3JB9 Rna Binding Protein Rna date Aug 09, 2015
title Cryo-Em Structure Of The Yeast Spliceosome At 3.6 Angstrom R
authors C.Yan, J.Hang, R.Wan, M.Huang, C.Wong, Y.Shi
compound source
Molecule: Pre-Mrna-Splicing Factor Spp42
Chain: A
Synonym: Complexed With Cdc5 Protein 6
 Organism_scientific: Schizosaccharomyces Pombe 972h-
Organism_common: Fission Yeast
Organism_taxid: 284812
Strain: 972 Atcc 24843

Molecule: Pre-Mrna-Splicing Factor Cwf10
Chain: B
Synonym: 114 Kda U5 Small Nuclear Ribonucleoprotein Compone Homolog, Complexed With Cdc5 Protein 10;
Organism_scientific: Schizosaccharomyces Pombe 972h-
Organism_common: Fission Yeast
Organism_taxid: 284812
Strain: 972 Atcc 24843

Molecule: U5 Snrna
Chain: C
Organism_scientific: Schizosaccharomyces Pombe
Organism_common: Fission Yeast
Organism_taxid: 4896

Molecule: Small Nuclear Ribonucleoprotein Sm D3
Chain: D, Z
Synonym: Sm-D3, Snrnp Core Protein D3
Organism_scientific: Schizosaccharomyces Pombe 972h-
Organism_common: Fission Yeast
Organism_taxid: 284812
Strain: 972 Atcc 24843

Molecule: Small Nuclear Ribonucleoprotein-Associated Protei
Chain: E, b
Synonym: Snrnp-B, Sm Protein B, Sm-B, Smb
Organism_scientific: Schizosaccharomyces Pombe 972h-
Organism_common: Fission Yeast
Organism_taxid: 284812
Strain: 972 Atcc 24843

Molecule: Small Nuclear Ribonucleoprotein Sm D1
Chain: F, f
Synonym: Sm-D1, Snrnp Core Protein D1
Organism_scientific: Schizosaccharomyces Pombe 972h-
Organism_common: Fission Yeast
Organism_taxid: 284812
Strain: 972 Atcc 24843

Molecule: Small Nuclear Ribonucleoprotein Sm D2
Chain: G, l
Synonym: Sm-D2, Complexed With Cdc5 Protein 9, Snrnp Core P
Organism_scientific: Schizosaccharomyces Pombe 972h-
Organism_common: Fission Yeast
Organism_taxid: 284812
Strain: 972 Atcc 24843

Molecule: Small Nuclear Ribonucleoprotein E
Chain: H, m
Synonym: Snrnp-E, Sm Protein E, Sm-E, Sme
Organism_scientific: Schizosaccharomyces Pombe 972h-
Organism_common: Fission Yeast
Organism_taxid: 284812
Strain: 972 Atcc 24843

Molecule: Small Nuclear Ribonucleoprotein F
Chain: I, n
Synonym: Snrnp-F, Sm Protein F, Sm-F, Smf
Organism_scientific: Schizosaccharomyces Pombe 972h-
Organism_common: Fission Yeast
Organism_taxid: 284812
Strain: 972 Atcc 24843

Molecule: Small Nuclear Ribonucleoprotein G
Chain: J, o
Synonym: Snrnp-G, Sm Protein G, Sm-G, Smg
Organism_scientific: Schizosaccharomyces Pombe 972h-
Organism_common: Fission Yeast
Organism_taxid: 284812
Strain: 972 Atcc 24843

Molecule: Pre-Mrna-Splicing Factor Prp5
Chain: K
Synonym: Complexed With Cdc5 Protein 1, Pre-Mrna-Processing 5;
Organism_scientific: Schizosaccharomyces Pombe 972h-
Organism_common: Fission Yeast
Organism_taxid: 284812
Strain: 972 Atcc 24843

Molecule: Pre-Mrna-Splicing Factor Cwf17
Chain: L
Synonym: Complexed With Cdc5 Protein 17
Organism_scientific: Schizosaccharomyces Pombe 972h-
Organism_common: Fission Yeast
Organism_taxid: 284812
Strain: 972 Atcc 24843

Molecule: Pre-Mrna-Processing Protein 45
Chain: M
Synonym: Complexed With Cdc5 Protein 13, Transcriptional Co Snw1;
Organism_scientific: Schizosaccharomyces Pombe 972h-
Organism_common: Fission Yeast
Organism_taxid: 284812
Strain: 972 Atcc 24843

Molecule: U6 Snrna
Chain: N
Organism_scientific: Schizosaccharomyces Pombe
Organism_common: Fission Yeast
Organism_taxid: 4896

Molecule: Rna (5'-R(Pgpupapupgpupapu)-3')
Chain: O
Organism_scientific: Schizosaccharomyces Pombe
Organism_common: Fission Yeast
Organism_taxid: 4896

Molecule: Rna (5'-R(Pupupupapupapcpupapapcpapc
Chain: Q
Other_details: Chain O And Q Come From One Rna Molecule. At (Q 501) Is Covalently Binding To Atom P G (Q 100).;
Organism_scientific: Schizosaccharomyces Pombe
Organism_common: Fission Yeast
Organism_taxid: 4896

Molecule: U2 Snrna
Chain: P
Organism_scientific: Schizosaccharomyces Pombe
Organism_common: Fission Yeast
Organism_taxid: 4896

Molecule: Pre-Mrna-Processing Factor 19
Chain: S, T, U, V
Synonym: Complexed With Cdc5 Protein 8
Ec: 6.3.2.-
Organism_scientific: Schizosaccharomyces Pombe 972h-
Organism_common: Fission Yeast
Organism_taxid: 284812
Strain: 972 Atcc 24843

Molecule: Pre-Mrna-Splicing Factor Cdc5
Chain: W
Synonym: Cell Division Control Protein 5
Organism_scientific: Schizosaccharomyces Pombe 972h-
Organism_common: Fission Yeast
Organism_taxid: 284812
Strain: 972 Atcc 24843

Molecule: Pre-Mrna-Splicing Factor Cwf2
Chain: Y
Synonym: Complexed With Cdc5 Protein 2, Pre-Mrna-Processing 3;
Organism_scientific: Schizosaccharomyces Pombe 972h-
Organism_common: Fission Yeast
Organism_taxid: 284812
Strain: 972 Atcc 24843

Molecule: Pre-Mrna-Splicing Factor Cwf5
Chain: a
Synonym: Complexed With Cdc5 Protein 5
Organism_scientific: Schizosaccharomyces Pombe 972h-
Organism_common: Fission Yeast
Organism_taxid: 284812
Strain: 972 Atcc 24843

Molecule: Pre-Mrna-Splicing Factor Cwf19
Chain: c
Synonym: Complexed With Cdc5 Protein 19
Organism_scientific: Schizosaccharomyces Pombe 972h-
Organism_common: Fission Yeast
Organism_taxid: 284812
Strain: 972 Atcc 24843

Molecule: Peptidyl-Prolyl Cis-Trans Isomerase Ppi1
Chain: d
Synonym: Ppiase Ppi1, Cyclophilin Ppi1, Rotamase Ppi1
Ec: 5.2.1.8
Organism_scientific: Schizosaccharomyces Pombe 972h-
Organism_common: Fission Yeast
Organism_taxid: 284812
Strain: 972 Atcc 24843

Molecule: Pre-Mrna-Splicing Factor Cwf14
Chain: e
Synonym: Complexed With Cdc5 Protein 14
Organism_scientific: Schizosaccharomyces Pombe 972h-
Organism_common: Fission Yeast
Organism_taxid: 284812
Strain: 972 Atcc 24843

Molecule: Pre-Mrna-Processing Factor 17
Chain: g
Organism_scientific: Schizosaccharomyces Pombe 972h-
Organism_common: Fission Yeast
Organism_taxid: 284812
Strain: 972 Atcc 24843

Molecule: Pre-Mrna-Splicing Factor Cwf15
Chain: h
Synonym: Complexed With Cdc5 Protein 15
Organism_scientific: Schizosaccharomyces Pombe 972h-
Organism_common: Fission Yeast
Organism_taxid: 284812
Strain: 972 Atcc 24843

Molecule: Pre-Mrna-Splicing Factor Cwf7
Chain: I
Synonym: Complexed With Cdc5 Protein 7, Splicing Factor 27
Organism_scientific: Schizosaccharomyces Pombe 972h-
Organism_common: Fission Yeast
Organism_taxid: 284812
Strain: 972 Atcc 24843

Molecule: Pre-Mrna-Splicing Factor Cwf4
Chain: R
Synonym: Complexed With Cdc5 Protein 4
Organism_scientific: Schizosaccharomyces Pombe 972h-
Organism_common: Fission Yeast
Organism_taxid: 284812
Strain: 972 Atcc 24843

Molecule: Pre-Mrna-Splicing Factor Cwf3
Chain: r
Synonym: Complexed With Cdc5 Protein 3
Organism_scientific: Schizosaccharomyces Pombe 972h-
Organism_common: Fission Yeast
Organism_taxid: 284812
Strain: 972 Atcc 24843

Molecule: Pre-Mrna-Splicing Factor Cwf11
Chain: X
Synonym: Complexed With Cdc5 Protein 11
Organism_scientific: Schizosaccharomyces Pombe 972h-
Organism_common: Fission Yeast
Organism_taxid: 284812
Strain: 972 Atcc 24843

Molecule: U2 Small Nuclear Ribonucleoprotein A'
Chain: j
Synonym: U2 Snrnp A'
Organism_scientific: Schizosaccharomyces Pombe 972h-
Organism_common: Fission Yeast
Organism_taxid: 284812
Strain: 972 Atcc 24843

Molecule: Probable U2 Small Nuclear Ribonucleoprotein B''
Chain: k
Synonym: U2 Snrnp B''
Organism_scientific: Schizosaccharomyces Pombe 972h-
Organism_common: Fission Yeast
Organism_taxid: 284812
Strain: 972 Atcc 24843

Molecule: Unknown Chain
Chain: x
Organism_scientific: Schizosaccharomyces Pombe 972h-
Organism_common: Fission Yeast
Organism_taxid: 284812
Strain: 972 Atcc 24843
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 3.60 Å
ligand ADP, GDP, MG, ZN enzyme Ligase E.C.6.3.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • thiol-dependent ubiquitin-sp...
  • metallopeptidase activity
  • ubiquitin-like protein-speci...


    • B


    E, b

  • U1 snRNP
    • F, f

  • U1 snRNP
    • G, l

  • U1 snRNP
    • H, m

  • U1 snRNP
    • I, n

  • U1 snRNP
    • J, o

  • U1 snRNP
    • L

  • spliceosomal complex
    • M


    S, T, U, V


    W


    X

  • spliceosomal complex
    • Y


    Z, D

  • U1 snRNP
    • a


    c

  • U2-type spliceosomal complex...
    • d
  • peptidyl-prolyl cis-trans is...


    • e

  • spliceosomal complex
    • g


    h


    i

  • spliceosomal complex
    • j


    k


    r, R


    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1739 Kb) [Save to disk]
  • Biological Unit Coordinates (3jb9.pdb1.gz) 1709 Kb
  • LPC: Ligand-Protein Contacts for 3JB9
  • CSU: Contacts of Structural Units for 3JB9
  • Retrieve 3JB9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3JB9 from S2C, [Save to disk]
    • View 3JB9 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 3JB9
  • 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: [3jb9_Y] [3jb9] [3jb9_U] [3jb9_L] [3jb9_P] [3jb9_J] [3jb9_k] [3jb9_K] [3jb9_a] [3jb9_g] [3jb9_H] [3jb9_e] [3jb9_b] [3jb9_l] [3jb9_h] [3jb9_Q] [3jb9_V] [3jb9_j] [3jb9_B] [3jb9_r] [3jb9_W] [3jb9_N] [3jb9_G] [3jb9_S] [3jb9_O] [3jb9_M] [3jb9_T] [3jb9_C] [3jb9_A] [3jb9_m] [3jb9_n] [3jb9_f] [3jb9_F] [3jb9_x] [3jb9_D] [3jb9_I] [3jb9_c] [3jb9_i] [3jb9_Z] [3jb9_d] [3jb9_E] [3jb9_R] [3jb9_o] [3jb9_X]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3JB9: [EFG_C] [EFG_IV] [HAT] [JAB_MPN] [LRRcap] [RRM] [SANT] [Sm] [Ubox] [WD40] [ZnF_C3H1 ] by SMART
    • Other resources with information on 3JB9
  • Community annotation for 3JB9 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