3VI6

Crystal Structure of human ribosomal protein L30e

• PDB DOI: https://doi.org/10.2210/pdb3VI6/pdb

• Classification: RIBOSOMAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-09-21 Released: 2011-12-21 
• Deposition Author(s): Kawaguchi, A., Ose, T., Yao, M., Tanaka, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 0.216 
• R-Value Work: 0.190 
• R-Value Observed: 0.191 

Literature

Crystallization and preliminary X-ray structure analysis of human ribosomal protein L30e

Kawaguchi, A., Ose, T., Yao, M., Tanaka, I.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 1516-1518

• PubMed: 22139155 
• DOI: https://doi.org/10.1107/S1744309111045131
• Primary Citation of Related Structures:  
  3VI6


• PubMed Abstract: 
  

  Many functions have been reported for the eukaryotic ribosomal protein L30e. L30e makes several inter-subunit and intra-subunit interactions with protein or RNA components of the 80S ribosome. Yeast L30e has been shown to bind to its own transcript to autoregulate expression at both the transcriptional and the translational levels. Furthermore, it has been reported that mammalian L30e is a component of the selenocysteine-incorporation machinery by binding to the selenocysteine-insertion sequence on mRNA. As high-resolution crystal structures of mammalian L30e are not available, the purification, crystallization and X-ray structure analysis of human L30e are presented here.

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Organizational Affiliation: 

Graduate School of Life Sciences, Hokkaido University, Hokkaido, Sapporo, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 13.96 kDa 
• Atom Count: 839 
• Modelled Residue Count: 97 
• Deposited Residue Count: 125 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L30	A	125	Homo sapiens	Mutation(s): 0  Gene Names: RPL30
UniProt & NIH Common Fund Data Resources
Find proteins for P62888 (Homo sapiens) Explore P62888  Go to UniProtKB:  P62888
PHAROS:  P62888 GTEx:  ENSG00000156482

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMT	B [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 0.216 
• R-Value Work: 0.190 
• R-Value Observed: 0.191 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.282	α = 90
b = 56.282	β = 90
c = 203.628	γ = 120

Software Package:

Software Name	Purpose
SERGUI	data collection
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-21 
Deposition Author(s): Kawaguchi, A., Ose, T., Yao, M., Tanaka, I.

Revision History  

• Version 1.0: 2011-12-21
  Type: Initial release
  
• Version 1.1: 2014-01-15
  Changes: Structure summary
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description