6C0F Ribosome date Dec 29, 2017
title Yeast Nucleolar Pre-60s Ribosomal Subunit (State 2)
authors Z.A.Sanghai, L.Miller, J.Barandun, M.Hunziker, M.Chaker-Margot, S
compound source
Molecule: Saccharomyces Cerevisiae S288c 35s Pre-Ribosomal Miscrna;
Chain: 1
 Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: 5.8s Rrna
Chain: 2
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: Its2
Chain: 6
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: Ribosome Biogenesis Protein Nsa1
Chain: A
Synonym: Nop7-Associated Protein 1
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: 60s Ribosomal Protein L3
Chain: B
Synonym: Large Ribosomal Subunit Protein Ul3,Maintenance Of Protein 8,Rp1,Trichodermin Resistance Protein,Yl1;
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: 60s Ribosomal Protein L4-A
Chain: C
Synonym: L2,Large Ribosomal Subunit Protein Ul4-A,Rp2,Yl2
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: Protein Mak16
Chain: D
Synonym: Maintenance Of Killer Protein 16
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: 60s Ribosomal Protein L6-A
Chain: E
Synonym: L17,Large Ribosomal Subunit Protein El6-A,Rp18,Yl1
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: 60s Ribosomal Protein L7-A
Chain: F
Synonym: L6,Large Ribosomal Subunit Protein Ul30-A,Rp11,Yl8
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: 60s Ribosomal Protein L8-A
Chain: G
Synonym: L4,L4-2,L7a-1,Large Ribosomal Subunit Protein El8- Maintenance Of Killer Protein 7,Rp6,Yl5;
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: Ribosome Production Factor 1
Chain: I
Synonym: Ribosome Biogenesis Protein Rpf1
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: Proteasome-Interacting Protein Cic1
Chain: K
Synonym: Core Interacting Component 1
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: 60s Ribosomal Protein L13-A
Chain: L
Synonym: Large Ribosomal Subunit Protein El13-A
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: 60s Ribosomal Protein L14-A
Chain: M
Synonym: Large Ribosomal Subunit Protein El14-A
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: 60s Ribosomal Protein L15-A
Chain: N
Synonym: L13,Large Ribosomal Subunit Protein El15-A,Rp15r,Y
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: 60s Ribosomal Protein L16-A
Chain: O
Synonym: L13a,L21,Large Ribosomal Subunit Protein Ul13-A,Rp
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: 60s Ribosomal Protein L17-A
Chain: P
Synonym: L20a,Large Ribosomal Subunit Protein Ul22-A,Yl17
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: 60s Ribosomal Protein L18-A
Chain: Q
Synonym: Large Ribosomal Subunit Protein El18-A,Rp28
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: 60s Ribosomal Protein L20-A
Chain: S
Synonym: L18a,Large Ribosomal Subunit Protein El20-A
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: 60s Ribosomal Protein L23-A
Chain: V
Synonym: L17a,Large Ribosomal Subunit Protein Ul14-A,Yl32
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: Nucleolar Gtp-Binding Protein 1
Chain: W
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: 60s Ribosomal Protein L26-A
Chain: Y
Synonym: L33,Large Ribosomal Subunit Protein Ul24-A,Yl33
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: Nucleolar Protein 16
Chain: 7
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: Ribosomal Rna-Processing Protein 14
Chain: 8
Synonym: Ribosome Biogenesis Protein Rrp14
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: Ribosome Biogenesis Protein Brx1
Chain: b
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: 60s Ribosomal Protein L32
Chain: e
Synonym: Large Ribosomal Subunit Protein El32
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: 60s Ribosomal Protein L33-A
Chain: f
Synonym: L37,Large Ribosomal Subunit Protein El33-A,Rp47,Yl
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: 60s Ribosomal Protein L35-A
Chain: h
Synonym: Large Ribosomal Subunit Protein Ul29-A
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: 60s Ribosomal Protein L36-A
Chain: I
Synonym: L39,Large Ribosomal Subunit Protein El36-A,Yl39
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: 60s Ribosomal Protein L37-A
Chain: j
Synonym: L43,Large Ribosomal Subunit Protein El37-A,Yl35,Yp
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: Brx1-Associated Peptide
Chain: x
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: Rrna-Processing Protein Ebp2
Chain: m
Synonym: Ebna1-Binding Protein Homolog
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: Pescadillo Homolog
Chain: n
Synonym: Nucleolar Protein 7,Ribosomal Rna-Processing Prote
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: Ribosome Biogenesis Protein 15
Chain: o
Synonym: Nucleolar Protein 15
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: Atp-Dependent Rna Helicase Has1
Chain: p
Synonym: Helicase Associated With Set1 Protein 1
Ec: 3.6.4.13
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: Protein Mak11
Chain: q
Synonym: Maintenance Of Killer Protein 11
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: Ribosome Biogenesis Protein Erb1
Chain: s
Synonym: Eukaryotic Ribosome Biogenesis Protein 1
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: Ribosome Biogenesis Protein Rlp7
Chain: t
Synonym: Ribosomal Protein L7-Like
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: Ribosome Biogenesis Protein Rlp24
Chain: u
Synonym: Ribosomal Protein L24-Like
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: Ribosome Biogenesis Protein Ssf1
Chain: v
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: Ribosomal Rna-Processing Protein 15
Chain: w
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: Eukaryotic Translation Initiation Factor 6
Chain: y
Synonym: Eif-6
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190

Molecule: Ribosomal Rna-Processing Protein 1
Chain: z
Organism_scientific: Saccharomyces Cerevisiae By4741
Organism_taxid: 1247190
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 3.70 Å
ligand ZN enzyme Hydrolase E.C.3.6.4.13 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
7


8


A


B

  • cytosolic large ribosomal su...
    • C

  • cytosolic large ribosomal su...
    • D


    E


    F


    G

  • cytosolic large ribosomal su...
    • I


    K


    L

  • cytosolic large ribosomal su...
    • M

  • cytosolic large ribosomal su...
    • N


    O

  • cytosolic large ribosomal su...
    • P


    Q

  • cytosolic large ribosomal su...
    • S

  • cytosolic large ribosomal su...
    • V

  • cytosolic large ribosomal su...
    • W


    Y


    b


    e

  • cytosolic large ribosomal su...
    • f


    h

  • cytosolic large ribosomal su...
    • i


    j

  • cytosolic large ribosomal su...
    • n


    o


    p


    s


    t


    u


    v


    w


    y


    z


    Primary referenceModular assembly of the nucleolar pre-60S ribosomal subunit., Sanghai ZA, Miller L, Molloy KR, Barandun J, Hunziker M, Chaker-Margot M, Wang J, Chait BT, Klinge S, Nature. 2018 Mar 5. pii: nature26156. doi: 10.1038/nature26156. PMID:29512650
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1715 Kb) [Save to disk]
  • Biological Unit Coordinates (6c0f.pdb1.gz) 1680 Kb
  • LPC: Ligand-Protein Contacts for 6C0F
  • CSU: Contacts of Structural Units for 6C0F
  • Retrieve 6C0F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6C0F from S2C, [Save to disk]
    • View 6C0F 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 6C0F
  • 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: [6c0f_w] [6c0f_P] [6c0f_y] [6c0f_N] [6c0f_I] [6c0f_O] [6c0f_e] [6c0f_h] [6c0f_C] [6c0f_8] [6c0f_z] [6c0f_W] [6c0f_v] [6c0f_L] [6c0f_F] [6c0f_p] [6c0f_t] [6c0f_A] [6c0f_Q] [6c0f_b] [6c0f_x] [6c0f_q] [6c0f_j] [6c0f_7] [6c0f_V] [6c0f_G] [6c0f_D] [6c0f_f] [6c0f_M] [6c0f_S] [6c0f_K] [6c0f_s] [6c0f_B] [6c0f_2] [6c0f_n] [6c0f_u] [6c0f_E] [6c0f_i] [6c0f_6] [6c0f_Y] [6c0f_o] [6c0f_1] [6c0f_m]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6C0F
  • Community annotation for 6C0F at PDBWiki (http://pdbwiki.org)

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