[English] 日本語
Yorodumi
- PDB-9esh: Structure of a B-state intermediate committed to discard (Bd-I state) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9esh
TitleStructure of a B-state intermediate committed to discard (Bd-I state)
Components
  • (Pre-mRNA-processing factor ...) x 2
  • (Pre-mRNA-splicing factor ...) x 16
  • (Small nuclear ribonucleoprotein ...) x 6
  • G-patch domain-containing protein C1486.03
  • Peptidyl-prolyl cis-trans isomerase ppi1
  • Pre-mRNA-processing protein 45
  • Putative pre-mRNA-splicing factor ATP-dependent RNA helicase C20H4.09
  • Small nuclear ribonucleoprotein-associated protein B
  • U2snRNA
  • U5snRNA
  • U6snRNA
  • UNK1
  • UNK2
  • Uncharacterized protein C20H4.06c
  • pre-mRNA
KeywordsSPLICING / Helicase / G-patch protein / discard pathway
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 / spliceosomal conformational changes to generate catalytic conformation / U2-type post-mRNA release spliceosomal complex / 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 / spliceosomal conformational changes to generate catalytic conformation / U2-type post-mRNA release spliceosomal complex / siRNA-mediated pericentric heterochromatin formation / post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step / pICln-Sm protein complex / U2-type catalytic step 1 spliceosome / pre-mRNA binding / snRNP binding / spindle pole body / SMN-Sm protein complex / spliceosomal tri-snRNP complex / regulatory ncRNA-mediated gene silencing / commitment complex / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / U2-type catalytic step 2 spliceosome / U2 snRNP / U1 snRNP / U4 snRNP / U2-type prespliceosome / precatalytic spliceosome / mRNA 5'-splice site recognition / spliceosomal complex assembly / spliceosomal tri-snRNP complex assembly / Prp19 complex / U5 snRNA binding / protein K63-linked ubiquitination / U5 snRNP / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / spliceosomal snRNP assembly / U1 snRNA binding / pericentric heterochromatin / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / spliceosomal complex / mRNA splicing, via spliceosome / RING-type E3 ubiquitin transferase / metallopeptidase activity / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / nuclear envelope / protein folding / protein-macromolecule adaptor activity / molecular adaptor activity / cysteine-type deubiquitinase activity / RNA helicase activity / RNA helicase / DNA repair / GTPase activity / mRNA binding / GTP binding / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
G patch domain-containing protein, N-terminal / Protein of unknown function (DUF1604) / GCF, C-terminal / GC-rich sequence DNA-binding factor-like protein / TFP11/STIP/Ntr1 / cwf21 / Slt11, RNA recognition motif / Pre-mRNA-splicing factor Cwc2, RNA recognition motif / Pre-mRNA-splicing factor SPF27 / Torus domain ...G patch domain-containing protein, N-terminal / Protein of unknown function (DUF1604) / GCF, C-terminal / GC-rich sequence DNA-binding factor-like protein / TFP11/STIP/Ntr1 / cwf21 / Slt11, RNA recognition motif / Pre-mRNA-splicing factor Cwc2, RNA recognition motif / Pre-mRNA-splicing factor SPF27 / Torus domain / Breast carcinoma amplified sequence 2 (BCAS2) / Torus domain / CWF11 family / Intron-binding protein aquarius, N-terminal / Intron-binding protein aquarius N-terminal / mRNA splicing factor SYF2 / SYF2 splicing factor / G-patch domain / : / : / mRNA splicing factor Cwf21 domain / cwf21 domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / 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 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / : / : / STL11, N-terminal / : / Pre-mRNA-splicing factor Syf1/CRNKL1 C-terminal HAT repeat / SKI-interacting protein SKIP, SNW domain / SKI-interacting protein, SKIP / SKIP/SNW domain / : / Pre-mRNA-splicing factor Syf1/CNRKL1 N-terminal HAT repeat / Pre-mRNA-splicing factor Cwf15/Cwc15 / Cwf15/Cwc15 cell cycle control protein / WD repeat Prp46/PLRG1-like / Pre-mRNA-splicing factor Cwc2/Slt11 / : / G10 protein / Pre-mRNA-splicing factor BUD31 / Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminal / : / : / pre-mRNA splicing factor component / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / DNA2/NAM7-like helicase / : / MIF4G domain / Myb-like DNA-binding domain / Anaphase-promoting complex subunit 4, WD40 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 / Modified RING finger domain / zinc finger / U-box domain / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / Snu114, GTP-binding domain / 116 kDa U5 small nuclear ribonucleoprotein component N-terminus / Pre-mRNA-splicing factor Syf1-like / : / Small nuclear ribonucleoprotein Sm D3 / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / Helicase-associated domain / Small nuclear ribonucleoprotein G / Helicase associated domain (HA2) Add an annotation / Small nuclear ribonucleoprotein F / Sm-like protein Lsm7/SmG / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Sm-like protein Lsm6/SmF / Myb-type HTH DNA-binding domain profile. / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats
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 / 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 / Pre-mRNA-splicing factor cwf5 / Pre-mRNA-splicing factor cwf14 / Small nuclear ribonucleoprotein G / Pre-mRNA-splicing factor cwf10 / Pre-mRNA-splicing factor cwf11 / Pre-mRNA-splicing factor cwf17 / Pre-mRNA-splicing factor cdc5 / Pre-mRNA-splicing factor cwf15 / Peptidyl-prolyl cis-trans isomerase ppi1 / Pre-mRNA-splicing factor cwf2 / Pre-mRNA-splicing factor cwf4 / Pre-mRNA-processing protein 45 / 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 / Pre-mRNA-splicing factor cwf7 / Small nuclear ribonucleoprotein E / G-patch domain-containing protein C1486.03 / Small nuclear ribonucleoprotein Sm D3
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSoni, K. / Wild, K. / Sinning, I.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)SI 586/6-1 Germany
German Research Foundation (DFG)Project-ID 439669440, TP B03 Germany
CitationJournal: 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
DepositionMar 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.2May 28, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: pre-mRNA
2: U2snRNA
5: U5snRNA
6: U6snRNA
A: Pre-mRNA-splicing factor spp42
B: Pre-mRNA-splicing factor cwf10
C: Pre-mRNA-splicing factor cwf17
D: Small nuclear ribonucleoprotein Sm D3
E: Small nuclear ribonucleoprotein-associated protein B
F: Small nuclear ribonucleoprotein Sm D1
G: Small nuclear ribonucleoprotein Sm D2
H: Small nuclear ribonucleoprotein E
I: Small nuclear ribonucleoprotein F
J: Small nuclear ribonucleoprotein G
K: Pre-mRNA-splicing factor prp5
L: Pre-mRNA-processing protein 45
M: Pre-mRNA-splicing factor cwf5
N: Pre-mRNA-splicing factor cwf11
O: Pre-mRNA-splicing factor cwf14
P: Pre-mRNA-splicing factor cwf2
Q: Pre-mRNA-splicing factor cwf15
R: Pre-mRNA-splicing factor cwf4
S: Pre-mRNA-processing factor 19
T: Pre-mRNA-processing factor 19
U: Pre-mRNA-processing factor 19
V: Pre-mRNA-processing factor 19
W: Pre-mRNA-splicing factor cdc5
X: Pre-mRNA-splicing factor cwf3
Y: Pre-mRNA-splicing factor syf2
Z: Pre-mRNA-splicing factor cwf7
a: Pre-mRNA-processing factor 17
b: Pre-mRNA-splicing factor cwf21
c: Pre-mRNA-splicing factor cwf22
d: Peptidyl-prolyl cis-trans isomerase ppi1
f: UNK1
m: G-patch domain-containing protein C1486.03
r: UNK2
y: Uncharacterized protein C20H4.06c
z: Putative pre-mRNA-splicing factor ATP-dependent RNA helicase C20H4.09
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,040,94252
Polymers2,039,23039
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: 9135.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast)
#2: RNA chain U2snRNA


Mass: 59207.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: GenBank: 5081
#3: RNA chain U5snRNA


Mass: 38191.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: GenBank: 5125
#4: RNA chain U6snRNA


Mass: 31863.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: GenBank: 891582601

-
Pre-mRNA-splicing factor ... , 16 types, 16 molecules ABCKMNOPQRWXYZbc

#5: 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
#6: 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
#7: 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
#15: 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
#17: 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
#18: 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
#19: 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
#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
#22: 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
#24: 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
#25: 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
#26: 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
#27: Protein Pre-mRNA-splicing factor cwf7 / Complexed with cdc5 protein 7 / Splicing factor 27


Mass: 21348.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9USV3
#29: 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
#30: 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

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

#8: 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
#10: 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
#11: 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
#12: 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
#13: 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
#14: 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

-
Protein , 7 types, 7 molecules ELdmryz

#9: 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
#16: 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
#31: 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
#33: 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
#34: Protein UNK2


Mass: 29464.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast)
#35: Protein Uncharacterized protein C20H4.06c


Mass: 60850.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9HE07
#36: 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

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

#23: 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
#28: 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

-
Protein/peptide , 1 types, 1 molecules f

#32: Protein/peptide UNK1


Mass: 1890.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast)

-
Non-polymers , 5 types, 13 molecules

#37: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#38: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#39: 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 / Feature type: SUBJECT OF INVESTIGATION
#40: Chemical ChemComp-GTP / GUANOSINE-5'-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
#41: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Bd-I complex / Type: COMPLEX / Entity ID: #1-#36 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Buffer solutionpH: 7.5
Details: 20 mM HEPES pH 7.5, 100 mM NaCl, 1.5 mM MgCl2, 0.01% IGEPAL CA-630
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2100 mMSodium chlorideNaCl1
31.5 mMMagnesium chlorideMgCl21
40.01 %IGEPAL CA-630(C2H4O)nC14H22O1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

-
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 FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm
Image recordingAverage exposure time: 1.491 sec. / Electron dose: 49.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 13096

-
Processing

EM software
IDNameVersionCategory
1PHENIX1.19.2_4158:model refinement
2SerialEMimage acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 929930
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61423 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00493232
ELECTRON MICROSCOPYf_angle_d0.779127200
ELECTRON MICROSCOPYf_dihedral_angle_d15.34435778
ELECTRON MICROSCOPYf_chiral_restr0.0514242
ELECTRON MICROSCOPYf_plane_restr0.00615465

+
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