6GVJ

Human Mps1 kinase domain with ordered activation loop

• PDB DOI: https://doi.org/10.2210/pdb6GVJ/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2018-06-21 Released: 2019-01-09 
• Deposition Author(s): Roorda, J.C., Hiruma, Y., Joosten, R.P., Perrakis, A.
• Funding Organization(s): Netherlands Organisation for Scientific Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 0.233 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 

Literature

A crystal structure of the human protein kinase Mps1 reveals an ordered conformation of the activation loop.

Roorda, J.C., Joosten, R.P., Perrakis, A., Hiruma, Y.

(2019) Proteins 87: 348-352

• PubMed: 30582207 
• DOI: https://doi.org/10.1002/prot.25651
• Primary Citation of Related Structures:  
  6GVJ


• PubMed Abstract: 
  

  Monopolar spindle 1 (Mps1) is a dual-specificity protein kinase, orchestrating faithful chromosome segregation during mitosis. All reported structures of the Mps1 kinase adopt the hallmarks of an inactive conformation, which includes a mostly disordered activation loop. Here, we present a 2.4 Å resolution crystal structure of an "extended" version of the Mps1 kinase domain, which shows an ordered activation loop. However, the other structural characteristics of an active kinase are not present. Our structure shows that the Mps1 activation loop can fit to the ATP binding pocket and interferes with ATP, but less so with inhibitors binding, partly explain the potency of various Mps1 inhibitors.

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Organizational Affiliation: 

Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 49.5 kDa 
• Atom Count: 2,277 
• Modelled Residue Count: 272 
• Deposited Residue Count: 429 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity protein kinase TTK	A	429	Homo sapiens	Mutation(s): 0  Gene Names: TTK, MPS1, MPS1L1 EC: 2.7.12.1
UniProt & NIH Common Fund Data Resources
Find proteins for P33981 (Homo sapiens) Explore P33981  Go to UniProtKB:  P33981
PHAROS:  P33981 GTEx:  ENSG00000112742

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	H [auth A], I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 0.233 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.825	α = 90
b = 102.613	β = 90
c = 110.973	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
xia2	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-01-09 
Deposition Author(s): Roorda, J.C., Hiruma, Y., Joosten, R.P., Perrakis, A.

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Funding Organization	Location	Grant Number
Netherlands Organisation for Scientific Research	Netherlands	722.015.008
Netherlands Organisation for Scientific Research	Netherlands	723.013.003

Revision History  

• Version 1.0: 2019-01-09
  Type: Initial release
  
• Version 1.1: 2019-03-20
  Changes: Data collection, Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description