[English] 日本語
Yorodumi
- PDB-9s2g: Revised structure of the fission yeast defective B* spliceosome (B*d) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9s2g
TitleRevised structure of the fission yeast defective B* spliceosome (B*d)
Components
  • (Pre-mRNA-processing factor ...) x 2
  • (Pre-mRNA-splicing factor ...) x 17
  • (Small nuclear ribonucleoprotein ...) x 6
  • (Uncharacterized protein ...) x 3
  • G-patch domain-containing protein C1486.03
  • Peptidyl-prolyl cis-trans isomerase ppi1
  • Pre-mRNA
  • Pre-mRNA-processing protein 45
  • Protein saf4
  • Putative pre-mRNA-splicing factor ATP-dependent RNA helicase C20H4.09
  • Small nuclear ribonucleoprotein-associated protein B
  • Stress response protein bis1
  • U2 snRNA
  • U5 snRNA
  • U6 snRNA
KeywordsSPLICING / Spliceosome / 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 complex disassembly / U2-type post-mRNA release spliceosomal complex / spliceosomal conformational changes to generate catalytic conformation / siRNA-mediated pericentric heterochromatin formation / post-mRNA release spliceosomal 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 complex disassembly / U2-type post-mRNA release spliceosomal complex / 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 / spindle pole body / SMN-Sm protein complex / spliceosomal tri-snRNP complex / commitment complex / U4 snRNP / snRNP binding / mRNA cis splicing, via spliceosome / U2-type catalytic step 2 spliceosome / regulatory ncRNA-mediated gene silencing / U2-type spliceosomal complex / pre-mRNA binding / U1 snRNP / U2 snRNP / U2-type prespliceosome / precatalytic spliceosome / mRNA 5'-splice site recognition / spliceosomal complex assembly / Prp19 complex / spliceosomal tri-snRNP complex assembly / U5 snRNP / U5 snRNA binding / pre-mRNA intronic binding / U2 snRNA binding / U6 snRNA binding / U1 snRNA binding / protein K63-linked ubiquitination / pericentric heterochromatin / U4/U6 x U5 tri-snRNP complex / spliceosomal snRNP assembly / catalytic step 2 spliceosome / spliceosomal complex / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / mRNA splicing, via spliceosome / RING-type E3 ubiquitin transferase / spindle / metallopeptidase activity / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / nuclear envelope / protein folding / molecular adaptor activity / microtubule / protein-macromolecule adaptor activity / RNA helicase activity / cysteine-type deubiquitinase activity / RNA helicase / DNA repair / mRNA binding / GTPase activity / nucleolus / GTP binding / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Leukocyte receptor cluster member 1-like / G patch domain-containing protein, N-terminal / G patch domain-containing protein, N-terminal / Nuclear protein DGCR14/ESS-2 / Nuclear protein Es2 / GCF, C-terminal / : / GC-rich sequence DNA-binding factor-like protein / Nineteen complex-related protein 2 / TFP11/STIP/Ntr1 ...Leukocyte receptor cluster member 1-like / G patch domain-containing protein, N-terminal / G patch domain-containing protein, N-terminal / Nuclear protein DGCR14/ESS-2 / Nuclear protein Es2 / GCF, C-terminal / : / GC-rich sequence DNA-binding factor-like protein / Nineteen complex-related protein 2 / TFP11/STIP/Ntr1 / mRNA splicing factor Cwf18-like / cwf18 pre-mRNA splicing factor / Saf4/Yju2 protein / Saf4/Yju2 protein / HAT (Half-A-TPR) repeat / cwf21 / Slt11, RNA recognition motif / Pre-mRNA-splicing factor Cwc2, RNA recognition motif / Torus domain / Torus domain / Pre-mRNA-splicing factor SPF27 / Breast carcinoma amplified sequence 2 (BCAS2) / CWF11 family / Intron-binding protein aquarius, N-terminal / Intron-binding protein aquarius N-terminal / mRNA splicing factor SYF2 / SYF2 splicing factor / : / : / mRNA splicing factor Cwf21 domain / cwf21 domain / G-patch domain / G-patch domain profile. / Pre-mRNA-processing factor 17 / Pre-mRNA-splicing factor 19 / Pre-mRNA-processing factor 19 / : / Prp19/Pso4-like / : / Pre-mRNA-splicing factor SYF1 middle HAT repeat / glycine rich nucleic binding domain / G-patch domain / : / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / : / Pre-mRNA-splicing factor Syf1/CRNKL1 C-terminal HAT repeat / : / STL11, N-terminal / SKI-interacting protein SKIP, SNW domain / Pre-mRNA-splicing factor Cwf15/Cwc15 / SKI-interacting protein, SKIP / SKIP/SNW domain / Cwf15/Cwc15 cell cycle control protein / WD repeat Prp46/PLRG1-like / Pre-mRNA-splicing factor Cwc2/Slt11 / : / Initiation factor eIF-4 gamma, MA3 / Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminal / : / : / : / MA3 domain / pre-mRNA splicing factor component / Pre-mRNA-splicing factor Syf1/CNRKL1 N-terminal HAT repeat / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / G10 protein / Pre-mRNA-splicing factor BUD31 / DNA2/NAM7-like helicase / : / MIF4G domain / Anaphase-promoting complex subunit 4, WD40 domain / Myb-like DNA-binding domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / Small nuclear ribonucleoprotein D1 / Anaphase-promoting complex subunit 4 WD40 domain / U-box domain profile. / Zinc finger, CCCH-type superfamily / Pre-mRNA-splicing factor Syf1-like / zinc finger / 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 / Modified RING finger domain / U-box domain / Small nuclear ribonucleoprotein Sm D2 / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Small nuclear ribonucleoprotein Sm D3 / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Helicase-associated domain / Small nuclear ribonucleoprotein E / Helicase associated domain (HA2) Add an annotation / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Sm-like protein Lsm7/SmG
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / Pre-mRNA-splicing factor prp5 ...GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / Pre-mRNA-splicing factor prp5 / Uncharacterized protein C17A2.08c / Pre-mRNA-processing factor 19 / Small nuclear ribonucleoprotein Sm D2 / Pre-mRNA-splicing factor cwf21 / Pre-mRNA-splicing factor spp42 / Small nuclear ribonucleoprotein Sm D1 / Pre-mRNA-processing factor 17 / Pre-mRNA-splicing factor syf2 / Small nuclear ribonucleoprotein F / Stress response protein bis1 / Pre-mRNA-splicing factor cwf5 / Protein saf4 / 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 / Small nuclear ribonucleoprotein-associated protein B / Putative pre-mRNA-splicing factor ATP-dependent RNA helicase C20H4.09 / Uncharacterized protein C20H4.06c / Pre-mRNA-splicing factor Cwf22 / Pre-mRNA-splicing factor cwf3 / Uncharacterized protein C5E4.10c / Pre-mRNA-splicing factor cwf7 / Small nuclear ribonucleoprotein E / G-patch domain-containing protein C1486.03 / Pre-mRNA-splicing factor cwf18 / Small nuclear ribonucleoprotein Sm D3
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
Schizosaccharomyces pombe DM3650 (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsBoreikaite, V. / Vorlaender, M.K. / Plaschka, C.
Funding supportEuropean Union, France, Austria, 5items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)ALTF 784-2023European Union
Human Frontier Science Program (HFSP)LT0013/2024-L France
Austrian Science FundESP7844224 Austria
European Research Council (ERC)ERC-2020-STG 949081European Union
Austrian Science FundDOC177-B Austria
Citation
#1: Journal: Nat Struct Mol Biol / Year: 2025
Title: Structures of aberrant spliceosome intermediates on their way to disassembly.
Authors: Komal Soni / Attila Horvath / Olexandr Dybkov / Merlin Schwan / Sasanan Trakansuebkul / Dirk Flemming / Klemens Wild / Henning Urlaub / Tamás Fischer / Irmgard Sinning /
Abstract: Intron removal during pre-mRNA splicing is of extraordinary complexity and its disruption causes a vast number of genetic diseases in humans. While key steps of the canonical spliceosome cycle have ...Intron removal during pre-mRNA splicing is of extraordinary complexity and its disruption causes a vast number of genetic diseases in humans. While key steps of the canonical spliceosome cycle have been revealed by combined structure-function analyses, structural information on an aberrant spliceosome committed to premature disassembly is not available. Here, we report two cryo-electron microscopy structures of post-B spliceosome intermediates from Schizosaccharomyces pombe primed for disassembly. We identify the DEAH-box helicase-G-patch protein pair (Gih35-Gpl1, homologous to human DHX35-GPATCH1) and show how it maintains catalytic dormancy. In both structures, Gpl1 recognizes a remodeled active site introduced by an overstabilization of the U5 loop I interaction with the 5' exon leading to a single-nucleotide insertion at the 5' splice site. Remodeling is communicated to the spliceosome surface and the Ntr1 complex that mediates disassembly is recruited. Our data pave the way for a targeted analysis of splicing quality control.
History
DepositionJul 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: Pre-mRNA
2: U2 snRNA
3: Stress response protein bis1
35: Putative pre-mRNA-splicing factor ATP-dependent RNA helicase C20H4.09
5: U5 snRNA
6: U6 snRNA
A: Pre-mRNA-splicing factor spp42
C: Pre-mRNA-splicing factor cwf10
CW: Pre-mRNA-splicing factor cwf22
E: Pre-mRNA-splicing factor cwf17
GP: Uncharacterized protein C20H4.06c (GPATCH1)
I: Pre-mRNA-splicing factor cwf3
J: Pre-mRNA-splicing factor cwf4
K: Pre-mRNA-splicing factor cwf7
L: Pre-mRNA-splicing factor cdc5
LG: Uncharacterized protein C5E4.10c (LENG1)
M: Pre-mRNA-splicing factor syf2
N: Pre-mRNA-splicing factor cwf14
O: Pre-mRNA-splicing factor cwf5
O2: Pre-mRNA-splicing factor cwf2
P: Pre-mRNA-splicing factor cwf15
PX: Uncharacterized protein C17A2.08c (PAXBP1)
Q: Pre-mRNA-splicing factor cwf11
R: Pre-mRNA-processing protein 45
S: Peptidyl-prolyl cis-trans isomerase ppi1
SR: Pre-mRNA-splicing factor cwf21
T: Pre-mRNA-splicing factor prp5
TF: G-patch domain-containing protein C1486.03
W: Pre-mRNA-processing factor 17
YB: Protein saf4
Z: Pre-mRNA-splicing factor cwf18
a: Small nuclear ribonucleoprotein Sm D3
b: Small nuclear ribonucleoprotein-associated protein B
c: Small nuclear ribonucleoprotein Sm D1
d: Small nuclear ribonucleoprotein Sm D2
e: Small nuclear ribonucleoprotein E
f: Small nuclear ribonucleoprotein F
g: Small nuclear ribonucleoprotein G
q: Pre-mRNA-processing factor 19
r: Pre-mRNA-processing factor 19
s: Pre-mRNA-processing factor 19
t: Pre-mRNA-processing factor 19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,170,34455
Polymers2,168,63242
Non-polymers1,71213
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
RNA chain , 4 types, 4 molecules 1256

#1: RNA chain Pre-mRNA


Mass: 9464.497 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast)
#2: 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) / References: GenBank: 5081
#5: 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) / References: GenBank: 5125
#6: 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) / References: GenBank: 891582601

-
Protein , 7 types, 7 molecules 335RSTFYBb

#3: Protein Stress response protein bis1 / Splicing factor ESS-2 homolog


Mass: 43084.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O59793
#4: Protein Putative pre-mRNA-splicing factor ATP-dependent RNA helicase C20H4.09 / DEAH-box helicase C20H4.09


Mass: 73113.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9HE06, RNA helicase
#24: 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 (fission yeast) / References: UniProt: Q09882
#25: 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 (fission yeast) / References: UniProt: P87051, peptidylprolyl isomerase
#28: Protein G-patch domain-containing protein C1486.03


Mass: 91791.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9UTK6
#30: Protein Protein saf4


Mass: 34751.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O60141
#33: Protein Small nuclear ribonucleoprotein-associated protein B / snRNP-B / Sm protein B / Sm-B / SmB


Mass: 15493.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q10163

-
Pre-mRNA-splicing factor ... , 17 types, 17 molecules ACCWEIJKLMNOO2PQSRTZ

#7: 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 (fission yeast) / References: UniProt: O14187
#8: 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 (fission yeast) / References: UniProt: O94316
#9: Protein Pre-mRNA-splicing factor cwf22 / Complexed with cdc5 protein 22


Mass: 102928.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9P6R9
#10: 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 (fission yeast) / References: UniProt: O94620
#12: Protein Pre-mRNA-splicing factor cwf3 / Complexed with cdc5 protein 3


Mass: 92759.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9P7R9
#13: Protein Pre-mRNA-splicing factor cwf4 / Complexed with cdc5 protein 4


Mass: 80964.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P87312
#14: 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 DM3650 (yeast) / References: UniProt: Q9USV3
#15: Protein Pre-mRNA-splicing factor cdc5 / Cell division control protein 5


Mass: 86981.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P39964
#17: Protein Pre-mRNA-splicing factor syf2


Mass: 28037.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O59733
#18: 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 (fission yeast) / References: UniProt: O74772
#19: Protein Pre-mRNA-splicing factor cwf5 / Complexed with cdc5 protein 5


Mass: 39640.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O59800
#20: Protein Pre-mRNA-splicing factor cwf2 / Complexed with cdc5 protein 2 / Pre-mRNA-processing protein 3


Mass: 44343.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P87126
#21: 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 (fission yeast) / References: UniProt: P78794
#23: 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 (fission yeast) / References: UniProt: O94508
#26: Protein Pre-mRNA-splicing factor cwf21 / Complexed with cdc5 protein 21


Mass: 34617.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O14161
#27: Protein Pre-mRNA-splicing factor prp5 / Complexed with cdc5 protein 1 / Pre-mRNA-processing protein 5


Mass: 52492.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O13615
#31: Protein Pre-mRNA-splicing factor cwf18 / Complexed with cdc5 protein 18


Mass: 16685.877 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9UU80

-
Uncharacterized protein ... , 3 types, 3 molecules GPLGPX

#11: Protein Uncharacterized protein C20H4.06c (GPATCH1)


Mass: 60850.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9HE07
#16: Protein Uncharacterized protein C5E4.10c (LENG1)


Mass: 23969.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9P7Z6
#22: Protein Uncharacterized protein C17A2.08c (PAXBP1)


Mass: 41937.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O13758

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

#29: 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 (fission yeast) / References: UniProt: O43071
#39: Protein
Pre-mRNA-processing factor 19 / Complexed with cdc5 protein 8 / RING-type E3 ubiquitin transferase PRP19


Mass: 54243.988 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast)
References: UniProt: O14011, RING-type E3 ubiquitin transferase

-
Small nuclear ribonucleoprotein ... , 6 types, 6 molecules acdefg

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


Mass: 11050.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9UUC6
#34: Protein Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / snRNP core protein D1


Mass: 13115.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O42661
#35: Protein Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / Complexed with cdc5 protein 9 / snRNP core protein D2


Mass: 13119.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O14036
#36: Protein Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / Sm-E / SmE


Mass: 9702.353 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9USZ3
#37: Protein Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / Sm-F / SmF


Mass: 8667.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O59734
#38: Protein Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / Sm-G / SmG


Mass: 8616.038 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74966

-
Non-polymers , 5 types, 13 molecules

#40: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#41: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#42: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6
#43: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


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


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Revised fission yeast defective B* spliceosome (B*D) / Type: COMPLEX / Entity ID: #1-#39 / Source: NATURAL
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 49.4 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
1Warpparticle selection
2PHENIX1.21.2_5419+SVNmodel refinement
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72631 / 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