5VY5

Rabbit muscle aldolase using 200keV

• PDB DOI: https://doi.org/10.2210/pdb5VY5/pdb
• EM Map EMD-8743: EMDB EMDataResource

• Classification: LYASE
• Organism(s): Oryctolagus cuniculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-05-24 Released: 2017-06-14 
• Deposition Author(s): Herzik Jr., M.A., Wu, M., Lander, G.C.
• Funding Organization(s): National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Achieving better-than-3- angstrom resolution by single-particle cryo-EM at 200 keV.

Herzik, M.A., Wu, M., Lander, G.C.

(2017) Nat Methods 14: 1075-1078

• PubMed: 28991891 
• DOI: https://doi.org/10.1038/nmeth.4461
• Primary Citation of Related Structures:  
  5VY3, 5VY4, 5VY5


• PubMed Abstract: 
  

  Nearly all single-particle cryo-EM structures resolved to better than 4-Å resolution have been determined using 300-keV transmission electron microscopes (TEMs). We demonstrate that it is possible to obtain reconstructions of macromolecular complexes of different sizes to better than 3-Å resolution using a 200-keV TEM. These structures are of sufficient quality to unambiguously assign amino acid rotameric conformations and identify ordered water molecules.

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Organizational Affiliation: 

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 157.05 kDa 
• Atom Count: 10,472 
• Modelled Residue Count: 1,372 
• Deposited Residue Count: 1,452 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructose-bisphosphate aldolase A	A [auth B], B [auth A], C, D	363	Oryctolagus cuniculus	Mutation(s): 0  Gene Names: ALDOA EC: 4.1.2.13
UniProt
Find proteins for P00883 (Oryctolagus cuniculus) Explore P00883  Go to UniProtKB:  P00883

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.11.1-2580
RECONSTRUCTION	RELION	2.0

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-06-14 
Deposition Author(s): Herzik Jr., M.A., Wu, M., Lander, G.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)	United States	DP2EB020402

Revision History  

• Version 1.0: 2017-06-14
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence, Data collection
• Version 1.2: 2017-10-25
  Changes: Database references
• Version 1.3: 2017-11-15
  Changes: Database references
• Version 1.4: 2018-07-18
  Changes: Data collection, Experimental preparation
• Version 1.5: 2019-12-11
  Changes: Author supporting evidence
• Version 1.6: 2024-03-13
  Changes: Data collection, Database references