21 domain-containing protein


Mass: 80630.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DFH0
#28: Protein MI domain-containing protein / Cwc22


Mass: 102389.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DML4
#29: Protein Intron-binding protein aquarius


Mass: 201450.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DR41

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RNA chain , 5 types, 5 molecules BFH53

#2: RNA chain U5 snRNA


Mass: 35370.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#5: RNA chain U6 snRNA


Mass: 32760.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#22: RNA chain U2 snRNA


Mass: 61386.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: GenBank: 2826764
#30: RNA chain RNA (5'-R(P*CP*CP*GP*AP*AP*CP*G)-3')


Mass: 2219.411 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#31: RNA chain RNA (173-mer)


Mass: 55292.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)

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Small nuclear ribonucleoprotein ... , 5 types, 5 molecules agedc

#7: Protein Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3


Mass: 13789.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8I0E2
#8: Protein Small nuclear ribonucleoprotein G / snRNP-G


Mass: 8532.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8HRS8
#9: Protein Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E


Mass: 10216.069 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IYZ2
#11: Protein Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2


Mass: 12630.687 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8I074
#12: Protein Small nuclear ribonucleoprotein Sm D1 / snRNP core protein D1


Mass: 12668.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3CTT9

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Non-polymers , 3 types, 11 molecules

#32: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#33: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#34: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Chlamydomonas C* complex / Type: COMPLEX / Entity ID: #1-#4, #6-#31 / Source: NATURAL
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 518369 / Symmetry type: POINT
RefinementHighest resolution: 2.6 Å

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