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- PDB-7dco: Cryo-EM structure of the activated spliceosome (Bact complex) at ... -

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Entry
Database: PDB / ID: 7dco
TitleCryo-EM structure of the activated spliceosome (Bact complex) at an atomic resolution of 2.5 angstrom
Components
  • (Pre-mRNA-processing ...) x 2
  • (Pre-mRNA-splicing factor ...) x 10
  • (Small nuclear ribonucleoprotein ...SnRNP) x 4
  • BJ4_G0014900.mRNA.1.CDS.1
  • BJ4_G0027490.mRNA.1.CDS.1
  • BJ4_G0037700.mRNA.1.CDS.1
  • BJ4_G0056610.mRNA.1.CDS.1
  • BRR2 isoform 1
  • BUD31 isoform 1
  • CDC40 isoform 1
  • CLF1 isoform 1
  • CWC22 isoform 1
  • CWC27 isoform 1
  • HLJ1_G0043010.mRNA.1.CDS.1
  • HLJ1_G0053790.mRNA.1.CDS.1
  • HLJ1_G0054350.mRNA.1.CDS.1
  • HSH155 isoform 1
  • HSH49 isoform 1
  • PRP11 isoform 1
  • PRP8 isoform 1
  • PRP9 isoform 1
  • Pre-mRNA leakage protein 1
  • RDS3 complex subunit 10
  • RSE1 isoform 1
  • SMD1 isoform 1
  • SNT309 isoform 1
  • SNU114 isoform 1
  • SX2_G0027210.mRNA.1.CDS.1
  • SYF1 isoform 1
  • Sm protein F
  • U2 snRNAU2 spliceosomal RNA
  • U5 snRNAU5 spliceosomal RNA
  • U6 snRNAU6 spliceosomal RNA
  • pre-mRNAPrimary transcript
KeywordsSPLICING / RNA splicing / spliceosome / Bact complex / Prp2 / Spp2 / ATPase/helicase / activation
Function / homology
Function and homology information


maintenance of RNA location / RES complex / protein serine/threonine phosphatase inhibitor activity / snoRNA splicing / negative regulation of protein dephosphorylation / generation of catalytic spliceosome for first transesterification step / miRNA processing / U4/U6 snRNP / Prp19 complex / 7-methylguanosine cap hypermethylation ...maintenance of RNA location / RES complex / protein serine/threonine phosphatase inhibitor activity / snoRNA splicing / negative regulation of protein dephosphorylation / generation of catalytic spliceosome for first transesterification step / miRNA processing / U4/U6 snRNP / Prp19 complex / 7-methylguanosine cap hypermethylation / ATP-dependent activity, acting on RNA / U2-type catalytic step 1 spliceosome / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / commitment complex / U2-type prespliceosome assembly / U4 snRNP / U2 snRNP / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / generation of catalytic spliceosome for second transesterification step / ATPase activator activity / mRNA 5'-splice site recognition / U5 snRNP / spliceosomal snRNP assembly / mRNA export from nucleus / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / RNA splicing / helicase activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / spliceosomal complex / mRNA processing / mRNA splicing, via spliceosome / nucleic acid binding / RNA helicase activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA helicase / nuclear speck / GTPase activity / mRNA binding / GTP binding / ATP hydrolysis activity / DNA binding / RNA binding / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Pre-mRNA-splicing factor Spp2-like / Spp2/MOS2, G-patch domain / Pre-mRNA-splicing factor CWC24-like / G-patch domain / cwf21 / Torus domain / Pre-mRNA-splicing factor Cwc2, RNA recognition motif / Torus domain / mRNA splicing factor Cwf21 domain / cwf21 domain ...Pre-mRNA-splicing factor Spp2-like / Spp2/MOS2, G-patch domain / Pre-mRNA-splicing factor CWC24-like / G-patch domain / cwf21 / Torus domain / Pre-mRNA-splicing factor Cwc2, RNA recognition motif / Torus domain / mRNA splicing factor Cwf21 domain / cwf21 domain / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / BUD31/G10-related, conserved site / : / : / G10 protein signature 1. / G10 protein signature 2. / G-patch domain / glycine rich nucleic binding domain / Pre-mRNA-splicing factor Cwf15/Cwc15 / HAT (Half-A-TPR) repeat / Cwf15/Cwc15 cell cycle control protein / Splicing factor 3A subunit 1 / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / Pre-mRNA-splicing factor Cwc2/Slt11 / Splicing factor 3A subunit 1, conserved domain / Pre-mRNA splicing factor PRP21 like protein / G10 protein / Domain of unknown function DUF382 / Pre-mRNA-splicing factor BUD31 / Domain of unknown function (DUF382) / Zinc finger, C3HC4 type (RING finger) / : / Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminal / pre-mRNA splicing factor component / SWAP/Surp / SWAP/Surp superfamily / Surp module / SURP motif repeat profile. / Suppressor-of-White-APricot splicing regulator / 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) / Zinc finger, CCCH-type superfamily / U2A'/phosphoprotein 32 family A, C-terminal / occurring C-terminal to leucine-rich repeats / Leucine-rich repeat / : / Helicase associated domain (HA2), ratchet-like / zinc finger / Pre-mRNA-splicing factor Syf1-like / Snu114, GTP-binding domain / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation / 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 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / Myb domain / FHA domain / : / Forkhead-associated (FHA) domain / Sm domain profile. / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Myb-like DNA-binding domain / 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 / SMAD/FHA domain superfamily / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / : / : ...GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / : / : / Pre-mRNA-splicing factor CLF1 / : / : / Pre-mRNA-splicing factor CWC24 / SNU114 isoform 1 / : / : / : / Pre-mRNA-splicing factor CWC21 / : / BJ4_G0014900.mRNA.1.CDS.1 / : / : / : / Pre-mRNA-splicing factor CWC2 / : / RDS3 isoform 1 / : / U2 small nuclear ribonucleoprotein A' / : / MSL1 isoform 1 / Small nuclear ribonucleoprotein Sm D3 / BUD31 isoform 1 / : / Sm protein F / : / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein Sm D2 / HLJ1_G0022770.mRNA.1.CDS.1 / HLJ1_G0043010.mRNA.1.CDS.1 / : / : / RDS3 complex subunit 10 / Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2 / Pre-mRNA-splicing factor PRP21 / Small nuclear ribonucleoprotein G / Pre-mRNA-splicing factor SPP2 / Pre-mRNA-splicing factor CEF1 / Pre-mRNA-splicing factor CWC15 / Pre-mRNA leakage protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsBai, R. / Wan, R. / Yan, C. / Qi, J. / Zhang, P. / Lei, J. / Shi, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930059 China
CitationJournal: Science / Year: 2021
Title: Mechanism of spliceosome remodeling by the ATPase/helicase Prp2 and its coactivator Spp2.
Authors: Rui Bai / Ruixue Wan / Chuangye Yan / Qi Jia / Jianlin Lei / Yigong Shi /
Abstract: Spliceosome remodeling, executed by conserved adenosine triphosphatase (ATPase)/helicases including Prp2, enables precursor messenger RNA (pre-mRNA) splicing. However, the structural basis for the ...Spliceosome remodeling, executed by conserved adenosine triphosphatase (ATPase)/helicases including Prp2, enables precursor messenger RNA (pre-mRNA) splicing. However, the structural basis for the function of the ATPase/helicases remains poorly understood. Here, we report atomic structures of Prp2 in isolation, Prp2 complexed with its coactivator Spp2, and Prp2-loaded activated spliceosome and the results of structure-guided biochemical analysis. Prp2 weakly associates with the spliceosome and cannot function without Spp2, which stably associates with Prp2 and anchors on the spliceosome, thus tethering Prp2 to the activated spliceosome and allowing Prp2 to function. Pre-mRNA is loaded into a featured channel between the N and C halves of Prp2, where Leu from the N half and Arg from the C half prevent backward sliding of pre-mRNA toward its 5'-end. Adenosine 5'-triphosphate binding and hydrolysis trigger interdomain movement in Prp2, which drives unidirectional stepwise translocation of pre-mRNA toward its 3'-end. These conserved mechanisms explain the coupling of spliceosome remodeling to pre-mRNA splicing.
History
DepositionOct 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: 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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Assembly

Deposited unit
A: PRP8 isoform 1
B: U5 snRNA
C: SNU114 isoform 1
D: BRR2 isoform 1
d: Small nuclear ribonucleoprotein Sm D3
a: BJ4_G0014900.mRNA.1.CDS.1
b: SMD1 isoform 1
c: BJ4_G0037700.mRNA.1.CDS.1
e: Small nuclear ribonucleoprotein E
f: Sm protein F
g: Small nuclear ribonucleoprotein G
F: U6 snRNA
G: pre-mRNA
H: U2 snRNA
o: HLJ1_G0053790.mRNA.1.CDS.1
p: BJ4_G0027490.mRNA.1.CDS.1
h: BJ4_G0014900.mRNA.1.CDS.1
i: Small nuclear ribonucleoprotein E
j: Sm protein F
k: Small nuclear ribonucleoprotein G
l: Small nuclear ribonucleoprotein Sm D3
m: SMD1 isoform 1
n: BJ4_G0037700.mRNA.1.CDS.1
u: PRP9 isoform 1
w: Pre-mRNA-splicing factor PRP21
v: PRP11 isoform 1
1: HSH155 isoform 1
2: HLJ1_G0043010.mRNA.1.CDS.1
3: RSE1 isoform 1
4: HSH49 isoform 1
5: BJ4_G0056610.mRNA.1.CDS.1
6: RDS3 complex subunit 10
L: Pre-mRNA-splicing factor CEF1
s: Pre-mRNA-processing factor 19
t: Pre-mRNA-processing factor 19
q: Pre-mRNA-processing factor 19
r: Pre-mRNA-processing factor 19
K: SNT309 isoform 1
N: BUD31 isoform 1
T: HLJ1_G0054350.mRNA.1.CDS.1
P: Pre-mRNA-processing protein 45
Q: Pre-mRNA-splicing factor SLT11
R: Pre-mRNA-splicing factor CWC2
S: Pre-mRNA-splicing factor CWC15
Y: Pre-mRNA leakage protein 1
X: SX2_G0027210.mRNA.1.CDS.1
Z: Pre-mRNA-splicing factor CWC26
W: CDC40 isoform 1
U: Pre-mRNA-splicing factor CWC21
V: CWC22 isoform 1
M: Pre-mRNA-splicing factor CWC24
z: CWC27 isoform 1
y: Pre-mRNA-splicing factor SPP2
J: CLF1 isoform 1
I: SYF1 isoform 1
x: Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,914,32080
Polymers2,911,97056
Non-polymers2,35024
Water30,8781714
1


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

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Components

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Protein , 27 types, 31 molecules ACDahbmcnfjopuv123456KNTYXWVzJI

#1: Protein PRP8 isoform 1


Mass: 279867.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PW68
#3: Protein SNU114 isoform 1


Mass: 114174.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PW35
#4: Protein BRR2 isoform 1


Mass: 246470.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q2I8
#6: Protein BJ4_G0014900.mRNA.1.CDS.1 / HLJ1_G0014660.mRNA.1.CDS.1 / SMB1 isoform 1 / Y55_G0014800.mRNA.1.CDS.1


Mass: 22426.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q0I3
#7: Protein SMD1 isoform 1


Mass: 16296.798 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q0W7
#8: Protein BJ4_G0037700.mRNA.1.CDS.1 / HLJ1_G0037800.mRNA.1.CDS.1 / HN1_G0037500.mRNA.1.CDS.1 / Y55_G0037640.mRNA.1.CDS.1


Mass: 12876.066 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6L0ZK95
#10: Protein Sm protein F


Mass: 9669.945 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q5K4
#15: Protein HLJ1_G0053790.mRNA.1.CDS.1 / LEA1 isoform 1 / Y55_G0053650.mRNA.1.CDS.1


Mass: 27232.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q2G3
#16: Protein BJ4_G0027490.mRNA.1.CDS.1 / HN1_G0027200.mRNA.1.CDS.1 / MSL1 isoform 1 / SX2_G0029270.mRNA.1.CDS.1 / Y55_G0027550.mRNA.1.CDS.1


Mass: 12850.944 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q318
#18: Protein PRP9 isoform 1


Mass: 63126.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PZ67
#20: Protein PRP11 isoform 1


Mass: 29962.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q100
#21: Protein HSH155 isoform 1


Mass: 110166.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PSM1
#22: Protein HLJ1_G0043010.mRNA.1.CDS.1


Mass: 27503.838 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6L0ZSI9
#23: Protein RSE1 isoform 1


Mass: 153956.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PUP5
#24: Protein HSH49 isoform 1


Mass: 24534.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q466
#25: Protein BJ4_G0056610.mRNA.1.CDS.1 / EM14S01-3B_G0056430.mRNA.1.CDS.1 / HLJ1_G0056610.mRNA.1.CDS.1 / HN1_G0056420.mRNA.1.CDS.1 / JXXY16. ...EM14S01-3B_G0056430.mRNA.1.CDS.1 / HLJ1_G0056610.mRNA.1.CDS.1 / HN1_G0056420.mRNA.1.CDS.1 / JXXY16.1_G0056310.mRNA.1.CDS.1 / RDS3 isoform 1 / SX2_G0056170.mRNA.1.CDS.1 / XXYS1_G0055940.mRNA.1.CDS.1 / Y55_G0056510.mRNA.1.CDS.1


Mass: 12283.573 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q1K7
#26: Protein RDS3 complex subunit 10 / Splicing factor 3b subunit


Mass: 9888.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0C074
#29: Protein SNT309 isoform 1 / Y55_G0056570.mRNA.1.CDS.1


Mass: 20741.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q641
#30: Protein BUD31 isoform 1 / EM14S01-3B_G0005920.mRNA.1.CDS.1 / HLJ1_G0006010.mRNA.1.CDS.1 / JXXY16.1_G0005970.mRNA.1.CDS.1 / ...EM14S01-3B_G0005920.mRNA.1.CDS.1 / HLJ1_G0006010.mRNA.1.CDS.1 / JXXY16.1_G0005970.mRNA.1.CDS.1 / Pre-mRNA-splicing factor BUD31 / SX2_G0005960.mRNA.1.CDS.1 / XXYS1_G0005950.mRNA.1.CDS.1 / Y55_G0006020.mRNA.1.CDS.1


Mass: 18484.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q3N1
#31: Protein HLJ1_G0054350.mRNA.1.CDS.1 / Pre-mRNA-splicing factor PRP46


Mass: 37639.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6L0ZMZ1
#36: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q07930
#37: Protein SX2_G0027210.mRNA.1.CDS.1


Mass: 14880.456 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6L1ALU2
#39: Protein CDC40 isoform 1


Mass: 52128.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PYD5
#41: Protein CWC22 isoform 1


Mass: 67386.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q1E9
#43: Protein CWC27 isoform 1


Mass: 35080.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q291
#45: Protein CLF1 isoform 1 / Pre-mRNA-splicing factor CLF1


Mass: 82555.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PT67
#46: Protein SYF1 isoform 1


Mass: 100344.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q0A4

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RNA chain , 4 types, 4 molecules BFGH

#2: 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 (brewer's yeast) / References: GenBank: 1039023403
#12: RNA chain U6 snRNA / U6 spliceosomal RNA


Mass: 35883.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1039022925
#13: RNA chain pre-mRNA / Primary transcript


Mass: 44772.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#14: 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 (brewer's yeast)

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Small nuclear ribonucleoprotein ... , 4 types, 6 molecules deigkl

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


Mass: 11240.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q3H8
#9: Protein Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E


Mass: 10385.098 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q895
#11: Protein Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / SmG


Mass: 8490.809 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40204
#17: Protein Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3


Mass: 8882.204 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q3H8

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Pre-mRNA-splicing factor ... , 10 types, 10 molecules wLQRSZUMyx

#19: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P32524
#27: Protein Pre-mRNA-splicing factor CEF1 / PRP nineteen-associated complex protein 85 / PRP19-associated complex protein 85


Mass: 67837.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q03654
#33: Protein Pre-mRNA-splicing factor SLT11


Mass: 40988.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q0Z2
#34: Protein Pre-mRNA-splicing factor CWC2


Mass: 29742.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q155
#35: Protein Pre-mRNA-splicing factor CWC15 / Complexed with CEF1 protein 15


Mass: 19975.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q03772
#38: Protein Pre-mRNA-splicing factor CWC26


Mass: 14039.636 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6L1AYM3
#40: Protein Pre-mRNA-splicing factor CWC21


Mass: 15793.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PZG6
#42: Protein Pre-mRNA-splicing factor CWC24


Mass: 29797.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PVM6
#44: Protein Pre-mRNA-splicing factor SPP2 / Spliceosome maturation protein SPP2 / Suppressor of PRP protein 2


Mass: 20685.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q02521
#47: Protein Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2 / Pre-mRNA-processing protein 2


Mass: 99947.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P20095, RNA helicase

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Pre-mRNA-processing ... , 2 types, 5 molecules stqrP

#28: Protein
Pre-mRNA-processing factor 19


Mass: 56629.777 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: A0A6A5PQI0, RING-type E3 ubiquitin transferase
#32: Protein Pre-mRNA-processing protein 45


Mass: 42548.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PTY9

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Non-polymers , 6 types, 1738 molecules

#48: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
#49: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


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


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#51: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#52: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#53: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1714 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: the activated spliceosome Bact complex / Type: COMPLEX / Entity ID: #1-#50 / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: Quantifoil
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 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 705371 / Symmetry type: POINT

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