5Z3G Ribosome date Jan 06, 2018
title Cryo-Em Structure Of A Nucleolar Pre-60s Ribosome (Rpf1-Tap)
authors X.Zhu, D.Zhou, K.Ye
compound source
Molecule: 25s Rrna
Chain: A
 Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: 5.8s Rrna
Chain: B
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Its2 Rna
Chain: C
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Ribosome Biogenesis Protein Rlp7
Chain: D
Synonym: Ribosomal Protein L7-Like
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: Ribosome Biogenesis Protein 15
Chain: E
Synonym: Nucleolar Protein 15
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: 60s Ribosomal Protein L3
Chain: F
Synonym: Large Ribosomal Subunit Protein Ul3,Maintenance Of Protein 8,Rp1,Trichodermin Resistance Protein,Yl1;
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: 60s Ribosomal Protein L4-A
Chain: G
Synonym: L2,Large Ribosomal Subunit Protein Ul4-A,Rp2,Yl2
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: Proteasome-Interacting Protein Cic1
Chain: H
Synonym: Core Interacting Component 1
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: 60s Ribosomal Protein L6-A
Chain: I
Synonym: L17,Large Ribosomal Subunit Protein El6-A,Rp18,Yl1
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: 60s Ribosomal Protein L7-A
Chain: J
Synonym: L6,Large Ribosomal Subunit Protein Ul30-A,Rp11,Yl8
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: 60s Ribosomal Protein L8-A
Chain: K
Synonym: L4,L4-2,L7a-1,Large Ribosomal Subunit Protein El8- Maintenance Of Killer Protein 7,Rp6,Yl5;
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: 60s Ribosomal Protein L9-A
Chain: L
Synonym: L8,Large Ribosomal Subunit Protein Ul6-A,Rp24,Yl11
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: Nucleolar Protein 7
Chain: M
Synonym: Pescadillo Homolog,Ribosomal Rna-Processing Protei
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: Eukaryotic Translation Initiation Factor 6
Chain: N
Synonym: Eif-6
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: Ribosome Production Factor 1
Chain: O
Synonym: Ribosome Biogenesis Protein Rpf1
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: 60s Ribosomal Protein L13-A
Chain: P
Synonym: Large Ribosomal Subunit Protein El13-A
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: 60s Ribosomal Protein L14-A
Chain: Q
Synonym: Large Ribosomal Subunit Protein El14-A
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: 60s Ribosomal Protein L15-A
Chain: R
Synonym: L13,Large Ribosomal Subunit Protein El15-A,Rp15r,Y
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: 60s Ribosomal Protein L16-A
Chain: S
Synonym: L13a,L21,Large Ribosomal Subunit Protein Ul13-A,Rp
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: 60s Ribosomal Protein L17-A
Chain: T
Synonym: L20a,Large Ribosomal Subunit Protein Ul22-A,Yl17
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: 60s Ribosomal Protein L18-A
Chain: U
Synonym: Large Ribosomal Subunit Protein El18-A,Rp28
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: Ribosome Biogenesis Protein Nsa1
Chain: V
Synonym: Nop7-Associated Protein 1
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: 60s Ribosomal Protein L20-A
Chain: W
Synonym: L18a,Large Ribosomal Subunit Protein El20-A
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: Ribosomal Rna-Processing Protein 1
Chain: X
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: Atp-Dependent Rna Helicase Has1
Chain: Y
Synonym: Helicase Associated With Set1 Protein 1
Ec: 3.6.4.13
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: Protein Mak16
Chain: Z
Synonym: Maintenance Of Killer Protein 16
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: Ribosome Biogenesis Protein Brx1
Chain: a
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: Rrna-Processing Protein Ebp2
Chain: b
Synonym: Ebna1-Binding Protein Homolog
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: 60s Ribosomal Protein L26-A
Chain: c
Synonym: L33,Large Ribosomal Subunit Protein Ul24-A,Yl33
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: Unassigned
Chain: d
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: 60s Ribosomal Protein L32
Chain: I
Synonym: Large Ribosomal Subunit Protein El32
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: 60s Ribosomal Protein L33-A
Chain: j
Synonym: L37,Large Ribosomal Subunit Protein El33-A,Rp47,Yl
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: 60s Ribosomal Protein L35-A
Chain: l
Synonym: Large Ribosomal Subunit Protein Ul29-A
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: 60s Ribosomal Protein L36-A
Chain: m
Synonym: L39,Large Ribosomal Subunit Protein El36-A,Yl39
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c

Molecule: 60s Ribosomal Protein L37-A
Chain: n
Synonym: L43,Large Ribosomal Subunit Protein El37-A,Yl35,Yp
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 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 3.65 Å
ligand
enzyme Hydrolase E.C.3.6.4.13 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
D


E


F

  • cytosolic large ribosomal su...
    • G

  • cytosolic large ribosomal su...
    • H


    I


    J


    K

  • cytosolic large ribosomal su...
    • L


    M


    N


    O


    P

  • cytosolic large ribosomal su...
    • Q

  • cytosolic large ribosomal su...
    • R


    S

  • cytosolic large ribosomal su...
    • T


    U

  • cytosolic large ribosomal su...
    • V


    W

  • cytosolic large ribosomal su...
    • X


    Y


    Z


    a


    b


    c


    i

  • cytosolic large ribosomal su...
    • j


    l

  • cytosolic large ribosomal su...
    • m


    n

  • cytosolic large ribosomal su...
    • Primary referenceCryo-EM structure of an early precursor of large ribosomal subunit reveals a half-assembled intermediate., Zhou D, Zhu X, Zheng S, Tan D, Dong MQ, Ye K, Protein Cell. 2018 Mar 19. pii: 10.1007/s13238-018-0526-7. doi:, 10.1007/s13238-018-0526-7. PMID:29557065
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1567 Kb) [Save to disk]
  • Biological Unit Coordinates (5z3g.pdb1.gz) 1542 Kb
  • CSU: Contacts of Structural Units for 5Z3G
  • Retrieve 5Z3G in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5Z3G from S2C, [Save to disk]
    • View 5Z3G 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 5Z3G
  • 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: [5z3g_F] [5z3g_b] [5z3g_O] [5z3g_J] [5z3g_N] [5z3g_Z] [5z3g_S] [5z3g_K] [5z3g_j] [5z3g_A] [5z3g_V] [5z3g_l] [5z3g_d] [5z3g_Y] [5z3g_C] [5z3g_P] [5z3g_W] [5z3g_G] [5z3g_n] [5z3g_E] [5z3g_D] [5z3g_L] [5z3g_i] [5z3g_M] [5z3g_Q] [5z3g_T] [5z3g_U] [5z3g_R] [5z3g_c] [5z3g_B] [5z3g_I] [5z3g_m] [5z3g_a] [5z3g_X] [5z3g_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5Z3G
  • Community annotation for 5Z3G at PDBWiki (http://pdbwiki.org)

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