3JCM Transcription date Dec 23, 2015
title Cryo-Em Structure Of The Spliceosomal U4u6.U5 Tri-Snrnp
authors R.Wan, C.Yan, R.Bai, L.Wang, M.Huang, C.C.Wong, Y.Shi
compound source
Molecule: Pre-Mrna-Splicing Factor 8
Chain: A
 Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Strain: S288c

Molecule: U4u6 Small Nuclear Ribonucleoprotein Prp4
Chain: B
Synonym: Pre-Mrna-Processing Protein 4
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Strain: S288c

Molecule: Pre-Mrna-Processing Factor 31
Chain: I
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Strain: S288c

Molecule: Pre-Mrna-Splicing Factor 6
Chain: G
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Strain: S288c

Molecule: U4u6 Small Nuclear Ribonucleoprotein Prp3
Chain: K
Synonym: Pre-Mrna-Splicing Factor 3
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Strain: S288c

Molecule: Spliceosomal Protein Dib1
Chain: L
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Strain: S288c

Molecule: 13 Kda Ribonucleoprotein-Associated Protein
Chain: M
Synonym: Small Nuclear Ribonucleoprotein-Associated Protein
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Strain: S288c

Molecule: Pre-Mrna-Splicing Factor Snu114
Chain: H
Synonym: 114 Kda U5 Small Nuclear Ribonucleoprotein Compone Inhibitory Protein 10;
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Strain: S288c

Molecule: Pre-Mrna-Splicing Helicase Brr2
Chain: N
Synonym: Protein Snu246
Ec: 3.6.4.13
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Strain: S288c

Molecule: Small Nuclear Ribonucleoprotein Sm D3
Chain: R, J
Synonym: Sm-D3, Snrnp Core Protein D3
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Strain: S288c

Molecule: Small Nuclear Ribonucleoprotein-Associated Protei
Chain: S, O
Synonym: Snrnp-B, Sm Protein B, Sm-B, Smb
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Strain: S288c

Molecule: Small Nuclear Ribonucleoprotein Sm D1
Chain: T, P
Synonym: Sm-D1, Snrnp Core Protein D1
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Strain: S288c

Molecule: Small Nuclear Ribonucleoprotein Sm D2
Chain: U, Q
Synonym: Sm-D2, Snrnp Core Protein D2
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Strain: S288c

Molecule: Small Nuclear Ribonucleoprotein E
Chain: V, Y
Synonym: Snrnp-E, Sm Protein E, Sm-E, Sme
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Strain: S288c

Molecule: Small Nuclear Ribonucleoprotein F
Chain: W, Z
Synonym: Snrnp-F, Sm Protein F, Sm-F, Smf
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Strain: S288c

Molecule: Small Nuclear Ribonucleoprotein G
Chain: X, a
Synonym: Snrnp-G, Sm Protein G, Sm-G, Smg
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Strain: S288c

Molecule: U6 Snrna-Associated Sm-Like Protein Lsm8
Chain: b
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Strain: S288c

Molecule: U6 Snrna-Associated Sm-Like Protein Lsm2
Chain: c
Synonym: Small Nuclear Ribonucleoprotein D Homolog Snp3
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Strain: S288c

Molecule: U6 Snrna-Associated Sm-Like Protein Lsm3
Chain: d
Synonym: Smx4 Protein
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Strain: S288c

Molecule: U6 Snrna-Associated Sm-Like Protein Lsm6
Chain: e
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Strain: S288c

Molecule: U6 Snrna-Associated Sm-Like Protein Lsm5
Chain: f
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Strain: S288c

Molecule: U6 Snrna-Associated Sm-Like Protein Lsm7
Chain: g
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Strain: S288c

Molecule: U6 Snrna-Associated Sm-Like Protein Lsm4
Chain: h
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Strain: S288c

Molecule: Pre-Mrna
Chain: C
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Snr6 Snrna
Chain: D
Synonym: U6 Snrna
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Strain: S288c

Molecule: Snr14 Snrna
Chain: E
Synonym: U4 Snrna
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Strain: S288c

Molecule: Snr7-L Snrna
Chain: F
Synonym: U5 Snrna
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Strain: S288c
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, M7M enzyme Hydrolase E.C.3.6.4.13 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • metallopeptidase activity


    • B


    G


    H


    I


    J, R


    K


    L


    M


    N


    Q, U


    S, O


    T, P


    Y, V


    Z, W


    a, X


    b


    c


    d


    e


    f


    g


    h


    Primary referenceThe 3.8 A structure of the U4/U6.U5 tri-snRNP: Insights into spliceosome assembly and catalysis., Wan R, Yan C, Bai R, Wang L, Huang M, Wong CC, Shi Y, Science. 2016 Jan 29;351(6272):466-75. doi: 10.1126/science.aad6466. Epub 2016, Jan 7. PMID:26743623
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1214 Kb) [Save to disk]
  • Biological Unit Coordinates (3jcm.pdb1.gz) 1176 Kb
  • LPC: Ligand-Protein Contacts for 3JCM
  • CSU: Contacts of Structural Units for 3JCM
  • Retrieve 3JCM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3JCM from S2C, [Save to disk]
    • View 3JCM 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 3JCM
  • 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: [3jcm_R] [3jcm_V] [3jcm_Q] [3jcm_A] [3jcm_F] [3jcm_S] [3jcm_T] [3jcm_Z] [3jcm_Y] [3jcm_g] [3jcm_D] [3jcm_K] [3jcm_e] [3jcm] [3jcm_N] [3jcm_U] [3jcm_f] [3jcm_O] [3jcm_G] [3jcm_E] [3jcm_P] [3jcm_C] [3jcm_b] [3jcm_H] [3jcm_a] [3jcm_M] [3jcm_c] [3jcm_J] [3jcm_B] [3jcm_h] [3jcm_L] [3jcm_I] [3jcm_W] [3jcm_X] [3jcm_d]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3JCM: [AAA] [DEXDc] [DIM1] [EFG_C] [EFG_IV] [HAT] [HELICc] [JAB_MPN] [NOSIC] [SFM] [Sec63] [Sm] [TPR] [WD40 ] by SMART
    • Other resources with information on 3JCM
  • Community annotation for 3JCM at PDBWiki (http://pdbwiki.org)

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