5MPS Splicing date Dec 18, 2016
title Structure Of A Spliceosome Remodeled For Exon Ligation
authors S.M.Fica, C.Oubridge, W.P.Galej, M.E.Wilkinson, A.J.Newman, X.C. K.Nagai
compound source
Molecule: Yeast Ubc4 Gene For Ubiquitin-Conjugating Enzyme
Chain: I
Engineered: Yes
Other_details: Saccharomyces Cerevisiae Ubc4 Pre-Mrna Intro Vitro Transcribed.;
 Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Expression_system: In Vitro Transcription Vector Pt7-Fluc(D
Expression_system_taxid: 905932

Molecule: Ubc4 Gene Exon
Chain: E
Engineered: Yes
Other_details: Saccharomyces Cerevisiae Ubc4 Pre-Mrna Exon, Transcribed.;
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Ubc4
Expression_system: In Vitro Transcription Vector Pt7-Fluc(D
Expression_system_taxid: 905932

Molecule: U2 Snrna
Chain: 2
Engineered: Yes
Other_details: Saccharomyces Cerevisiae U2 Snrna
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Expression_system: Saccharomyces Cerevisiae
Expression_system_common: Baker'S Yeast
Expression_system_taxid: 4932

Molecule: Saccharomyces Cerevisiae Strain T.52_2h Chromosom Sequence;
Chain: 6
Engineered: Yes
Other_details: Saccharomyces Cerevisiae U6 Snrna
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Expression_system: Saccharomyces Cerevisiae
Expression_system_common: Baker'S Yeast
Expression_system_taxid: 4932

Molecule: U5 Snrna
Chain: 5
Engineered: Yes
Other_details: Saccharomyces Cerevisiae U5 Snrna
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Expression_system: Saccharomyces Cerevisiae
Expression_system_common: Baker'S Yeast
Expression_system_taxid: 4932

Molecule: Pre-Mrna-Splicing Factor 8
Chain: A
Other_details: Saccharomyces Cerevisiae Prp8 Protein
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Pre-Mrna-Splicing Factor Snu114
Chain: C
Synonym: 114 Kda U5 Small Nuclear Ribonucleoprotein Compone Inhibitory Protein 10;
Other_details: C Snu114 Protein
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Pre-Mrna-Splicing Factor Cwc22
Chain: H
Synonym: Complexed With Cef1 Protein 22
Other_details: Saccharomyces Cerevisiae Cwc22 Protein
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Pre-Mrna-Splicing Factor Prp46
Chain: J
Synonym: Complexed With Cef1 Protein 1,Prp Nineteen-Associa Complex Protein 50,Prp19-Associated Complex Protein 50,Pre- Processing Protein 46;
Other_details: Saccharomyces Cerevisiae Prp46 Protein
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Pre-Mrna-Processing Protein 45
Chain: K
Other_details: Saccharomyces Cerevisiae Prp45 Protein
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Pre-Mrna-Splicing Factor Bud31
Chain: L
Synonym: Bud Site Selection Protein 31,Complexed With Cef1 14;
Other_details: Saccharomyces Cerevisiae Bud31 Protein
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Pre-Mrna-Splicing Factor Cwc2
Chain: M
Synonym: Complexed With Cef1 Protein 2,Prp19-Associated Com Protein 40,Synthetic Lethal With Clf1 Protein 3;
Other_details: Saccharomyces Cerevisiae Cwc2 Protein
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Pre-Mrna-Splicing Factor Slt11
Chain: N
Synonym: Extracellular Mutant Protein 2,Synthetic Lethality Protein 11;
Other_details: Saccharomyces Cerevisiae Ecm2 Protein
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Pre-Mrna-Splicing Factor Cef1
Chain: O
Synonym: Prp Nineteen-Associated Complex Protein 85,Prp19-A Complex Protein 85;
Other_details: Saccharomyces Cerevisiae Cef1 Protein
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Pre-Mrna-Splicing Factor Cwc15
Chain: P
Synonym: Complexed With Cef1 Protein 15
Other_details: Saccharomyces Cerevisiae Cwc15 Protein
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Pre-Mrna-Splicing Factor Cwc21
Chain: R
Synonym: Complexed With Cef1 Protein 21
Other_details: Saccharomyces Cerevisiae Cwc21 Protein
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Pre-Mrna-Splicing Factor Clf1
Chain: S
Synonym: Crooked Neck-Like Factor 1,Prp19-Associated Comple 77,Synthetic Lethal With Cdc40 Protein 3;
Other_details: Saccharomyces Cerevisiae Clf1 Protein
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Pre-Mrna-Splicing Factor Syf1
Chain: T
Synonym: Prp19-Associated Complex Protein 90,Synthetic Leth Cdc40 Protein 1;
Other_details: Saccharomyces Cerevisiae Syf1 Protein
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Pre-Mrna-Splicing Factor 18
Chain: a
Other_details: Saccharomyces Cerevisiae Prp18 Protein
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Pre-Mrna-Splicing Factor Slu7
Chain: c
Synonym: Synthetic Lethal With U2 Snrna Protein 17,Syntheti With U5 Snrna Protein 7;
Other_details: Saccharomyces Cerevisiae Slu7 Protein
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Pre-Mrna-Processing Factor 17
Chain: o
Synonym: Cell Division Control Protein 40
Other_details: Saccharomyces Cerevisiae Prp17 Protein
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Unknown
Chain: X
Other_details: Unknown Protein Helices Within C-Star Comple
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Pre-Mrna-Splicing Factor Syf2
Chain: y
Synonym: Prp19 Complex Protein 31,Synthetic Lethal With Cdc 2;
Other_details: Saccharomyces Cerevisiae Syf2 Protein
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Small Nuclear Ribonucleoprotein-Associated Protei
Chain: b
Synonym: Snrnp-B,Sm Protein B,Smb
Other_details: Saccharomyces Cerevisiae Smb Protein
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Small Nuclear Ribonucleoprotein Sm D3
Chain: d
Synonym: Sm-D3,Snrnp Core Protein D3
Other_details: Saccharomyces Cerevisiae Smd3 Protein
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Small Nuclear Ribonucleoprotein E
Chain: e
Synonym: Snrnp-E,Sm Protein E,Sme
Other_details: Saccharomyces Cerevisiae Sme Protein
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Small Nuclear Ribonucleoprotein F
Chain: f
Synonym: Snrnp-F,Sm Protein F,Smf
Other_details: Saccharomyces Cerevisiae Smf Protein
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Small Nuclear Ribonucleoprotein G
Chain: g
Synonym: Snrnp-G,Sm Protein G,Smg
Other_details: Saccharomyces Cerevisiae Smg Protein
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Small Nuclear Ribonucleoprotein Sm D1
Chain: h
Synonym: Sm-D1,Snrnp Core Protein D1
Other_details: Saccharomyces Cerevisiae Smd1 Protein
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Small Nuclear Ribonucleoprotein Sm D2
Chain: j
Synonym: Sm-D2,Snrnp Core Protein D2
Other_details: Saccharomyces Cerevisiae Smd2 Protein
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 3.85 Å
ligand GTP, IHP, K, MG, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A
  • metallopeptidase activity


    • C


    H


    J


    K

  • U2-type catalytic step 1 spl...
  • U2-type catalytic step 2 spl...
    • L


    M

  • U2-type catalytic step 1 spl...
  • U2-type catalytic step 2 spl...
    • N


    O

  • U2-type catalytic step 1 spl...
    • P


    R


    S

  • U2-type catalytic step 1 spl...
  • U2-type catalytic step 2 spl...
    • T

  • U2-type catalytic step 1 spl...
  • U2-type catalytic step 2 spl...
    • a


    b


    c


    d


    e


    f


    g


    h


    j


    o


    y

  • U2-type catalytic step 1 spl...
  • U2-type catalytic step 2 spl...
    • Primary referenceStructure of a spliceosome remodelled for exon ligation., Fica SM, Oubridge C, Galej WP, Wilkinson ME, Bai XC, Newman AJ, Nagai K, Nature. 2017 Jan 11. doi: 10.1038/nature21078. PMID:28076345
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1237 Kb) [Save to disk]
  • Biological Unit Coordinates (5mps.pdb1.gz) 1186 Kb
  • LPC: Ligand-Protein Contacts for 5MPS
  • CSU: Contacts of Structural Units for 5MPS
  • Retrieve 5MPS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5MPS from S2C, [Save to disk]
    • View 5MPS in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 5MPS
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5mps_d] [5mps_f] [5mps_O] [5mps_I] [5mps_S] [5mps_c] [5mps_b] [5mps_a] [5mps_K] [5mps_5] [5mps_y] [5mps_A] [5mps_o] [5mps_e] [5mps_J] [5mps_P] [5mps_j] [5mps_6] [5mps_N] [5mps_E] [5mps_C] [5mps_L] [5mps_R] [5mps_T] [5mps_g] [5mps_M] [5mps] [5mps_X] [5mps_H] [5mps_h] [5mps_2]
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  • Domain organization of by SWISSPFAM
    • Other resources with information on 5MPS
  • Community annotation for 5MPS at PDBWiki (http://pdbwiki.org)

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