6EM4 Ribosome date Oct 01, 2017
title State B 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: 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
Strain: Atcc 204508 S288c

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
Strain: Atcc 204508 S288c

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
Strain: Atcc 204508 S288c

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
Strain: Atcc 204508 S288c

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
Strain: Atcc 204508 S288c

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
Strain: Atcc 204508 S288c

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
Strain: Atcc 204508 S288c

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
Strain: Atcc 204508 S288c

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
Strain: Atcc 204508 S288c

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
Strain: Atcc 204508 S288c

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
Strain: Atcc 204508 S288c

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
Strain: Atcc 204508 S288c

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
Strain: Atcc 204508 S288c

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
Strain: Atcc 204508 S288c

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
Strain: Atcc 204508 S288c

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
Strain: Atcc 204508 S288c

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
Strain: Atcc 204508 S288c

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
Strain: Atcc 204508 S288c

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
Strain: Atcc 204508 S288c

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
Strain: Atcc 204508 S288c

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
Strain: Atcc 204508 S288c

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
Strain: Atcc 204508 S288c

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
Strain: Atcc 204508 S288c

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
Strain: Atcc 204508 S288c

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
Strain: Atcc 204508 S288c

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
Strain: Atcc 204508 S288c

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
Strain: Atcc 204508 S288c

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
Strain: Atcc 204508 S288c

Molecule: 25s Ribosomal Rna
Chain: 1
Other_details: Backbone Model

Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932

Molecule: 5.8s Ribosomal Rna
Chain: 2
Other_details: Backbone Model

Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932

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
Strain: Atcc 204508 S288c

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
Strain: Atcc 204508 S288c

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
Strain: Atcc 204508 S288c

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
Strain: Atcc 204508 S288c

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
Strain: Atcc 204508 S288c

Molecule: Internal Transcribed Spacer 1
Chain: 6
Other_details: Backbone Model

Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932

Molecule: Ribosome Biogenesis Protein Erb1
Chain: H
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
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 4.10 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


    J


    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...
  • Y


    e

  • cytosolic large ribosomal su...
  • f


    h

  • cytosolic large ribosomal su...
  • i


    j

  • cytosolic large ribosomal su...
  • n


    o


    t


    u


    v


    x


    y


    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] (993 Kb) [Save to disk]
  • Biological Unit Coordinates (6em4.pdb1.gz) 914 Kb
  • CSU: Contacts of Structural Units for 6EM4
  • Retrieve 6EM4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6EM4 from S2C, [Save to disk]
  • View 6EM4 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 6EM4
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6em4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6em4_f] [6em4_H] [6em4_Y] [6em4_P] [6em4_E] [6em4_Q] [6em4_S] [6em4_o] [6em4_e] [6em4_D] [6em4_y] [6em4_B] [6em4_t] [6em4_i] [6em4_J] [6em4_n] [6em4_A] [6em4_v] [6em4_u] [6em4_4] [6em4_M] [6em4_x] [6em4_5] [6em4_h] [6em4_6] [6em4_F] [6em4_2] [6em4_K] [6em4_j] [6em4_O] [6em4_L] [6em4_1] [6em4_3] [6em4_N] [6em4_C] [6em4_G] [6em4_V]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6EM4
  • Community annotation for 6EM4 at PDBWiki (http://pdbwiki.org)

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