[English] 日本語
Yorodumi
- PDB-7dco: Cryo-EM structure of the activated spliceosome (Bact complex) at ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

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 / snoRNA splicing / generation of catalytic spliceosome for first transesterification step / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / U2-type catalytic step 1 spliceosome / Prp19 complex / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex ...maintenance of RNA location / RES complex / snoRNA splicing / generation of catalytic spliceosome for first transesterification step / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / U2-type catalytic step 1 spliceosome / Prp19 complex / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / ATP-dependent activity, acting on RNA / SMN-Sm protein complex / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / U2-type prespliceosome assembly / commitment complex / 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 / spliceosomal complex / mRNA processing / mRNA splicing, via spliceosome / RNA helicase activity / nucleic acid binding / RNA helicase / mRNA binding / GTPase activity / 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 / Splicing factor 3A subunit 1 / Splicing factor 3A subunit 1, conserved 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 / Splicing factor 3A subunit 1 / Splicing factor 3A subunit 1, conserved domain / Pre-mRNA splicing factor PRP21 like protein / mRNA splicing factor Cwf21 domain / cwf21 domain / SWAP/Surp / SWAP/Surp superfamily / Surp module / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / SURP motif repeat profile. / Suppressor-of-White-APricot splicing regulator / Domain of unknown function DUF382 / Domain of unknown function (DUF382) / 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 / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / Pre-mRNA-splicing factor Cwc2/Slt11 / Zinc finger, C3HC4 type (RING finger) / G10 protein / PHF5-like / Pre-mRNA-splicing factor BUD31 / PHF5-like protein / PSP, proline-rich / Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminal / PSP / pre-mRNA splicing factor component / proline-rich domain in spliceosome associated proteins / Splicing factor 3B subunit 5/RDS3 complex subunit 10 / : / Splicing factor 3B subunit 10 (SF3b10) / U2A'/phosphoprotein 32 family A, C-terminal / occurring C-terminal to leucine-rich repeats / Leucine-rich repeat / Pre-mRNA-splicing factor Syf1-like / Zinc finger, CCCH-type superfamily / 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 / : / Helicase associated domain (HA2), ratchet-like / zinc finger / 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 / 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 / Myb-type HTH DNA-binding domain profile. / Sm-like protein Lsm6/SmF / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / Forkhead associated domain / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / Forkhead-associated (FHA) domain profile. / FHA domain / Myb domain / Forkhead-associated (FHA) domain / : / Sm domain profile. / Myb-like DNA-binding domain / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / LSM domain superfamily / 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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-30637
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-30637
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

+
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

-
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)

-
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

-
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

-
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

-
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

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
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

-
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)

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more