6EM5 Ribosome date Oct 01, 2017
title State D Architectural Model (Nsa1-Tap Flag-Ytm1) - Visualizi Assembly Pathway Of Nucleolar Pre-60s Ribosomes
authors L.Kater, J.Cheng, C.Barrio-Garcia, E.Hurt, R.Beckmann
compound source
Molecule: 5.8s Ribosomal Rna
Chain: 2
Other_details: Backbone Model
 Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Internal Transcribed Spacer 2
Chain: 6
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: 60s Ribosomal Protein L13-A
Chain: L
Synonym: Large Ribosomal Subunit Protein El13-A
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: 60s Ribosomal Protein L14-A
Chain: M
Synonym: Large Ribosomal Subunit Protein El14-A
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: 60s Ribosomal Protein L15-A
Chain: N
Synonym: L13,Large Ribosomal Subunit Protein El15-A,Rp15r,Y
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: 60s Ribosomal Protein L18-A
Chain: Q
Synonym: Large Ribosomal Subunit Protein El18-A,Rp28
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: 60s Ribosomal Protein L19-A
Chain: R
Synonym: L23,Large Ribosomal Subunit Protein El19-A,Rp15l,R
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: 60s Ribosomal Protein L20-A
Chain: S
Synonym: L18a,Large Ribosomal Subunit Protein El20-A
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: 60s Ribosomal Protein L21-A
Chain: T
Synonym: Large Ribosomal Subunit Protein El21-A
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: 60s Ribosomal Protein L22-A
Chain: U
Synonym: L1c,Large Ribosomal Subunit Protein El22-A,Rp4,Yl3
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: 60s Ribosomal Protein L27-A
Chain: Z
Synonym: Large Ribosomal Subunit Protein El27-A
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: 60s Ribosomal Protein L30
Chain: c
Synonym: L32,Large Ribosomal Subunit Protein El30,Rp73,Yl38
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: 60s Ribosomal Protein L31-A
Chain: d
Synonym: L34,Large Ribosomal Subunit Protein El31-A,Yl28
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: 60s Ribosomal Protein L32
Chain: e
Synonym: Large Ribosomal Subunit Protein El32
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: 60s Ribosomal Protein L33-A
Chain: f
Synonym: L37,Large Ribosomal Subunit Protein El33-A,Rp47,Yl
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: 60s Ribosomal Protein L34-A
Chain: g
Synonym: Large Ribosomal Subunit Protein El34-A
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: 60s Ribosomal Protein L36-B
Chain: I
Synonym: L39,Large Ribosomal Subunit Protein El36-B,Yl39
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: 60s Ribosomal Protein L37-A
Chain: j
Synonym: L43,Large Ribosomal Subunit Protein El37-A,Yl35,Yp
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: 60s Ribosomal Protein L38
Chain: k
Synonym: Large Ribosomal Subunit Protein El38
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: 60s Ribosomal Protein L6-A
Chain: E
Synonym: L17,Large Ribosomal Subunit Protein El6-A,Rp18,Yl1
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

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;
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: 60s Ribosomal Protein L16-A
Chain: O
Synonym: L13a,L21,Large Ribosomal Subunit Protein Ul13-A,Rp
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: 60s Ribosomal Protein L23-A
Chain: V
Synonym: L17a,Large Ribosomal Subunit Protein Ul14-A,Yl32
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: 60s Ribosomal Protein L25
Chain: X
Synonym: Large Ribosomal Subunit Protein Ul23,Rp16l,Yl25,Yp
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: 60s Ribosomal Protein L26-A
Chain: Y
Synonym: L33,Large Ribosomal Subunit Protein Ul24-A,Yl33
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: 60s Ribosomal Protein L35-A
Chain: h
Synonym: Large Ribosomal Subunit Protein Ul29-A
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

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

Molecule: 60s Ribosomal Protein L4-A
Chain: C
Synonym: L2,Large Ribosomal Subunit Protein Ul4-A,Rp2,Yl2
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: 60s Ribosomal Protein L9-A
Chain: H
Synonym: L8,Large Ribosomal Subunit Protein Ul6-A,Rp24,Yl11
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Ribosome Biogenesis Protein Brx1
Chain: A
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Proteasome-Interacting Protein Cic1
Chain: K
Synonym: Core Interacting Component 1
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Ribosome Biogenesis Protein Erb1
Chain: m
Synonym: Eukaryotic Ribosome Biogenesis Protein 1
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Atp-Dependent Rna Helicase Has1
Chain: D
Synonym: Helicase Associated With Set1 Protein 1
Ec: 3.6.4.13
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Ribosome Assembly Factor Mrt4
Chain: W
Synonym: Mrna Turnover Protein 4
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: 60s Ribosome Subunit Biogenesis Protein Nip7
Chain: l
Synonym: Nuclear Import Protein 7
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Nucleolar Gtp-Binding Protein 1
Chain: b
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Ribosome Biogenesis Protein 15
Chain: o
Synonym: Nucleolar Protein 15
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Pescadillo Homolog
Chain: n
Synonym: Nucleolar Protein 7,Ribosomal Rna-Processing Prote
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Ribosome Biogenesis Protein Nsa2
Chain: r
Synonym: Nop7-Associated Protein 2
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Nuclear Gtp-Binding Protein Nug1
Chain: s
Synonym: Nuclear Gtpase 1
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Ribosome Biogenesis Protein Rlp7
Chain: t
Synonym: Ribosomal Protein L7-Like
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Eukaryotic Translation Initiation Factor 6
Chain: y
Synonym: Eif-6
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Upf0642 Protein Ybl028c
Chain: z
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Ribosome Biogenesis Protein Ytm1
Chain: p
Synonym: Microtubule-Associated Protein Ytm1
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: 25s Rrna (Cytosine(2870)-C(5))-Methyltransferase
Chain: q
Synonym: Nucleolar Protein 2
Ec: 2.1.1.310
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Ribosome Biogenesis Protein Rlp24
Chain: u
Synonym: Ribosomal Protein L24-Like
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Nucleolar Protein 16
Chain: v
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: 27s Pre-Rrna (Guanosine(2922)-2'-O)-Methyltransfe
Chain: w
Synonym: 2'-O-Ribose Rna Methyltransferase Spb1,Adomet-Depe Methyltransferase Spb1,S-Adenosyl-L-Methionine-Dependent Methyltransferase,Suppressor Of Pab1 Protein 1;
Ec: 2.1.1.167
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Nucleolar Complex-Associated Protein 3
Chain: I
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Rrna-Processing Protein Ebp2
Chain: J
Synonym: Ebna1-Binding Protein Homolog
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Ribosome Production Factor 1
Chain: x
Synonym: Ribosome Biogenesis Protein Rpf1
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Protein Mak16
Chain: 3
Synonym: Maintenance Of Killer Protein 16
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Ribosomal Rna-Processing Protein 1
Chain: 4
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Ribosome Biogenesis Protein Nsa1
Chain: 5
Synonym: Nop7-Associated Protein 1
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: 25s Ribosomal Rna
Chain: 1
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: 60s Ribosomal Protein L7-A
Chain: F
Synonym: L6,Large Ribosomal Subunit Protein Ul30-A,Rp11,Yl8
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: 60s Ribosomal Protein L17-A
Chain: P
Synonym: L20a,Large Ribosomal Subunit Protein Ul22-A,Yl17
Other_details: Backbone Model
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
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 4.30 Å
ligand
enzyme Hydrolase E.C.3.6.4.13 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
3


4


5


A


B

  • cytosolic large ribosomal su...
    • C

  • cytosolic large ribosomal su...
    • D


    E


    F


    G

  • cytosolic large ribosomal su...
    • H


    I


    J


    K


    L

  • cytosolic large ribosomal su...
    • M

  • cytosolic large ribosomal su...
    • N


    O

  • cytosolic large ribosomal su...
    • P


    Q

  • cytosolic large ribosomal su...
    • R

  • cytosolic large ribosomal su...
    • S

  • cytosolic large ribosomal su...
    • T

  • cytosolic large ribosomal su...
    • U


    V

  • cytosolic large ribosomal su...
    • W


    X

  • cytosolic large ribosomal su...
    • Y


    Z

  • cytosolic large ribosomal su...
    • b


    c

  • cytosolic large ribosomal su...
    • d


    e

  • cytosolic large ribosomal su...
    • f


    g

  • preribosome, large subunit p...
    • h

  • cytosolic large ribosomal su...
    • i


    j

  • cytosolic large ribosomal su...
    • k

  • cytosolic large ribosomal su...
    • l


    m


    n


    o


    p


    q


    r


    s


    t


    u


    v


    w


    x


    y


    z


    Primary referenceVisualizing the Assembly Pathway of Nucleolar Pre-60S Ribosomes., Kater L, Thoms M, Barrio-Garcia C, Cheng J, Ismail S, Ahmed YL, Bange G, Kressler D, Berninghausen O, Sinning I, Hurt E, Beckmann R, Cell. 2017 Dec 14;171(7):1599-1610.e14. doi: 10.1016/j.cell.2017.11.039. PMID:29245012
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1603 Kb) [Save to disk]
  • Biological Unit Coordinates (6em5.pdb1.gz) 1486 Kb
  • CSU: Contacts of Structural Units for 6EM5
  • Retrieve 6EM5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6EM5 from S2C, [Save to disk]
    • View 6EM5 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 6EM5
  • 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: [6em5_z] [6em5_K] [6em5_A] [6em5_v] [6em5_Y] [6em5_k] [6em5_F] [6em5_5] [6em5_4] [6em5_t] [6em5_g] [6em5_n] [6em5_Z] [6em5_T] [6em5_3] [6em5_O] [6em5_r] [6em5_P] [6em5_w] [6em5_6] [6em5_i] [6em5_l] [6em5_c] [6em5_X] [6em5_2] [6em5_D] [6em5_B] [6em5_I] [6em5_U] [6em5_Q] [6em5_W] [6em5_L] [6em5_M] [6em5_R] [6em5_J] [6em5_S] [6em5_s] [6em5_E] [6em5_j] [6em5_p] [6em5_q] [6em5_1] [6em5_u] [6em5_N] [6em5_H] [6em5_d] [6em5_V] [6em5_C] [6em5_h] [6em5_y] [6em5_m] [6em5_b] [6em5_e] [6em5_f] [6em5_x] [6em5_G] [6em5_o]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6EM5
  • Community annotation for 6EM5 at PDBWiki (http://pdbwiki.org)

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