5GMK

Cryo-EM structure of the Catalytic Step I spliceosome (C complex) at 3.4 angstrom resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 Å
  • Aggregation State: Particle
  • Reconstruction Method: Single Particle

Literature

Macromolecules
Sequence Display for 5GMK

Classification: RNA BINDING PROTEIN / RNA

Total Structure Weight: 2023545.50


Macromolecule Entities
Molecule Chains Length Organism Details
Pre-mRNA-splicing factor 8 A 2413 Saccharomyces cerevisiae Gene Name(s): PRP8 DBF3 DNA39 RNA8 SLT21 USA2 YHR165C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Pre-mRNA-splicing factor SNU114 C 1008 Saccharomyces cerevisiae Gene Name(s): SNU114 GIN10 YKL173W YKL637
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Pre-mRNA-splicing factor CWC21 J 135 Saccharomyces cerevisiae Gene Name(s): CWC21 YDR482C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Pre-mRNA-splicing factor PRP46 O 451 Saccharomyces cerevisiae Gene Name(s): PRP46 CWC1 NTC50 YPL151C P2594
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Pre-mRNA-processing protein 45 P 379 Saccharomyces cerevisiae Gene Name(s): PRP45 FUN20 YAL032C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Pre-mRNA-splicing factor SLT11 Q 364 Saccharomyces cerevisiae Gene Name(s): ECM2 Gene View SLT11 YBR065C YBR0614
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Pre-mRNA-splicing factor CWC2 R 339 Saccharomyces cerevisiae Gene Name(s): CWC2 NTC40 SLC3 YDL209C D1041
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Pre-mRNA-splicing factor CWC15 S 175 Saccharomyces cerevisiae Gene Name(s): CWC15 Gene View YDR163W YD8358.17
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Pre-mRNA-splicing factor BUD31 T 157 Saccharomyces cerevisiae Gene Name(s): BUD31 Gene View CWC14 YCR063W YCR63W YCR903
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Pre-mRNA-splicing factor CWC22 Z 577 Saccharomyces cerevisiae Gene Name(s): CWC22 Gene View YGR278W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Pre-mRNA-splicing factor CEF1 c 587 Saccharomyces cerevisiae Gene Name(s): CEF1 NTC85 YMR213W YM8261.07
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Pre-mRNA-splicing factor CLF1 d 687 Saccharomyces cerevisiae Gene Name(s): CLF1 NTC77 SYF3 YLR117C L2952
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Protein CWC16 F 278 Saccharomyces cerevisiae Gene Name(s): YJU2 CWC16 YKL095W YKL442
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Pre-mRNA-splicing factor CWC25 G 179 Saccharomyces cerevisiae Gene Name(s): CWC25 Gene View YNL245C N0901
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Pre-mRNA-splicing factor ISY1 H 235 Saccharomyces cerevisiae Gene Name(s): ISY1 Gene View NTC30 UTR3 YJR050W J1657
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Pre-mRNA-splicing factor SYF2 I 215 Saccharomyces cerevisiae Gene Name(s): SYF2 Gene View NTC31 YGR129W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Pre-mRNA-splicing factor SYF1 v 859 Saccharomyces cerevisiae Gene Name(s): SYF1 NTC90 YDR416W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Pre-mRNA-processing factor 17 n 455 Saccharomyces cerevisiae Gene Name(s): CDC40 Gene View PRP17 SLU4 XRS2 YDR364C D9481.11
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Pre-mRNA-processing factor 19 o, p, q, r 503 Saccharomyces cerevisiae EC#: 6.3.2 IUBMB
Gene Name(s): PRP19 PSO4 YLL036C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Pre-mRNA-splicing factor SNT309 t 175 Saccharomyces cerevisiae Gene Name(s): SNT309 NTC25 YPR101W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Small nuclear ribonucleoprotein-associated protein B k, s 196 Saccharomyces cerevisiae Gene Name(s): SMB1 YER029C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Small nuclear ribonucleoprotein E i, u 94 Saccharomyces cerevisiae Gene Name(s): SME1 YOR159C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Small nuclear ribonucleoprotein F h, w 86 Saccharomyces cerevisiae Gene Name(s): SMX3 YPR182W P9705.4
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Small nuclear ribonucleoprotein G j, x 77 Saccharomyces cerevisiae Gene Name(s): SMX2 SNP2 YFL017W-A YFL017Bw
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Small nuclear ribonucleoprotein Sm D3 l, y 101 Saccharomyces cerevisiae Gene Name(s): SMD3 YLR147C L9634.6
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Small nuclear ribonucleoprotein Sm D1 m, z 146 Saccharomyces cerevisiae Gene Name(s): SMD1 YGR074W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Small nuclear ribonucleoprotein Sm D2 e, g 110 Saccharomyces cerevisiae Gene Name(s): SMD2 YLR275W L9328.5
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
U2 small nuclear ribonucleoprotein B'' a 111 Saccharomyces cerevisiae Gene Name(s): MSL1 Gene View YIR009W YIB9W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
U2 small nuclear ribonucleoprotein A' b 238 Saccharomyces cerevisiae Gene Name(s): LEA1 YPL213W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
U5 snRNA D 214 Saccharomyces cerevisiae
U6 snRNA E 112 Saccharomyces cerevisiae
U2 snRNA L 1175 Saccharomyces cerevisiae
Intron_BPS M 29 Saccharomyces cerevisiae
5'-Exon B 13 Saccharomyces cerevisiae
5'-Splicing Site N 15 Saccharomyces cerevisiae

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GTP
Query on GTP

C GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

F, Q, R, T ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

C, E MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
UNK
Query on UNK
c, d, v L-PEPTIDE LINKING C4 H9 N O2 --

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 Å
  • Reconstruction Method: Single Particle

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-07-14
  • Released Date: 2016-08-17
  • Deposition author(s): Wan, R., Yan, C., Bai, R., Huang, G., Shi, Y.

Revision History

  • Version 1_0: 2016-08-17

    Type: Initial release

  • Version 1_1: 2016-09-07

    Type: Database references, Other

  • Version 1_2: 2016-09-14

    Type: Other

  • Version 1_3: 2016-11-02

    Type: Other

  • Version 1_4: 2016-12-21

    Type: Structure summary