9B0T | pdb_00009b0t

Cryo-EM structure of E227Q variant of uMtCK1 in complex with transition state analog


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9B0T

This is version 1.2 of the entry. See complete history

Literature

Structural basis for substrate binding, catalysis, and inhibition of cancer target mitochondrial creatine kinase by a covalent inhibitor.

Demir, M.Koepping, L.Li, Y.Fujimoto, L.Bobkov, A.Zhao, J.Hitosugi, T.Sergienko, E.

(2025) Structure 33: 786-797.e3

  • DOI: https://doi.org/10.1016/j.str.2025.01.008
  • Primary Citation Related Structures: 
    9B04, 9B05, 9B0T, 9B0U, 9B14, 9B16

  • PubMed Abstract: 

    Mitochondrial creatine kinases (MtCKs) are key players in maintaining energy homeostasis in cells that work with cytosolic creatine kinases for energy transport from mitochondria to cytoplasm. The inhibition of breast cancer growth by cyclocreatine targeting CKs indicates dependence of cancer cells on the "energy shuttle" for cell growth and survival. Hence, understanding key mechanistic features of creatine kinases and their inhibition plays an important role in the development of cancer therapeutics. Herein, we present mutational and structural investigations on understudied ubiquitous MtCK that showed closure of the loop comprising His61 is specific to and relies on creatine binding and mechanism of phosphoryl transfer depends on electrostatics of active site. We demonstrate that previously identified pan-CK covalent inhibitor CKi inhibit breast cancer cell proliferation; however, our biochemical and structural data indicated that inhibition by CKi is highly dependent on covalent link formation and conformational changes upon creatine binding are not observed.


  • Organizational Affiliation
    • Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA. Electronic address: mdemir@sbpdiscovery.org.

Macromolecule Content 

  • Total Structure Weight: 385.94 kDa 
  • Atom Count: 21,704 
  • Modeled Residue Count: 2,872 
  • Deposited Residue Count: 3,344 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Creatine kinase U-type, mitochondrial
A, B, C, D, E
A, B, C, D, E, F, G, H
418Homo sapiensMutation(s): 1 
Gene Names: CKMT1ACKMTCKMT1B
EC: 2.7.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for P12532 (Homo sapiens)
Explore P12532 
Go to UniProtKB:  P12532
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12532
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
(Subject of Investigation/LOI)

Query on ADP



Download:Ideal Coordinates CCD File
DA [auth F]
HA [auth G]
J [auth A]
LA [auth H]
N [auth B]
DA [auth F],
HA [auth G],
J [auth A],
LA [auth H],
N [auth B],
R [auth C],
V [auth D],
Z [auth E]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
CRN
(Subject of Investigation/LOI)

Query on CRN



Download:Ideal Coordinates CCD File
CA [auth F]
GA [auth G]
I [auth A]
KA [auth H]
M [auth B]
CA [auth F],
GA [auth G],
I [auth A],
KA [auth H],
M [auth B],
Q [auth C],
U [auth D],
Y [auth E]
N-[(E)-AMINO(IMINO)METHYL]-N-METHYLGLYCINE
C4 H9 N3 O2
CVSVTCORWBXHQV-UHFFFAOYSA-N
NO3
(Subject of Investigation/LOI)

Query on NO3



Download:Ideal Coordinates CCD File
AA [auth E]
EA [auth F]
IA [auth G]
K [auth A]
MA [auth H]
AA [auth E],
EA [auth F],
IA [auth G],
K [auth A],
MA [auth H],
O [auth B],
S [auth C],
W [auth D]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
BA [auth E]
FA [auth F]
JA [auth G]
L [auth A]
NA [auth H]
BA [auth E],
FA [auth F],
JA [auth G],
L [auth A],
NA [auth H],
P [auth B],
T [auth C],
X [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Office of the DirectorUnited StatesOD026926
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA030199
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA251910

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-12
    Type: Initial release
  • Version 1.1: 2025-02-19
    Changes: Data collection, Database references
  • Version 1.2: 2025-04-16
    Changes: Data collection, Database references