1U12

M. loti cyclic nucleotide binding domain mutant

• PDB DOI: https://doi.org/10.2210/pdb1U12/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Mesorhizobium japonicum MAFF 303099
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-07-14 Released: 2004-11-30 
• Deposition Author(s): Clayton, G.M., Silverman, W.R., Heginbotham, L., Morais-Cabral, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.281 
• R-Value Work: 0.253 
• R-Value Observed: 0.253 

Literature

Structural Basis of Ligand Activation in a Cyclic Nucleotide Regulated Potassium Channel

Clayton, G.M., Silverman, W.R., Heginbotham, L., Morais-Cabral, J.H.

(2004) Cell 119: 615-627

• PubMed: 15550244 
• DOI: https://doi.org/10.1016/j.cell.2004.10.030
• Primary Citation of Related Structures:  
  1U12, 1VP6


• PubMed Abstract: 
  

  Here we describe the initial functional characterization of a cyclic nucleotide regulated ion channel from the bacterium Mesorhizobium loti and present two structures of its cyclic nucleotide binding domain, with and without cAMP. The domains are organized as dimers with the interface formed by the linker regions that connect the nucleotide binding pocket to the pore domain. Together, structural and functional data suggest the domains form two dimers on the cytoplasmic face of the channel. We propose a model for gating in which ligand binding alters the structural relationship within a dimer, directly affecting the position of the adjacent transmembrane helices.

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Organizational Affiliation: 

Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, CT 06520, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33.27 kDa 
• Atom Count: 1,918 
• Modelled Residue Count: 258 
• Deposited Residue Count: 276 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cyclic nucleotide binding domain	A, B	138	Mesorhizobium japonicum MAFF 303099	Mutation(s): 1
UniProt
Find proteins for Q98GN8 (Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)) Explore Q98GN8  Go to UniProtKB:  Q98GN8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	AA [auth B], BA [auth B], C [auth A], CA [auth B], D [auth A], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], N [auth A], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
SO4	O [auth A], P [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
K	MA [auth B], Q [auth A], R [auth A], S [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.281 
• R-Value Work: 0.253 
• R-Value Observed: 0.253 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.126	α = 90
b = 57.126	β = 90
c = 193.037	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-11-30 
Deposition Author(s): Clayton, G.M., Silverman, W.R., Heginbotham, L., Morais-Cabral, J.H.

Revision History  

• Version 1.0: 2004-11-30
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations
• Version 1.4: 2024-02-14
  Changes: Data collection