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- PDB-5zwo: Cryo-EM structure of the yeast B complex at average resolution of... -

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Entry
Database: PDB / ID: 5zwo
TitleCryo-EM structure of the yeast B complex at average resolution of 3.9 angstrom
Components
  • (Pre-mRNA-splicing factor ...) x 11
  • (Small nuclear ribonucleoprotein ...SnRNP) x 6
  • (U2 small nuclear ribonucleoprotein ...) x 2
  • (U2 snRNP component ...) x 2
  • (U4/U6 small nuclear ribonucleoprotein ...) x 2
  • (U6 snRNA-associated Sm-like protein ...) x 7
  • 13 kDa ribonucleoprotein-associated protein
  • 23 kDa U4/U6.U5 small nuclear ribonucleoprotein component
  • 66 kDa U4/U6.U5 small nuclear ribonucleoprotein component
  • Cold sensitive U2 snRNA suppressor 1
  • Pre-mRNA leakage protein 1
  • Pre-mRNA-processing factor 31
  • Pre-mRNA-splicing helicase BRR2
  • Pre-mRNAPrimary transcript
  • Protein HSH49
  • RDS3 complex subunit 10
  • Small nuclear ribonucleoprotein-associated protein B
  • Spliceosomal protein DIB1Spliceosome
  • U2 snRNAU2 spliceosomal RNA
  • U4 snRNAU4 spliceosomal RNA
  • U5 snRNAU5 spliceosomal RNA
  • U6 snRNAU6 spliceosomal RNA
KeywordsSPLICING / spliceosome / assembly / B complex
Function / homology
Function and homology information


maintenance of RNA location / maturation of 5S rRNA / RES complex / spliceosomal conformational changes to generate catalytic conformation / mRNA decay by 5' to 3' exoribonuclease / snoRNA splicing / Lsm1-7-Pat1 complex / U6 snRNP / snoRNA guided rRNA 2'-O-methylation / positive regulation of RNA binding ...maintenance of RNA location / maturation of 5S rRNA / RES complex / spliceosomal conformational changes to generate catalytic conformation / mRNA decay by 5' to 3' exoribonuclease / snoRNA splicing / Lsm1-7-Pat1 complex / U6 snRNP / snoRNA guided rRNA 2'-O-methylation / positive regulation of RNA binding / box C/D sno(s)RNA 3'-end processing / generation of catalytic spliceosome for first transesterification step / deadenylation-dependent decapping of nuclear-transcribed mRNA / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / box C/D methylation guide snoRNP complex / splicing factor binding / U4/U6 snRNP / P-body assembly / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / sno(s)RNA-containing ribonucleoprotein complex / U4 snRNA binding / SMN-Sm protein complex / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / U2-type prespliceosome assembly / commitment complex / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / poly(U) RNA binding / nuclear-transcribed mRNA catabolic process / U3 snoRNA binding / U1 snRNP / U2-type prespliceosome / tRNA processing / precatalytic spliceosome / spliceosomal complex assembly / generation of catalytic spliceosome for second transesterification step / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA 3'-splice site recognition / mRNA 5'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / spliceosomal snRNP assembly / U2 snRNA binding / U6 snRNA binding / mRNA export from nucleus / pre-mRNA intronic binding / maturation of SSU-rRNA / U1 snRNA binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / small-subunit processome / P-body / spliceosomal complex / mRNA splicing, via spliceosome / rRNA processing / metallopeptidase activity / cytosolic large ribosomal subunit / RNA helicase activity / nucleic acid binding / RNA helicase / response to xenobiotic stimulus / mRNA binding / GTPase activity / GTP binding / nucleolus / ATP hydrolysis activity / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1320 / Surp module / Pre-mRNA-splicing factor Prp9, N-terminal / Pre-mRNA-splicing factor PRP9 N-terminus / U4/U6.U5 small nuclear ribonucleoprotein component Snu23 / Pre-mRNA-splicing factor 38 / Ist3-like, RNA recognition motif / PRP38 family / SNU66/SART1 family / Bud13 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1320 / Surp module / Pre-mRNA-splicing factor Prp9, N-terminal / Pre-mRNA-splicing factor PRP9 N-terminus / U4/U6.U5 small nuclear ribonucleoprotein component Snu23 / Pre-mRNA-splicing factor 38 / Ist3-like, RNA recognition motif / PRP38 family / SNU66/SART1 family / Bud13 / HIND motif / SART-1 family / Pre-mRNA-splicing factor of RES complex / HIND motif / Pre-mRNA processing factor 4 (PRP4)-like / Splicing Factor Motif, present in Prp18 and Pr04 / Prp31 C-terminal / U4/U6 small nuclear ribonucleoprotein Prp31 / Prp31 C terminal domain / Pre-mRNA-splicing factor 3 / U4/U6 small nuclear ribonucleoprotein Prp3 / Sm-like protein Lsm8 / pre-mRNA processing factor 3 domain / Small nuclear ribonucleoprotein Prp3, C-terminal domain / Small nuclear ribonucleoprotein Prp3, C-terminal domain / U6 snRNA-associated Sm-like protein Lsm1/8 / Dim1 family / U6 snRNA-associated Sm-like protein LSm2 / Sm-like protein Lsm4 / Mitosis protein DIM1 / Mitosis protein DIM1 / Sm-like protein Lsm7 / PRP1 splicing factor, N-terminal / Sm-like protein LSm5 / Sm-like protein Lsm3 / U6 snRNA-associated Sm-like protein Lsm3 / PRP1 splicing factor, N-terminal / Splicing factor 3A subunit 1 / Splicing factor 3A subunit 1, conserved domain / Pre-mRNA splicing factor PRP21 like protein / SF3A2 domain / Pre-mRNA-splicing factor SF3a complex subunit 2 (Prp11) / Splicing factor SF3a60 /Prp9 subunit, C-terminal / SF3A3 domain / SF3B4, RNA recognition motif 1 / SF3a60/Prp9 C-terminal / Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9 / SWAP/Surp / SWAP/Surp superfamily / Surp module / SURP motif repeat profile. / Suppressor-of-White-APricot splicing regulator / Domain of unknown function DUF382 / Domain of unknown function (DUF382) / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / Zinc-finger of C2H2 type / PHF5-like / PHF5-like protein / PSP, proline-rich / PSP / proline-rich domain in spliceosome associated proteins / Splicing factor 3B subunit 5/RDS3 complex subunit 10 / Splicing factor 3B subunit 10 (SF3b10) / Matrin/U1-C, C2H2-type zinc finger / Splicing factor 3B subunit 1-like / Zinc finger matrin-type profile. / U2A'/phosphoprotein 32 family A, C-terminal / occurring C-terminal to leucine-rich repeats / Leucine-rich repeat / Pre-mRNA-splicing factor Syf1-like / NOSIC / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / NOSIC (NUC001) domain / Nop domain / Nop domain superfamily / Nop, C-terminal domain / snoRNA binding domain, fibrillarin / Nop domain profile. / H/ACA ribonucleoprotein complex, subunit Nhp2-like / Snu114, GTP-binding domain / Zinc-finger double-stranded RNA-binding / Zinc finger, double-stranded RNA binding / Sec63 Brl 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 / Sec63 domain / Sec63 Brl domain / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / Ribosomal protein L30/S12 / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Sm-like protein Lsm7/SmG / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / SH3 type barrels. - #100
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / RDS3 complex subunit 10 / Pre-mRNA-splicing factor 6 / Pre-mRNA-splicing factor PRP9 / U4/U6 small nuclear ribonucleoprotein PRP4 / Pre-mRNA-splicing factor PRP21 ...GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / RDS3 complex subunit 10 / Pre-mRNA-splicing factor 6 / Pre-mRNA-splicing factor PRP9 / U4/U6 small nuclear ribonucleoprotein PRP4 / Pre-mRNA-splicing factor PRP21 / Pre-mRNA-splicing helicase BRR2 / Pre-mRNA-splicing factor 8 / Pre-mRNA-splicing factor SNU114 / U6 snRNA-associated Sm-like protein LSm2 / Pre-mRNA-splicing factor SPP381 / 13 kDa ribonucleoprotein-associated protein / Small nuclear ribonucleoprotein-associated protein B / U6 snRNA-associated Sm-like protein LSm4 / U6 snRNA-associated Sm-like protein LSm5 / Small nuclear ribonucleoprotein G / U2 snRNP component IST3 / U2 small nuclear ribonucleoprotein B'' / Small nuclear ribonucleoprotein Sm D3 / Pre-mRNA-splicing factor CWC26 / U6 snRNA-associated Sm-like protein LSm8 / Pre-mRNA-processing factor 31 / U2 snRNP component HSH155 / U6 snRNA-associated Sm-like protein LSm7 / Small nuclear ribonucleoprotein F / U6 snRNA-associated Sm-like protein LSm3 / Pre-mRNA-splicing factor 38 / Small nuclear ribonucleoprotein Sm D1 / Cold sensitive U2 snRNA suppressor 1 / U4/U6 small nuclear ribonucleoprotein PRP3 / Pre-mRNA-splicing factor RSE1 / Small nuclear ribonucleoprotein Sm D2 / U6 snRNA-associated Sm-like protein LSm6 / Spliceosomal protein DIB1 / Pre-mRNA-splicing factor RDS3 / Pre-mRNA-splicing factor PRP11 / Pre-mRNA leakage protein 1 / U2 small nuclear ribonucleoprotein A' / Small nuclear ribonucleoprotein E / 23 kDa U4/U6.U5 small nuclear ribonucleoprotein component / 66 kDa U4/U6.U5 small nuclear ribonucleoprotein component / Protein HSH49
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsBai, R. / Wan, R. / Yan, C. / Shi, Y.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31430020 China
National Natural Science Foundation of China31621092 China
Ministry of Science and Technology (China)2016YFA0501100 China
CitationJournal: Science / Year: 2018
Title: Structures of the fully assembled spliceosome before activation.
Authors: Rui Bai / Ruixue Wan / Chuangye Yan / Jianlin Lei / Yigong Shi /
Abstract: The precatalytic spliceosome (B complex) is preceded by the pre-B complex. Here we report the cryo-electron microscopy structures of the pre-B and B complexes at average resolutions of 3.3 to 4.6 ...The precatalytic spliceosome (B complex) is preceded by the pre-B complex. Here we report the cryo-electron microscopy structures of the pre-B and B complexes at average resolutions of 3.3 to 4.6 and 3.9 angstroms, respectively. In the pre-B complex, the duplex between the 5' splice site (5'SS) and U1 small nuclear RNA (snRNA) is recognized by Yhc1, Luc7, and the Sm ring. In the B complex, U1 small nuclear ribonucleoprotein is dissociated, the 5'-exon-5'SS sequences are translocated near U6 snRNA, and three B-specific proteins may orient the precursor messenger RNA. In both complexes, U6 snRNA is anchored to loop I of U5 snRNA, and the duplex between the branch point sequence and U2 snRNA is recognized by the SF3b complex. Structural analysis reveals the mechanism of assembly and activation for the yeast spliceosome.
History
DepositionMay 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Pre-mRNA-splicing factor 8
K: U4/U6 small nuclear ribonucleoprotein PRP4
L: Pre-mRNA-processing factor 31
N: Pre-mRNA-splicing factor 6
J: U4/U6 small nuclear ribonucleoprotein PRP3
E: Spliceosomal protein DIB1
M: 13 kDa ribonucleoprotein-associated protein
C: Pre-mRNA-splicing factor SNU114
z: U6 snRNA-associated Sm-like protein LSm8
q: U6 snRNA-associated Sm-like protein LSm2
r: U6 snRNA-associated Sm-like protein LSm3
x: U6 snRNA-associated Sm-like protein LSm6
t: U6 snRNA-associated Sm-like protein LSm5
y: U6 snRNA-associated Sm-like protein LSm7
s: U6 snRNA-associated Sm-like protein LSm4
F: U6 snRNA
B: U5 snRNA
O: 66 kDa U4/U6.U5 small nuclear ribonucleoprotein component
d: Small nuclear ribonucleoprotein Sm D3
a: Small nuclear ribonucleoprotein-associated protein B
b: Small nuclear ribonucleoprotein Sm D1
c: Small nuclear ribonucleoprotein Sm D2
e: Small nuclear ribonucleoprotein E
f: Small nuclear ribonucleoprotein F
g: Small nuclear ribonucleoprotein G
I: U4 snRNA
D: Pre-mRNA-splicing helicase BRR2
P: Small nuclear ribonucleoprotein-associated protein B
Q: Small nuclear ribonucleoprotein Sm D1
R: Small nuclear ribonucleoprotein Sm D2
S: Small nuclear ribonucleoprotein Sm D3
T: Small nuclear ribonucleoprotein E
U: Small nuclear ribonucleoprotein F
V: Small nuclear ribonucleoprotein G
G: Pre-mRNA
1: U2 snRNP component HSH155
2: Cold sensitive U2 snRNA suppressor 1
3: Pre-mRNA-splicing factor RSE1
4: Protein HSH49
5: Pre-mRNA-splicing factor RDS3
6: RDS3 complex subunit 10
X: U2 snRNP component IST3
Y: Pre-mRNA-splicing factor CWC26
Z: Pre-mRNA leakage protein 1
H: U2 snRNA
h: Small nuclear ribonucleoprotein-associated protein B
i: Small nuclear ribonucleoprotein E
j: Small nuclear ribonucleoprotein F
k: Small nuclear ribonucleoprotein G
l: Small nuclear ribonucleoprotein Sm D3
m: Small nuclear ribonucleoprotein Sm D1
n: Small nuclear ribonucleoprotein Sm D2
o: U2 small nuclear ribonucleoprotein A'
p: U2 small nuclear ribonucleoprotein B''
u: Pre-mRNA-splicing factor PRP9
w: Pre-mRNA-splicing factor PRP21
v: Pre-mRNA-splicing factor PRP11
W: 23 kDa U4/U6.U5 small nuclear ribonucleoprotein component
0: Pre-mRNA-splicing factor 38
9: Pre-mRNA-splicing factor SPP381
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,604,02562
Polymers2,603,47860
Non-polymers5472
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Pre-mRNA-splicing factor ... , 11 types, 11 molecules ANC35Yuwv09

#1: Protein Pre-mRNA-splicing factor 8


Mass: 279867.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P33334
#4: Protein Pre-mRNA-splicing factor 6


Mass: 104370.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P19735
#8: Protein Pre-mRNA-splicing factor SNU114 / 114 kDa U5 small nuclear ribonucleoprotein component / Growth inhibitory protein 10


Mass: 114174.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P36048
#31: Protein Pre-mRNA-splicing factor RSE1 / RNA splicing and ER to Golgi transport factor 1 / Spliceosome-associated protein 130


Mass: 153956.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: Q04693
#33: Protein Pre-mRNA-splicing factor RDS3 / Regulator of drug sensitivity 3


Mass: 12283.573 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: Q06835
#36: Protein Pre-mRNA-splicing factor CWC26 / Bud site selection protein 13 / Complexed with CEF1 protein 26 / Synthetic lethal with CLF1 protein 7


Mass: 30529.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P46947
#41: Protein Pre-mRNA-splicing factor PRP9


Mass: 63126.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P19736
#42: Protein Pre-mRNA-splicing factor PRP21


Mass: 33111.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P32524
#43: Protein Pre-mRNA-splicing factor PRP11


Mass: 29962.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: Q07350
#45: Protein Pre-mRNA-splicing factor 38 / Pre-mRNA-processing factor 38


Mass: 27995.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: Q00723
#46: Protein Pre-mRNA-splicing factor SPP381 / Suppressor of PRP38-1 mutation


Mass: 33830.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P38282

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U4/U6 small nuclear ribonucleoprotein ... , 2 types, 2 molecules KJ

#2: Protein U4/U6 small nuclear ribonucleoprotein PRP4 / Pre-mRNA-processing protein 4


Mass: 52506.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P20053
#5: Protein U4/U6 small nuclear ribonucleoprotein PRP3 / Pre-mRNA-splicing factor 3


Mass: 55974.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: Q03338

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Protein , 11 types, 13 molecules LEMOaPhD246ZW

#3: Protein Pre-mRNA-processing factor 31


Mass: 56382.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P49704
#6: Protein Spliceosomal protein DIB1 / Spliceosome


Mass: 16798.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: Q06819
#7: Protein 13 kDa ribonucleoprotein-associated protein / Small nuclear ribonucleoprotein-associated protein 1


Mass: 13582.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P39990
#18: Protein 66 kDa U4/U6.U5 small nuclear ribonucleoprotein component


Mass: 66544.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: Q12420
#20: Protein Small nuclear ribonucleoprotein-associated protein B / snRNP-B / Sm protein B / SmB


Mass: 22426.990 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P40018
#27: Protein Pre-mRNA-splicing helicase BRR2 / Protein Snu246


Mass: 246470.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P32639, RNA helicase
#30: Protein Cold sensitive U2 snRNA suppressor 1


Mass: 50339.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: Q02554
#32: Protein Protein HSH49


Mass: 24534.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: Q99181
#34: Protein RDS3 complex subunit 10 / Splicing factor 3b subunit


Mass: 10045.401 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P0C074
#37: Protein Pre-mRNA leakage protein 1


Mass: 23685.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: Q07930
#44: Protein 23 kDa U4/U6.U5 small nuclear ribonucleoprotein component


Mass: 22717.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: Q12368

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U6 snRNA-associated Sm-like protein ... , 7 types, 7 molecules zqrxtys

#9: Protein U6 snRNA-associated Sm-like protein LSm8


Mass: 12403.378 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P47093
#10: Protein U6 snRNA-associated Sm-like protein LSm2 / Small nuclear ribonucleoprotein D homolog SNP3


Mass: 11177.888 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P38203
#11: Protein U6 snRNA-associated Sm-like protein LSm3 / SmX4 protein


Mass: 10039.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P57743
#12: Protein U6 snRNA-associated Sm-like protein LSm6


Mass: 9406.579 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: Q06406
#13: Protein U6 snRNA-associated Sm-like protein LSm5


Mass: 10432.954 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P40089
#14: Protein U6 snRNA-associated Sm-like protein LSm7


Mass: 13027.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P53905
#15: Protein U6 snRNA-associated Sm-like protein LSm4


Mass: 21298.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P40070

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RNA chain , 5 types, 5 molecules FBIGH

#16: RNA chain U6 snRNA / U6 spliceosomal RNA


Mass: 35846.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c
#17: RNA chain U5 snRNA / U5 spliceosomal RNA


Mass: 68643.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c
#26: RNA chain U4 snRNA / U4 spliceosomal RNA


Mass: 51492.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c
#28: RNA chain Pre-mRNA / Primary transcript


Mass: 19067.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c
#38: RNA chain U2 snRNA / U2 spliceosomal RNA


Mass: 376324.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c

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Small nuclear ribonucleoprotein ... , 6 types, 18 molecules dSlbQmcRneTifUjgVk

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


Mass: 11240.139 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P43321
#21: Protein Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / snRNP core protein D1


Mass: 16296.798 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: Q02260
#22: Protein Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2


Mass: 12876.066 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: Q06217
#23: Protein Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / SmE


Mass: 10385.098 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: Q12330
#24: Protein Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / SmF


Mass: 9669.945 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P54999
#25: Protein Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / SmG


Mass: 8490.809 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P40204

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U2 snRNP component ... , 2 types, 2 molecules 1X

#29: Protein U2 snRNP component HSH155


Mass: 110166.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P49955
#35: Protein U2 snRNP component IST3 / Increased sodium tolerance protein 3 / U2 snRNP protein SNU17


Mass: 17121.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P40565

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U2 small nuclear ribonucleoprotein ... , 2 types, 2 molecules op

#39: Protein U2 small nuclear ribonucleoprotein A' / U2 snRNP A' / Looks exceptionally like U2A protein 1


Mass: 27232.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: Q08963
#40: Protein U2 small nuclear ribonucleoprotein B'' / U2 snRNP B''


Mass: 12850.944 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P40567

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Non-polymers , 2 types, 2 molecules

#47: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: yeast fully assembled spliceosomal B complex before activation
Type: CELL / Entity ID: #1-#46 / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
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 FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
10RELION2initial Euler assignment
11RELION2final Euler assignment
12RELION2classification
13RELION23D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 342588 / Symmetry type: POINT
RefinementHighest resolution: 3.9 Å

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