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- PDB-3jb9: Cryo-EM structure of the yeast spliceosome at 3.6 angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 3jb9
TitleCryo-EM structure of the yeast spliceosome at 3.6 angstrom resolution
Components
  • (Pre-mRNA-processing factor ...) x 2
  • (Pre-mRNA-splicing factor ...) x 14
  • (Small nuclear ribonucleoprotein ...) x 6
  • Peptidyl-prolyl cis-trans isomerase ppi1
  • Pre-mRNA-processing protein 45
  • Probable U2 small nuclear ribonucleoprotein B''
  • RNA (5'-R(P*GP*UP*AP*UP*GP*UP*AP*U)-3')
  • RNA (5'-R(P*UP*UP*UP*AP*UP*AP*CP*UP*AP*AP*CP*AP*C)-3')
  • Small nuclear ribonucleoprotein-associated protein B
  • U2 small nuclear ribonucleoprotein A'
  • U2 snRNA
  • U5 snRNA
  • U6 snRNA
  • unknown chain
KeywordsRNA BINDING PROTEIN/RNA / Spliceosome / U2/U5/U6 / Lariat / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


nucleolar peripheral inclusion body / mRNA Splicing - Major Pathway / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / spliceosomal conformational changes to generate catalytic conformation / siRNA-mediated pericentric heterochromatin formation / post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step / pICln-Sm protein complex ...nucleolar peripheral inclusion body / mRNA Splicing - Major Pathway / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / spliceosomal conformational changes to generate catalytic conformation / siRNA-mediated pericentric heterochromatin formation / post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step / pICln-Sm protein complex / U2-type catalytic step 1 spliceosome / pre-mRNA binding / snRNP binding / regulatory ncRNA-mediated gene silencing / SMN-Sm protein complex / spliceosomal tri-snRNP complex / U2-type spliceosomal 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 / spliceosomal complex assembly / mRNA 5'-splice site recognition / 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 / pericentric heterochromatin / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / 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 / spliceosomal complex / RING-type E3 ubiquitin transferase / mRNA splicing, via spliceosome / metallopeptidase activity / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / nuclear envelope / protein folding / molecular adaptor activity / cysteine-type deubiquitinase activity / DNA repair / GTPase activity / mRNA binding / GTP binding / DNA binding / RNA binding / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Cwf19-like protein, C-terminal domain-2 / Cwf19-like, C-terminal domain-1 / Cwf19-like protein / Protein similar to CwfJ C-terminus 2 / Protein similar to CwfJ C-terminus 1 / HAT (Half-A-TPR) repeat / Slt11, RNA recognition motif / Pre-mRNA-splicing factor Cwc2, RNA recognition motif / Pre-mRNA-splicing factor SPF27 / Torus domain ...Cwf19-like protein, C-terminal domain-2 / Cwf19-like, C-terminal domain-1 / Cwf19-like protein / Protein similar to CwfJ C-terminus 2 / Protein similar to CwfJ C-terminus 1 / HAT (Half-A-TPR) repeat / Slt11, RNA recognition motif / Pre-mRNA-splicing factor Cwc2, RNA recognition motif / Pre-mRNA-splicing factor SPF27 / Torus domain / Breast carcinoma amplified sequence 2 (BCAS2) / Torus domain / CWF11 family / Intron-binding protein aquarius, N-terminal / Intron-binding protein aquarius N-terminal / Pre-mRNA-processing factor 17 / : / : / Pre-mRNA-splicing factor SYF1 middle HAT repeat / Pre-mRNA-splicing factor 19 / Pre-mRNA-processing factor 19 / Prp19/Pso4-like / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / : / : / Pre-mRNA-splicing factor Syf1/CRNKL1 C-terminal HAT repeat / : / STL11, N-terminal / : / Pre-mRNA-splicing factor Syf1/CNRKL1 N-terminal HAT repeat / 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 / : / Anaphase-promoting complex subunit 4, WD40 domain / Leucine Rich repeats (2 copies) / Myb-like DNA-binding domain / U2 small nuclear ribonucleoprotein A' / Small nuclear ribonucleoprotein D1 / U-box domain profile. / Anaphase-promoting complex subunit 4 WD40 domain / HIT-like superfamily / Modified RING finger domain / U-box domain / Zinc finger, CCCH-type superfamily / zinc finger / Leucine-rich repeat / 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 / SH3 type barrels. - #100 / 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. / Cyclophilin-like / Cyclophilin / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / Myb domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / : / Myb-like DNA-binding domain / Sm domain profile. / Alpha-Beta Horseshoe / 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
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-DIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / Pre-mRNA-splicing factor prp5 / Pre-mRNA-processing factor 19 / Small nuclear ribonucleoprotein Sm D2 / Pre-mRNA-splicing factor spp42 / Small nuclear ribonucleoprotein Sm D1 ...ADENOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-DIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / Pre-mRNA-splicing factor prp5 / Pre-mRNA-processing factor 19 / Small nuclear ribonucleoprotein Sm D2 / Pre-mRNA-splicing factor spp42 / Small nuclear ribonucleoprotein Sm D1 / Pre-mRNA-processing factor 17 / Small nuclear ribonucleoprotein F / Pre-mRNA-splicing factor cwf5 / Pre-mRNA-splicing factor cwf14 / Small nuclear ribonucleoprotein G / Pre-mRNA-splicing factor cwf10 / Pre-mRNA-splicing factor cwf11 / Pre-mRNA-splicing factor cwf17 / Pre-mRNA-splicing factor cdc5 / Pre-mRNA-splicing factor cwf15 / Peptidyl-prolyl cis-trans isomerase ppi1 / Pre-mRNA-splicing factor cwf2 / Pre-mRNA-splicing factor cwf4 / Pre-mRNA-processing protein 45 / Pre-mRNA-splicing factor cwf19 / Small nuclear ribonucleoprotein-associated protein B / Probable U2 small nuclear ribonucleoprotein B'' / Pre-mRNA-splicing factor cwf3 / Pre-mRNA-splicing factor cwf7 / U2 small nuclear ribonucleoprotein A' / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein Sm D3
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
Schizosaccharomyces pombe (fission yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsYan, C. / Hang, J. / Wan, R. / Huang, M. / Wong, C. / Shi, Y.
CitationJournal: Science / Year: 2015
Title: Structure of a yeast spliceosome at 3.6-angstrom resolution.
Authors: Chuangye Yan / Jing Hang / Ruixue Wan / Min Huang / Catherine C L Wong / Yigong Shi /
Abstract: Splicing of precursor messenger RNA (pre-mRNA) in yeast is executed by the spliceosome, which consists of five small nuclear ribonucleoproteins (snRNPs), NTC (nineteen complex), NTC-related proteins ...Splicing of precursor messenger RNA (pre-mRNA) in yeast is executed by the spliceosome, which consists of five small nuclear ribonucleoproteins (snRNPs), NTC (nineteen complex), NTC-related proteins (NTR), and a number of associated enzymes and cofactors. Here, we report the three-dimensional structure of a Schizosaccharomyces pombe spliceosome at 3.6-angstrom resolution, revealed by means of single-particle cryogenic electron microscopy. This spliceosome contains U2 and U5 snRNPs, NTC, NTR, U6 small nuclear RNA, and an RNA intron lariat. The atomic model includes 10,574 amino acids from 37 proteins and four RNA molecules, with a combined molecular mass of approximately 1.3 megadaltons. Spp42 (Prp8 in Saccharomyces cerevisiae), the key protein component of the U5 snRNP, forms a central scaffold and anchors the catalytic center. Both the morphology and the placement of protein components appear to have evolved to facilitate the dynamic process of pre-mRNA splicing. Our near-atomic-resolution structure of a central spliceosome provides a molecular framework for mechanistic understanding of pre-mRNA splicing.
History
DepositionAug 9, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: cell / database_2 ...cell / database_2 / em_image_scans / em_software / struct_conn
Item: _cell.Z_PDB / _cell.length_a ..._cell.Z_PDB / _cell.length_a / _cell.length_b / _cell.length_c / _em_software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Dec 11, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other
Category: atom_site / atom_sites ...atom_site / atom_sites / em_software / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _em_software.image_processing_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id
Revision 2.1Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Assembly

Deposited unit
A: Pre-mRNA-splicing factor spp42
B: Pre-mRNA-splicing factor cwf10
C: U5 snRNA
D: Small nuclear ribonucleoprotein Sm D3
E: Small nuclear ribonucleoprotein-associated protein B
F: Small nuclear ribonucleoprotein Sm D1
G: Small nuclear ribonucleoprotein Sm D2
H: Small nuclear ribonucleoprotein E
I: Small nuclear ribonucleoprotein F
J: Small nuclear ribonucleoprotein G
K: Pre-mRNA-splicing factor prp5
L: Pre-mRNA-splicing factor cwf17
M: Pre-mRNA-processing protein 45
N: U6 snRNA
O: RNA (5'-R(P*GP*UP*AP*UP*GP*UP*AP*U)-3')
Q: RNA (5'-R(P*UP*UP*UP*AP*UP*AP*CP*UP*AP*AP*CP*AP*C)-3')
P: U2 snRNA
S: Pre-mRNA-processing factor 19
T: Pre-mRNA-processing factor 19
U: Pre-mRNA-processing factor 19
V: Pre-mRNA-processing factor 19
W: Pre-mRNA-splicing factor cdc5
Y: Pre-mRNA-splicing factor cwf2
a: Pre-mRNA-splicing factor cwf5
c: Pre-mRNA-splicing factor cwf19
d: Peptidyl-prolyl cis-trans isomerase ppi1
e: Pre-mRNA-splicing factor cwf14
g: Pre-mRNA-processing factor 17
h: Pre-mRNA-splicing factor cwf15
i: Pre-mRNA-splicing factor cwf7
R: Pre-mRNA-splicing factor cwf4
r: Pre-mRNA-splicing factor cwf3
X: Pre-mRNA-splicing factor cwf11
j: U2 small nuclear ribonucleoprotein A'
k: Probable U2 small nuclear ribonucleoprotein B''
Z: Small nuclear ribonucleoprotein Sm D3
b: Small nuclear ribonucleoprotein-associated protein B
f: Small nuclear ribonucleoprotein Sm D1
l: Small nuclear ribonucleoprotein Sm D2
m: Small nuclear ribonucleoprotein E
n: Small nuclear ribonucleoprotein F
o: Small nuclear ribonucleoprotein G
x: unknown chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,789,82556
Polymers1,788,40043
Non-polymers1,42513
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Pre-mRNA-splicing factor ... , 14 types, 14 molecules ABKLWYacehiRrX

#1: Protein Pre-mRNA-splicing factor spp42 / Complexed with cdc5 protein 6


Mass: 274917.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: O14187
#2: Protein Pre-mRNA-splicing factor cwf10 / 114 kDa U5 small nuclear ribonucleoprotein component homolog / Complexed with cdc5 protein 10


Mass: 111445.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: O94316
#11: Protein Pre-mRNA-splicing factor prp5 / Complexed with cdc5 protein 1 / Pre-mRNA-processing protein 5


Mass: 48909.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: O13615
#12: Protein Pre-mRNA-splicing factor cwf17 / Complexed with cdc5 protein 17


Mass: 37477.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: O94620
#19: Protein Pre-mRNA-splicing factor cdc5 / Cell division control protein 5


Mass: 75128.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: P39964
#20: Protein Pre-mRNA-splicing factor cwf2 / Complexed with cdc5 protein 2 / Pre-mRNA-processing protein 3


Mass: 41838.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: P87126
#21: Protein Pre-mRNA-splicing factor cwf5 / Complexed with cdc5 protein 5


Mass: 37133.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: O59800
#22: Protein Pre-mRNA-splicing factor cwf19 / Complexed with cdc5 protein 19


Mass: 74547.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: Q09909
#24: Protein Pre-mRNA-splicing factor cwf14 / Complexed with cdc5 protein 14


Mass: 17122.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: O74772
#26: Protein Pre-mRNA-splicing factor cwf15 / Complexed with cdc5 protein 15


Mass: 30478.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: P78794
#27: Protein Pre-mRNA-splicing factor cwf7 / Complexed with cdc5 protein 7 / Splicing factor 27


Mass: 21348.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: Q9USV3
#28: Protein Pre-mRNA-splicing factor cwf4 / Complexed with cdc5 protein 4


Mass: 67082.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: P87312
#29: Protein Pre-mRNA-splicing factor cwf3 / Complexed with cdc5 protein 3


Mass: 72172.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: Q9P7R9
#30: Protein Pre-mRNA-splicing factor cwf11 / Complexed with cdc5 protein 11


Mass: 148532.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: O94508

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RNA chain , 5 types, 5 molecules CNOQP

#3: RNA chain U5 snRNA


Mass: 38191.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast)
#14: RNA chain U6 snRNA


Mass: 31863.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast)
#15: RNA chain RNA (5'-R(P*GP*UP*AP*UP*GP*UP*AP*U)-3')


Mass: 2528.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast)
#16: RNA chain RNA (5'-R(P*UP*UP*UP*AP*UP*AP*CP*UP*AP*AP*CP*AP*C)-3')


Mass: 4047.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: chain O and Q come from one RNA molecule. atom O2' A (Q 501) is covalently binding to atom P G (Q 100).
Source: (natural) Schizosaccharomyces pombe (fission yeast)
#17: RNA chain U2 snRNA


Mass: 59207.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast)

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Small nuclear ribonucleoprotein ... , 6 types, 12 molecules DZFfGlHmInJo

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


Mass: 11050.884 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: Q9UUC6
#6: Protein Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / snRNP core protein D1


Mass: 13115.422 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: O42661
#7: Protein Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / Complexed with cdc5 protein 9 / snRNP core protein D2


Mass: 13119.311 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: O14036
#8: Protein Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / Sm-E / SmE


Mass: 9702.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: Q9USZ3
#9: Protein Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / Sm-F / SmF


Mass: 8667.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: O59734
#10: Protein Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / Sm-G / SmG


Mass: 8616.038 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: O74966

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Protein , 6 types, 7 molecules EbMdjkx

#5: Protein Small nuclear ribonucleoprotein-associated protein B / snRNP-B / Sm protein B / Sm-B / SmB


Mass: 15493.004 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: Q10163
#13: Protein Pre-mRNA-processing protein 45 / Complexed with cdc5 protein 13 / Transcriptional coregulator snw1


Mass: 62798.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: Q09882
#23: Protein Peptidyl-prolyl cis-trans isomerase ppi1 / PPIase ppi1 / Cyclophilin ppi1 / Rotamase ppi1


Mass: 16884.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: P87051, peptidylprolyl isomerase
#31: Protein U2 small nuclear ribonucleoprotein A' / U2 snRNP A'


Mass: 27260.381 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: Q9USX8
#32: Protein Probable U2 small nuclear ribonucleoprotein B'' / U2 snRNP B''


Mass: 12685.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: Q7LL14
#33: Protein unknown chain


Mass: 35081.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843

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Pre-mRNA-processing factor ... , 2 types, 5 molecules STUVg

#18: Protein
Pre-mRNA-processing factor 19 / Complexed with cdc5 protein 8


Mass: 54243.988 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843
References: UniProt: O14011, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#25: Protein Pre-mRNA-processing factor 17


Mass: 63211.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: O43071

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Non-polymers , 4 types, 13 molecules

#34: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#35: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#36: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#37: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Details

Sequence detailsTHERE ARE MANY UNK RESIDUES IN CHAIN K, W, Y, a(LOWER CASE), R, r(LOWER CASE). THE COMPLETE ...THERE ARE MANY UNK RESIDUES IN CHAIN K, W, Y, a(LOWER CASE), R, r(LOWER CASE). THE COMPLETE SEQUENCE OF THESE CHAINS CORRESPOND TO EACH UNP DATABASE SEQUENCE. CHAIN K UNP O13615, CHAIN W UNP P39964, CHAIN Y UNP P87126, CHAIN a(LOWER CASE) UNP O59800, CHAIN R UNP P87312, CHAIN r(LOWER CASE) UNP Q9P7R9, BUT THE AUTHOR IS NOT SURE WHICH PART CORRESPONDS WITH UNK RESIDUES. SO THE RESIDUE NUMBERS OF ALL UNK ARE MEANINGLESS. ABOUT CHAIN x(LOWER CASE), THE AUTHOR COULD OBSERVE THESE RESIDUES, BUT CAN NOT ASSIGN TO THE SEQRES OF THIS CHAIN. SO THE RESIDUE NUMBERS IN CHAIN x(LOWER CASE) ARE MEANINGLESS.

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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: spliceosome / Type: COMPLEX
Buffer solutionName: CEB buffer / pH: 8 / Details: CEB buffer
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: carbon coated grid
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Method: Blot for 2.5 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Mar 29, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1.5 nm / Nominal defocus min: 3 nm / Cs: 1.4 mm / Camera length: 0 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingFilm or detector model: GATAN K2 (4k x 4k)

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Processing

EM softwareName: RELION / Category: 3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 112795 / Details: (Single particle--Applied symmetry: C1) / Symmetry type: POINT
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
14I43

4i43

14I431PDBexperimental model
23J7P

3j7p

13J7P2PDBexperimental model
34WZJ

4wzj

14WZJ3PDBexperimental model
44YVD

4yvd

14YVD4PDBexperimental model
52XL2

2xl2

12XL25PDBexperimental model
62BAY

2bay

12BAY6PDBexperimental model
73LRV

3lrv

13LRV7PDBexperimental model
81GV2

1gv2

11GV28PDBexperimental model
93U1L

3u1l

13U1L9PDBexperimental model
102YTC

2ytc

12YTC10PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms79585 6900 66 0 86551

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