1YSH

Localization and dynamic behavior of ribosomal protein L30e

• PDB DOI: https://doi.org/10.2210/pdb1YSH/pdb
• EM Map EMD-1125: EMDB EMDataResource
• NAKB: 1YSH

• Classification: STRUCTURAL PROTEIN/RNA
• Organism(s): synthetic construct, Triticum aestivum, Oryza sativa
• Mutation(s): No 


• Deposited: 2005-02-08 Released: 2005-07-05 
• Deposition Author(s): Halic, M., Becker, T., Frank, J., Spahn, C.M., Beckmann, R.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 9.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Localization and dynamic behavior of ribosomal protein L30e

Halic, M., Becker, T., Frank, J., Spahn, C.M., Beckmann, R.

(2005) Nat Struct Mol Biol 12: 467-468

• PubMed: 15864315 
• DOI: https://doi.org/10.1038/nsmb933
• Primary Citation of Related Structures:  
  1YSH


• PubMed Abstract: 
  

  The ribosomal protein L30e is an indispensable component of the eukaryotic 80S ribosome, where it is part of the large (60S) ribosomal subunit. Here, we determined the localization of L30e in the cryo-EM map of the 80S wheat germ (wg) ribosome at a resolution of 9.5 A. L30e is part of the interface between large and small subunits, where it dynamically participates in the formation of the two intersubunit bridges eB9 and B4.

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Organizational Affiliation: 

Institute of Biochemistry, Charité, University Medical School Berlin, Monbijoustrasse 2, 10117 Berlin, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 82.63 kDa 
• Atom Count: 5,576 
• Modelled Residue Count: 424 
• Deposited Residue Count: 424 
• Unique protein chains: 3
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ribosomal protein L30	D [auth C]	104	Triticum aestivum	Mutation(s): 0
UniProt
Find proteins for Q5I7K9 (Triticum aestivum) Explore Q5I7K9  Go to UniProtKB:  Q5I7K9

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
ribosomal protein L37a	E [auth D]	73	Oryza sativa	Mutation(s): 0
UniProt
Find proteins for P0DKK1 (Oryza sativa subsp. japonica) Explore P0DKK1  Go to UniProtKB:  P0DKK1

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
40S RIBOSOMAL PROTEIN S13	F [auth E]	84	Oryza sativa	Mutation(s): 0
UniProt
Find proteins for Q69UI2 (Oryza sativa subsp. japonica) Explore Q69UI2  Go to UniProtKB:  Q69UI2

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (28-MER)	A	28	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (34-MER)	B [auth F]	34	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (101-MER)	C [auth B]	101	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 9.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	SPIDER

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-07-05 
Deposition Author(s): Halic, M., Becker, T., Frank, J., Spahn, C.M., Beckmann, R.

Revision History  

• Version 1.0: 2005-07-05
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-12-18
  Changes: Data collection, Database references, Source and taxonomy
• Version 1.4: 2024-10-09
  Changes: Data collection, Database references, Structure summary