1VP6 | pdb_00001vp6

M.loti ion channel cylic nucleotide binding domain

• PDB DOI: https://doi.org/10.2210/pdb1VP6/pdb
• Entry: 1VP6 supersedes: 1PF0

• Classification: MEMBRANE PROTEIN
• Organism(s): Mesorhizobium loti
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-10-14 Released: 2004-10-26 
• 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: 1.70 Å
• R-Value Free: 
  0.219 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

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 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: 31.1 kDa 
• Atom Count: 2,316 
• Modeled Residue Count: 266 
• Deposited Residue Count: 276 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic-nucleotide binding domain of mesorhizobium loti CNG potassium channel	A, B [auth C]	138	Mesorhizobium loti	Mutation(s): 0
UniProt
Find proteins for Q98GN8 (Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)) Explore Q98GN8  Go to UniProtKB:  Q98GN8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CMP	O [auth A], T [auth C]	ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE C10 H12 N5 O6 P IVOMOUWHDPKRLL-KQYNXXCUSA-N
BR	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], P [auth C], Q [auth C], R [auth C], S [auth C]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.219 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.324	α = 90
b = 80.292	β = 99.16
c = 50.419	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
SOLVE	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-10-26 
Deposition Author(s): Clayton, G.M., Silverman, W.R., Heginbotham, L., Morais-Cabral, J.H.
• This entry supersedes: 1PF0

Revision History  

• Version 1.0: 2004-10-26
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations