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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 / Prp19 complex / snRNP binding / pICln-Sm protein complex / U2-type catalytic step 1 spliceosome / pre-mRNA binding / SMN-Sm protein complex / spliceosomal tri-snRNP complex ...post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step / U12-type spliceosomal complex / Prp19 complex / snRNP binding / pICln-Sm protein complex / U2-type catalytic step 1 spliceosome / pre-mRNA binding / SMN-Sm protein complex / spliceosomal tri-snRNP complex / P granule / mRNA cis splicing, via spliceosome / commitment complex / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / cyclosporin A binding / spliceosomal complex assembly / protein K63-linked ubiquitination / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / chloroplast / helicase activity / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / spliceosomal complex / RING-type E3 ubiquitin transferase / mRNA splicing, via spliceosome / mRNA processing / ubiquitin-protein transferase activity / metallopeptidase activity / ubiquitin protein ligase activity / protein folding / DNA repair / GTPase activity / mRNA binding / GTP binding / DNA binding / RNA binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Torus domain / Torus domain / Myb-like domain profile. / : / : / Intron-binding protein aquarius, beta-barrel / Intron-binding protein aquarius insert domain / Pre-mRNA-splicing factor SPF27 / Breast carcinoma amplified sequence 2 (BCAS2) / mRNA splicing factor SYF2 ...Torus domain / Torus domain / Myb-like domain profile. / : / : / Intron-binding protein aquarius, beta-barrel / Intron-binding protein aquarius insert domain / Pre-mRNA-splicing factor SPF27 / Breast carcinoma amplified sequence 2 (BCAS2) / mRNA splicing factor SYF2 / SYF2 splicing factor / Intron-binding protein aquarius, N-terminal / Intron-binding protein aquarius N-terminal / : / : / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / Pre-mRNA-processing factor 17 / HAT (Half-A-TPR) repeat / Pre-mRNA-splicing factor 19 / Pre-mRNA-processing factor 19 / Prp19/Pso4-like / : / STL11, N-terminal / DNA2/NAM7 helicase, helicase domain / : / AAA domain / DNA2/NAM7-like helicase / WD repeat Prp46/PLRG1-like / : / : / : / SKI-interacting protein SKIP, SNW domain / SKI-interacting protein, SKIP / SKIP/SNW domain / Myb-like DNA-binding domain / Pre-mRNA-splicing factor Cwf15/Cwc15 / Cwf15/Cwc15 cell cycle control protein / 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 / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / MIF4G domain / Small nuclear ribonucleoprotein D1 / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / U-box domain profile. / Modified RING finger domain / U-box domain / Zinc finger, CCCH-type superfamily / zinc finger / Pre-mRNA-splicing factor Syf1-like / Snu114, GTP-binding domain / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / 116 kDa U5 small nuclear ribonucleoprotein component N-terminus / : / 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 / Myb-type HTH DNA-binding domain profile. / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Sm-like protein Lsm6/SmF / 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 / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / PROCT domain / Prp8 RNase domain IV, fingers region
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 domain-containing protein / 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 domain-containing protein / 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: To Be Published
Title: Structure of a Step II catalytically activated spliceosome form Chlamydomonas reinhardtii
Authors: Lu, Y. / Zhan, X.
History
DepositionDec 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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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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