3EGV

Ribosomal protein L11 methyltransferase (PrmA) in complex with trimethylated ribosomal protein L11


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.213 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 

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This is version 2.0 of the entry. See complete history


Literature

Multiple-site trimethylation of ribosomal protein L11 by the PrmA methyltransferase.

Demirci, H.Gregory, S.T.Dahlberg, A.E.Jogl, G.

(2008) Structure 16: 1059-1066

  • DOI: https://doi.org/10.1016/j.str.2008.03.016
  • Primary Citation of Related Structures:  
    3CJQ, 3CJR, 3CJS, 3CJT, 3EGV

  • PubMed Abstract: 

    Ribosomal protein L11 is a universally conserved component of the large subunit, and plays a significant role during initiation, elongation, and termination of protein synthesis. In Escherichia coli, the lysine methyltransferase PrmA trimethylates the N-terminal alpha-amino group and the epsilon-amino groups of Lys3 and Lys39. Here, we report four PrmA-L11 complex structures in different orientations with respect to the PrmA active site. Two structures capture the L11 N-terminal alpha-amino group in the active site in a trimethylated post-catalytic state and in a dimethylated state with bound S-adenosyl-L-homocysteine. Two other structures show L11 in a catalytic orientation to modify Lys39 and in a noncatalytic orientation. The comparison of complex structures in different orientations with a minimal substrate recognition complex shows that the binding mode remains conserved in all L11 orientations, and that substrate orientation is brought about by the unusual interdomain flexibility of PrmA.


  • Organizational Affiliation

    Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L11 methyltransferase254Thermus thermophilus HB8Mutation(s): 0 
Gene Names: prmATTHA0656
EC: 2.1.1
UniProt
Find proteins for Q84BQ9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q84BQ9 
Go to UniProtKB:  Q84BQ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84BQ9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11147Thermus thermophilus HB8Mutation(s): 1 
Gene Names: rpl11rplKTTHA0247
UniProt
Find proteins for Q5SLP6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SLP6 
Go to UniProtKB:  Q5SLP6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SLP6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download Ideal Coordinates CCD File 
C [auth A]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
IOD
Query on IOD

Download Ideal Coordinates CCD File 
I [auth B]IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.213 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.547α = 90
b = 134.547β = 90
c = 48.944γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SAHClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-01-18
    Changes: Non-polymer description
  • Version 1.3: 2017-03-01
    Changes: Non-polymer description
  • Version 1.4: 2023-08-30
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Advisory, Atomic model, Data collection, Derived calculations