3IYY | pdb_00003iyy

Coordinates of the b1b bridge-forming protein structures fitted into the Cryo-EM map of EFG.GDPNP-bound E.coli 70S ribosome(EMD-1363)

• PDB DOI: https://doi.org/10.2210/pdb3IYY/pdb
• EM Map EMD-1363: EMDB EMDataResource

• Classification: RIBOSOMAL PROTEIN
• Organism(s): Escherichia coli O55:H7 str. CB9615
• Mutation(s): No 


• Deposited: 2010-07-23 Released: 2010-09-01 
• Deposition Author(s): Shasmal, M., Chakraborty, B., Sengupta, J.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 10.9 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

Intrinsic molecular properties of the protein-protein bridge facilitate ratchet-like motion of the ribosome.

Shasmal, M., Chakraborty, B., Sengupta, J.

(2010) Biochem Biophys Res Commun 399: 192-197

• PubMed: 20643101 
• DOI: https://doi.org/10.1016/j.bbrc.2010.07.053
• Primary Citation of Related Structures:  
  3IYX, 3IYY


• PubMed Abstract: 
  

  The ribosomal intersubunit bridges maintain the overall architecture of the ribosome and thereby play a pivotal role in the dynamics of translation. The only protein-protein bridge, b1b, is formed by the two proteins, S13 and L5 of the small and large ribosomal subunits, respectively. B1b absorbs the largest movement during ratchet-like motion, and its two proteins reorganize in different constellations during this motion of the ribosome. Our results in this study of b1b in the Escherichia coli 70S ribosome suggest that the intrinsic molecular features of the bridging proteins allow the bridge to modulate the ratchet-like motion in a controlled manner. Additionally, another large subunit protein, L31, seems to participate with S13 and L5 in the formation, dynamics, and stabilization of this bridge.

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Organizational Affiliation: 

Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Calcutta 700032, India.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 41.35 kDa 
• Atom Count: 361 
• Modelled Residue Count: 361 
• Deposited Residue Count: 367 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L31	A	70	Escherichia coli O55:H7 str. CB9615	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L5	B [auth F]	179	Escherichia coli O55:H7 str. CB9615	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S13	C [auth M]	118	Escherichia coli O55:H7 str. CB9615	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 10.9 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	SPIDER

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-01 
Deposition Author(s): Shasmal, M., Chakraborty, B., Sengupta, J.

Revision History  

• Version 1.0: 2010-09-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-07-18
  Changes: Data collection
• Version 1.3: 2019-12-18
  Changes: Other
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references, Refinement description