5MQ0 Splicing date Dec 19, 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
 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: 5'-Exon Of Ubc4 Pre-Mrna
Chain: E
Engineered: Yes
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: S.Cerevisiae Chromosome II Reading Frame Orf Ybr2
Chain: 2
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Saccharomyces Cerevisiae Strain T.52_2h Chromosom Sequence;
Chain: 6
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Saccharomyces Cerevisiae Strain Wi_c_mbsp_4 Chrom Sequence;
Chain: 5
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

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

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

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

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

Molecule: Unknown Protein
Chain: X
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;
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

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

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

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

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

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

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

Molecule: Small Nuclear Ribonucleoprotein Sm D2
Chain: j, m
Synonym: Sm-D2,Snrnp Core Protein D2
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Pre-Mrna-Splicing Factor Atp-Dependent Rna Helica
Chain: V
Ec: 3.6.4.13
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: U2 Small Nuclear Ribonucleoprotein A'
Chain: W
Synonym: U2 Snrnp A',Looks Exceptionally Like U2a Protein 1
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: U2 Small Nuclear Ribonucleoprotein B''
Chain: Y
Synonym: U2 Snrnp B''
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: 3'-Exon Of Ubc4 Pre-Mrna, Bound By Prp22 Helicase
Chain: 3
Engineered: Yes
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: Pre-Mrna-Splicing Factor Snt309
Chain: s
Synonym: Prp19-Associated Complex Protein 25,Synergistic To Mutation Protein 309;
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Pre-Mrna-Processing Factor 19
Chain: t, u, v, w
Ec: 6.3.2.-
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 4.17 Å
ligand GTP, IHP, K, MG, ZN enzyme Hydrolase E.C.3.6.4.13 BRENDA
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...
    • V


    W


    Y


    a


    c


    d, n


    e, p


    g, r


    h, l


    j, m


    k, b


    o


    q, f


    s

  • U2-type catalytic step 1 spl...
    • u, t, v, w

  • U2-type catalytic step 1 spl...
    • 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] (1619 Kb) [Save to disk]
  • Biological Unit Coordinates (5mq0.pdb1.gz) 1541 Kb
  • LPC: Ligand-Protein Contacts for 5MQ0
  • CSU: Contacts of Structural Units for 5MQ0
  • Retrieve 5MQ0 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5MQ0 from S2C, [Save to disk]
    • View 5MQ0 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 5MQ0
  • 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: [5mq0_w] [5mq0_E] [5mq0_T] [5mq0_W] [5mq0_H] [5mq0_b] [5mq0_s] [5mq0_l] [5mq0_2] [5mq0_Y] [5mq0_j] [5mq0_I] [5mq0_v] [5mq0_S] [5mq0_a] [5mq0_u] [5mq0_d] [5mq0_r] [5mq0_p] [5mq0_g] [5mq0_e] [5mq0_C] [5mq0_3] [5mq0_N] [5mq0_c] [5mq0_k] [5mq0_n] [5mq0_K] [5mq0_h] [5mq0_m] [5mq0_R] [5mq0_P] [5mq0_6] [5mq0_y] [5mq0_X] [5mq0_5] [5mq0_L] [5mq0_M] [5mq0_f] [5mq0_O] [5mq0_q] [5mq0_o] [5mq0_A] [5mq0_t] [5mq0] [5mq0_J] [5mq0_V]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5MQ0
  • Community annotation for 5MQ0 at PDBWiki (http://pdbwiki.org)

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science