6EMF | pdb_00006emf

Crystal structure of Rrp1 from Chaetomium thermophilum in space group C2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 
    0.232 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6EMF

This is version 1.4 of the entry. See complete history

Literature

Visualizing the Assembly Pathway of Nucleolar Pre-60S Ribosomes.

Kater, L.Thoms, M.Barrio-Garcia, C.Cheng, J.Ismail, S.Ahmed, Y.L.Bange, G.Kressler, D.Berninghausen, O.Sinning, I.Hurt, E.Beckmann, R.

(2017) Cell 171: 1599-1610.e14

  • DOI: https://doi.org/10.1016/j.cell.2017.11.039
  • Primary Citation Related Structures: 
    6ELZ, 6EM1, 6EM3, 6EM4, 6EM5, 6EMF, 6EMG, 6EN7

  • PubMed Abstract: 

    Eukaryotic 60S ribosomal subunits are comprised of three rRNAs and ∼50 ribosomal proteins. The initial steps of their formation take place in the nucleolus, but, owing to a lack of structural information, this process is poorly understood. Using cryo-EM, we solved structures of early 60S biogenesis intermediates at 3.3 Å to 4.5 Å resolution, thereby providing insights into their sequential folding and assembly pathway. Besides revealing distinct immature rRNA conformations, we map 25 assembly factors in six different assembly states. Notably, the Nsa1-Rrp1-Rpf1-Mak16 module stabilizes the solvent side of the 60S subunit, and the Erb1-Ytm1-Nop7 complex organizes and connects through Erb1's meandering N-terminal extension, eight assembly factors, three ribosomal proteins, and three 25S rRNA domains. Our structural snapshots reveal the order of integration and compaction of the six major 60S domains within early nucleolar 60S particles developing stepwise from the solvent side around the exit tunnel to the central protuberance.


  • Organizational Affiliation
    • Gene Center Munich and Center of Integrated Protein Science-Munich (CiPS-M), Department of Biochemistry, Feodor-Lynen-Str. 25, University of Munich, 81377 Munich, Germany.

Macromolecule Content 

  • Total Structure Weight: 66.87 kDa 
  • Atom Count: 3,891 
  • Modeled Residue Count: 461 
  • Deposited Residue Count: 580 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
G0S4M2
A, B
290Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: CTHT_0031510
UniProt
Find proteins for G0S4M2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S4M2 
Go to UniProtKB:  G0S4M2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0S4M2
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PRO

Query on PRO



Download:Ideal Coordinates CCD File
H [auth B],
I [auth B]
PROLINE
C5 H9 N O2
ONIBWKKTOPOVIA-BYPYZUCNSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free:  0.232 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.72α = 90
b = 74.675β = 90.53
c = 68.795γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-27
    Type: Initial release
  • Version 1.1: 2018-01-31
    Changes: Author supporting evidence
  • Version 1.2: 2019-10-16
    Changes: Data collection
  • Version 1.3: 2019-11-13
    Changes: Data collection, Database references
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references