Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 39.76 kDa 
• Atom Count: 2582 
• Modelled Residue Count: 318 
• Deposited Residue Count: 350 
• Unique protein chains: 1

3W8Q

Structure of the Human Mitogen-Activated Protein Kinase Kinase 1 (MEK1)

• PDB DOI: 10.2210/pdb3W8Q/pdb

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


• Deposited: 2013-03-20 Released: 2014-03-26 
• Deposition Author(s): Nakae, S., Kitamura, M., Shirai, T., Tada, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.268 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 

Literature

Structure of mitogen-activated protein kinase kinase 1 in the DFG-out conformation.

Nakae, S., Kitamura, M., Fujiwara, D., Sawa, M., Shirai, T., Fujii, I., Tada, T.

(2021) Acta Crystallogr F Struct Biol Commun 77: 459-464

• PubMed: 34866601 
• DOI: 10.1107/S2053230X21011687
• Primary Citation of Related Structures:  
  3W8Q


• PubMed Abstract: 
  

Eukaryotic protein kinases contain an Asp-Phe-Gly (DFG) motif, the conformation of which is involved in controlling the catalytic activity, at the N-terminus of the activation segment. The motif can be switched between active-state (DFG-in) and inactive-state (DFG-out) conformations: however, the mechanism of conformational change is poorly understood, partly because there are few reports of the DFG-out conformation. Here, a novel crystal structure of nonphosphorylated human mitogen-activated protein kinase kinase 1 (MEK1; amino acids 38-381) complexed with ATP-γS is reported in which MEK1 adopts the DFG-out conformation. The crystal structure revealed that the structural elements (the αC helix and HRD motif) surrounding the active site are involved in the formation/stabilization of the DFG-out conformation. The ATP-γS molecule was bound to the canonical ATP-binding site in a different binding mode that has never been found in previously determined crystal structures of MEK1. This novel ATP-γS binding mode provides a starting point for the design of high-affinity inhibitors of nonphosphorylated inactive MEK1 that adopts the DFG-out conformation.

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Organizational Affiliation: 

Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity mitogen-activated protein kinase kinase 1	A	350	Homo sapiens	Mutation(s): 2  Gene Names: MAP2K1, MEK1, PRKMK1 EC: 2.7.12.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q02750 (Homo sapiens) Explore Q02750  Go to UniProtKB:  Q02750
PHAROS:  Q02750

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AGS	B [auth A]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C10 H16 N5 O12 P3 S NLTUCYMLOPLUHL-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.268 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.815	α = 90
b = 96.191	β = 90
c = 138.617	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-03-20 
• Released Date: 2014-03-26 
Deposition Author(s): Nakae, S., Kitamura, M., Shirai, T., Tada, T.

Revision History  

• Version 1.0: 2014-03-26
  Type: Initial release
  
• Version 1.1: 2021-12-22
  Changes: Database references, Derived calculations