3J3X | pdb_00003j3x

Independent reconstruction of Mm-cpn cryo-EM density map from half dataset in the closed state (training map)

• PDB DOI: https://doi.org/10.2210/pdb3J3X/pdb
• EM Map EMD-5645: EMDB EMDataResource

• Classification: CHAPERONE
• Organism(s): Methanococcus maripaludis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-05-02 Released: 2013-05-29 
• Deposition Author(s): DiMaio, F., Zhang, J., Chiu, W., Baker, D.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Cryo-EM model validation using independent map reconstructions.

Dimaio, F., Zhang, J., Chiu, W., Baker, D.

(2013) Protein Sci 22: 865-868

• PubMed: 23592445 
• DOI: https://doi.org/10.1002/pro.2267
• Primary Citation of Related Structures:  
  3J3X


• PubMed Abstract: 
  

  An increasing number of cryo-electron microscopy (cryo-EM) density maps are being generated with suitable resolution to trace the protein backbone and guide sidechain placement. Generating and evaluating atomic models based on such maps would be greatly facilitated by independent validation metrics for assessing the fit of the models to the data. We describe such a metric based on the fit of atomic models with independent test maps from single particle reconstructions not used in model refinement. The metric provides a means to determine the proper balance between the fit to the density and model energy and stereochemistry during refinement, and is likely to be useful in determining values of model building and refinement metaparameters quite generally.

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Organizational Affiliation: 
• Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D8  (Explore in 3D)
Global Stoichiometry: Homo 16-mer - A16 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 915.39 kDa 
• Atom Count: 61,264 
• Modeled Residue Count: 8,160 
• Deposited Residue Count: 8,512 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chaperonin	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	532	Methanococcus maripaludis	Mutation(s): 0
UniProt
Find proteins for Q6LX38 (Methanococcus maripaludis (strain DSM 14266 / JCM 13030 / NBRC 101832 / S2 / LL)) Explore Q6LX38  Go to UniProtKB:  Q6LX38

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	EMAN

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-29 
Deposition Author(s): DiMaio, F., Zhang, J., Chiu, W., Baker, D.

Revision History  

• Version 1.0: 2013-05-29
  Type: Initial release
  
• Version 1.1: 2013-06-12
  Changes: Database references
• Version 1.2: 2018-07-18
  Changes: Data collection
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Refinement description