Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 94.16 kDa 
• Atom Count: 6338 
• Modelled Residue Count: 794 
• Deposited Residue Count: 822 
• Unique protein chains: 1

5K11

Cryo-EM structure of isocitrate dehydrogenase (IDH1) in inhibitor-bound state

• PDB DOI: 10.2210/pdb5K11/pdb
• EM Map EMD-8193:EMDBEMDataResource

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus
• Mutation(s): No 


• Deposited: 2016-05-17 Released: 2016-06-08 
• Deposition Author(s): Merk, A., Bartesaghi, A., Banerjee, S., Falconieri, V., Rao, P., Earl, L., Milne, J., Subramaniam, S.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Breaking Cryo-EM Resolution Barriers to Facilitate Drug Discovery.

Merk, A., Bartesaghi, A., Banerjee, S., Falconieri, V., Rao, P., Davis, M.I., Pragani, R., Boxer, M.B., Earl, L.A., Milne, J.L., Subramaniam, S.

(2016) Cell 165: 1698-1707

• PubMed: 27238019 
• DOI: 10.1016/j.cell.2016.05.040
• Primary Citation of Related Structures:  
  5K0Z, 5K10, 5K11, 5K12


• PubMed Abstract: 
  

Recent advances in single-particle cryoelecton microscopy (cryo-EM) are enabling generation of numerous near-atomic resolution structures for well-ordered protein complexes with sizes ≥ ∼200 kDa. Whether cryo-EM methods are equally useful for high-resolution structural analysis of smaller, dynamic protein complexes such as those involved in cellular metabolism remains an important question. Here, we present 3.8 Å resolution cryo-EM structures of the cancer target isocitrate dehydrogenase (93 kDa) and identify the nature of conformational changes induced by binding of the allosteric small-molecule inhibitor ML309. We also report 2.8-Å- and 1.8-Å-resolution structures of lactate dehydrogenase (145 kDa) and glutamate dehydrogenase (334 kDa), respectively. With these results, two perceived barriers in single-particle cryo-EM are overcome: (1) crossing 2 Å resolution and (2) obtaining structures of proteins with sizes < 100 kDa, demonstrating that cryo-EM can be used to investigate a broad spectrum of drug-target interactions and dynamic conformational states.

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Organizational Affiliation: 

Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate dehydrogenase [NADP] cytoplasmic	A, B	411	Homo sapiens	Mutation(s): 0  Gene Names: IDH1, PICD EC: 1.1.1.42
UniProt & NIH Common Fund Data Resources
Find proteins for O75874 (Homo sapiens) Explore O75874  Go to UniProtKB:  O75874
PHAROS:  O75874 GTEx:  ENSG00000138413

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	C [auth A], D [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-05-17 
• Released Date: 2016-06-08 
Deposition Author(s): Merk, A., Bartesaghi, A., Banerjee, S., Falconieri, V., Rao, P., Earl, L., Milne, J., Subramaniam, S.

Revision History  

• Version 1.0: 2016-06-08
  Type: Initial release
  
• Version 1.1: 2016-06-29
  Changes: Database references
• Version 1.2: 2016-11-23
  Changes: Other
• Version 1.3: 2018-07-18
  Changes: Data collection, Experimental preparation