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- PDB-9esh: Structure of a B-state intermediate committed to discard (Bd-I state) -

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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 / regulatory ncRNA-mediated gene silencing / SMN-Sm protein complex / spliceosomal tri-snRNP complex / U2-type spliceosomal complex / commitment complex / mRNA cis splicing, via spliceosome / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / mRNA 5'-splice site recognition / spliceosomal tri-snRNP complex assembly / Prp19 complex / protein K63-linked ubiquitination / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / spliceosomal snRNP assembly / pericentric heterochromatin / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / peptidyl-prolyl cis-trans isomerase activity / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / spliceosomal complex / RING-type E3 ubiquitin transferase / mRNA splicing, via spliceosome / 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 / cytosol / cytoplasm
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 SYF1 middle HAT repeat / Pre-mRNA-splicing factor 19 / Pre-mRNA-processing factor 19 / Prp19/Pso4-like / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / : / : / Pre-mRNA-splicing factor Syf1/CRNKL1 C-terminal HAT repeat / : / STL11, N-terminal / : / Pre-mRNA-splicing factor Syf1/CNRKL1 N-terminal HAT repeat / SKI-interacting protein SKIP, SNW domain / SKI-interacting protein, SKIP / SKIP/SNW domain / 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 / DNA2/NAM7-like helicase / : / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / 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 / U-box domain profile. / Anaphase-promoting complex subunit 4 WD40 domain / Modified RING finger domain / U-box domain / Zinc finger, CCCH-type superfamily / 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 / Pre-mRNA-splicing factor Syf1-like / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Helicase-associated domain / 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 / 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
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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

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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

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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

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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

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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)

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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

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Details

Has ligand of interestY
Has protein modificationN

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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: 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

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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 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

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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

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