7XDE

Cryo-EM structures of human mitochondrial NAD(P)+-dependent malic enzyme in apo form

• PDB DOI: https://doi.org/10.2210/pdb7XDE/pdb
• EM Map EMD-33145: EMDB EMDataResource

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-03-26 Released: 2023-03-29 
• Deposition Author(s): Wang, C.H., Hsieh, J.T., Ho, M.C., Hung, H.C.
• Funding Organization(s): Academia Sinica (Taiwan), Ministry of Science and Technology (MoST, Taiwan)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.72 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Suppression of the human malic enzyme 2 modifies energy metabolism and inhibits cellular respiration

Hsieh, J.Y., Chen, K.C., Wang, C.H., Liu, G.Y., Ye, J.A., Chou, Y.T., Lin, Y.C., Lyu, C.J., Chang, R.Y., Liu, Y.L., Li, Y.H., Lee, M.R., Ho, M.C., Hung, H.C.

(2023) Commun Biol 6: 548

• DOI: https://doi.org/10.1038/s42003-023-04930-y

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: electron microscopy

Macromolecule Content

• Total Structure Weight: 264.74 kDa 
• Atom Count: 17,896 
• Modelled Residue Count: 2,248 
• Deposited Residue Count: 2,336 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent malic enzyme, mitochondrial	A, B, C, D	584	Homo sapiens	Mutation(s): 0  Gene Names: ME2 EC: 1.1.1.38
UniProt & NIH Common Fund Data Resources
Find proteins for P23368 (Homo sapiens) Explore P23368  Go to UniProtKB:  P23368
PHAROS:  P23368 GTEx:  ENSG00000082212

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.72 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-03-29 
Deposition Author(s): Wang, C.H., Hsieh, J.T., Ho, M.C., Hung, H.C.

---

Funding Organization	Location	Grant Number
Academia Sinica (Taiwan)	Taiwan	--
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	--

Revision History  

• Version 1.0: 2023-03-29
  Type: Initial release
  
• Version 1.1: 2023-05-31
  Changes: Database references