5LJ5 Splicing date Jul 17, 2016
title Overall Structure Of The Yeast Spliceosome Immediately After Branching.
authors W.P.Galej, M.F.Wilkinson, S.M.Fica, C.Oubridge, A.J.Newman, K.Nag
compound source
Molecule: U5 Snrna (Small Nuclear Rna)
Chain: U
 Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932

Molecule: Exon 1 (5' Exon) Of Ubc4 Pre-Mrna
Chain: E
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932

Molecule: Intron Of Ubc4 Pre-Mrna
Chain: I
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932

Molecule: U2 Snrna (Small Nuclear Rna)
Chain: Z
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932

Molecule: U6 Snrna (Small Nuclear Rna)
Chain: V
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932

Molecule: Pre-Mrna-Splicing Factor 8
Chain: A
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932

Molecule: Pre-Mrna-Splicing Helicase Brr2
Chain: B
Synonym: Protein Snu246
Ec: 3.6.4.13
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932

Molecule: Protein Cwc16
Chain: D
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932

Molecule: Pre-Mrna-Splicing Factor Cwc25
Chain: F
Synonym: Complexed With Cef1 Protein 25
Organism_scientific: Saccharomyces Cerevisiae
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_taxid: 4932

Molecule: Pre-Mrna-Splicing Factor Isy1
Chain: G
Synonym: Interactor Of Syf1,Prp19-Associated Complex Protei
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932

Molecule: Cwc22
Chain: H
Organism_scientific: Saccharomyces Cerevisiae
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_taxid: 4932

Molecule: Pre-Mrna-Processing Protein 45
Chain: K
Organism_scientific: Saccharomyces Cerevisiae
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_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_taxid: 4932

Molecule: Pre-Mrna-Splicing Factor Slt11
Chain: N
Synonym: Extracellular Mutant Protein 2,Synthetic Lethality Protein 11;
Organism_scientific: Saccharomyces Cerevisiae
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_taxid: 4932

Molecule: Cwc15
Chain: P
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932

Molecule: Pre-Mrna-Splicing Factor Cwc21
Chain: R
Synonym: Complexed With Cef1 Protein 21
Organism_scientific: Saccharomyces Cerevisiae
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_taxid: 4932

Molecule: Pre-Mrna-Splicing Factor Syf1
Chain: T
Synonym: Prp19-Associated Complex Protein 90,Synthetic Leth Cdc40 Protein 1;
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932

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

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

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

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

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

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

Molecule: Small Nuclear Ribonucleoprotein Sm D2
Chain: j, m
Synonym: Sm-D2,Snrnp Core Protein D2
Organism_scientific: Saccharomyces Cerevisiae
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_taxid: 4932

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

Molecule: Pre-Mrna-Splicing Factor Atp-Dependent Rna Helica
Chain: Q
Ec: 3.6.4.13
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932

Molecule: Pre-Mrna-Processing Factor 19
Chain: t, u, v, w
Ec: 6.3.2.-
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932

Molecule: Pre-Mrna-Splicing Factor Snt309
Chain: s
Synonym: Prp19-Associated Complex Protein 25,Synergistic To Mutation Protein 309;
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932

Molecule: Unknown
Chain: x
Organism_scientific: Saccharomyces Cerevisiae
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 3.80 Å
ligand GTP, MG, ZN enzyme Hydrolase E.C.3.6.4.13 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • metallopeptidase activity


    • B


    C


    D


    F


    G

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


    Q


    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...
    • W


    Y


    d, n


    e, p


    g, r


    h, l


    j, m


    k, b


    q, f


    s

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

  • U2-type catalytic step 1 spl...
    • Primary referenceCryo-EM structure of the spliceosome immediately after branching., Galej WP, Wilkinson ME, Fica SM, Oubridge C, Newman AJ, Nagai K, Nature. 2016 Jul 26. doi: 10.1038/nature19316. PMID:27459055
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1790 Kb) [Save to disk]
  • Biological Unit Coordinates (5lj5.pdb1.gz) 1723 Kb
  • LPC: Ligand-Protein Contacts for 5LJ5
  • CSU: Contacts of Structural Units for 5LJ5
  • Retrieve 5LJ5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5LJ5 from S2C, [Save to disk]
    • View 5LJ5 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 5LJ5
  • 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: [5lj5_F] [5lj5_A] [5lj5_e] [5lj5_L] [5lj5_U] [5lj5_I] [5lj5_r] [5lj5_M] [5lj5_d] [5lj5_Y] [5lj5_v] [5lj5_x] [5lj5_Z] [5lj5_T] [5lj5_O] [5lj5_D] [5lj5_H] [5lj5_E] [5lj5_K] [5lj5_R] [5lj5_J] [5lj5_Q] [5lj5_S] [5lj5_t] [5lj5] [5lj5_m] [5lj5_p] [5lj5_G] [5lj5_w] [5lj5_h] [5lj5_n] [5lj5_u] [5lj5_g] [5lj5_l] [5lj5_P] [5lj5_C] [5lj5_q] [5lj5_s] [5lj5_W] [5lj5_B] [5lj5_b] [5lj5_N] [5lj5_j] [5lj5_k] [5lj5_f] [5lj5_V]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5LJ5: [AAA] [Cir_N] [DEXDc] [EFG_C] [EFG_IV] [HA2] [HAT] [HELICc] [JAB_MPN] [LRRcap] [MA3] [MIF4G] [RRM] [SANT] [Sec63] [Sm] [Ubox] [WD40] [cwf21 ] by SMART
    • Other resources with information on 5LJ5
  • Community annotation for 5LJ5 at PDBWiki (http://pdbwiki.org)

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