9CRA

CryoEM Structure of the C-terminally truncated form of human NAD Kinase bound to NAD

• PDB DOI: https://doi.org/10.2210/pdb9CRA/pdb
• EM Map EMD-45856: EMDB EMDataResource

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


• Deposited: 2024-07-21 Released: 2025-01-08 
• Deposition Author(s): Li, Y., Chen, Z., Mary, C., Labesse, G., Hoxhaj, G.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), Welch Foundation, Agence Nationale de la Recherche (ANR), Fondation pour la Recherche Medicale (FRM)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.34 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

CryoEM Structure of the C-terminally truncated form of human NAD Kinase

Li, Y., Chen, Z., Mary, C., Labesse, G., Hoxhaj, G.

To be published.

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: 166.93 kDa 
• Atom Count: 9,842 
• Modelled Residue Count: 1,247 
• Deposited Residue Count: 1,492 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD kinase	A, B, C, D	373	Homo sapiens	Mutation(s): 0  Gene Names: NADK EC: 2.7.1.23
UniProt & NIH Common Fund Data Resources
Find proteins for O95544 (Homo sapiens) Explore O95544  Go to UniProtKB:  O95544
PHAROS:  O95544 GTEx:  ENSG00000008130

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: 2.34 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	Coot
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-08 
Deposition Author(s): Li, Y., Chen, Z., Mary, C., Labesse, G., Hoxhaj, G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01GM143236
Welch Foundation	United States	I-2067-20210327
Welch Foundation	United States	I-2067-20240404
Agence Nationale de la Recherche (ANR)	France	ANR-20-CE18-0025
Fondation pour la Recherche Medicale (FRM)	France	EQU202303016265

Revision History  

• Version 1.0: 2025-01-08
  Type: Initial release