8HFH

CENP-E motor domain in complex with AMPPNP and Mg2+

• PDB DOI: https://doi.org/10.2210/pdb8HFH/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-11-10 Released: 2023-03-08 
• Deposition Author(s): Shibuya, A., Yokoyama, H.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.206 
• R-Value Work: 0.161 
• R-Value Observed: 0.165 

Literature

Crystal structure of the motor domain of centromere-associated protein E in complex with a non-hydrolysable ATP analogue.

Shibuya, A., Suzuki, A., Ogo, N., Sawada, J.I., Asai, A., Yokoyama, H.

(2023) FEBS Lett 597: 1138-1148

• PubMed: 36823439 
• DOI: https://doi.org/10.1002/1873-3468.14602
• Primary Citation of Related Structures:  
  8HFH


• PubMed Abstract: 
  

  Centromere-associated protein E (CENP-E) is a kinesin motor protein essential for mitosis and a new target for anticancer agents with less side effects. To rationally design anticancer drug candidates based on structure, it is important to determine the three-dimensional structure of the CENP-E motor domain bound to its inhibitor. Here, we report the first crystal structure of the CENP-E motor domain in complex with a non-hydrolysable ATP analogue, adenylyl-imidodiphosphate (AMPPNP). Furthermore, the structure is compared with the ADP-bound form of the CENP-E motor domain as well as the AMPPNP-bound forms of other kinesins. This study indicates that helix α4 of CENP-E participates in the slow binding of CENP-E to microtubules. These results will contribute to the development of anticancer drugs targeting CENP-E.

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Organizational Affiliation: 

Faculty of Pharmaceutical Sciences, Tokyo University of Science, Chiba, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 40.47 kDa 
• Atom Count: 2,909 
• Modelled Residue Count: 321 
• Deposited Residue Count: 353 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Centromere-associated protein E	A	353	Homo sapiens	Mutation(s): 1  Gene Names: CENPE
UniProt & NIH Common Fund Data Resources
Find proteins for Q02224 (Homo sapiens) Explore Q02224  Go to UniProtKB:  Q02224
PHAROS:  Q02224 GTEx:  ENSG00000138778

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP (Subject of Investigation/LOI)	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
IMD	G [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
MG (Subject of Investigation/LOI)	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	D [auth A], E [auth A], F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.206 
• R-Value Work: 0.161 
• R-Value Observed: 0.165 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.576	α = 90
b = 46.215	β = 90
c = 73.718	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-03-08 
Deposition Author(s): Shibuya, A., Yokoyama, H.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History  

• Version 1.0: 2023-03-08
  Type: Initial release
  
• Version 1.1: 2023-05-10
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description