3CL1

M. loti cyclic-nucleotide binding domain, cyclic-GMP bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural and Energetic Analysis of Activation by a Cyclic Nucleotide Binding Domain.

Altieri, S.L.Clayton, G.M.Silverman, W.R.Olivares, A.O.De La Cruz, E.M.Thomas, L.R.Morais-Cabral, J.H.

(2008) J Mol Biol 381: 655-669

  • DOI: https://doi.org/10.1016/j.jmb.2008.06.011
  • Primary Citation of Related Structures:  
    3CL1, 3CLP, 3CO2

  • PubMed Abstract: 

    MlotiK1 is a prokaryotic homolog of cyclic-nucleotide-dependent ion channels that contains an intracellular C-terminal cyclic nucleotide binding (CNB) domain. X-ray structures of the CNB domain have been solved in the absence of ligand and bound to cAMP. Both the full-length channel and CNB domain fragment are easily expressed and purified, making MlotiK1 a useful model system for dissecting activation by ligand binding. We have used X-ray crystallography to determine three new MlotiK1 CNB domain structures: a second apo configuration, a cGMP-bound structure, and a second cAMP-bound structure. In combination, the five MlotiK1 CNB domain structures provide a unique opportunity for analyzing, within a single protein, the structural differences between the apo state and the bound state, and the structural variability within each state. With this analysis as a guide, we have probed the nucleotide selectivity and importance of specific residue side chains in ligand binding and channel activation. These data help to identify ligand-protein interactions that are important for ligand dependence in MlotiK1 and, more globally, in the class of nucleotide-dependent proteins.


  • Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mll3241 protein
A, B
140N/AMutation(s): 0 
UniProt
Find proteins for Q98GN8 (Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099))
Explore Q98GN8 
Go to UniProtKB:  Q98GN8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ98GN8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PCG
Query on PCG

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B]
CYCLIC GUANOSINE MONOPHOSPHATE
C10 H12 N5 O7 P
ZOOGRGPOEVQQDX-UUOKFMHZSA-N
POL
Query on POL

Download Ideal Coordinates CCD File 
J [auth B]N-PROPANOL
C3 H8 O
BDERNNFJNOPAEC-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
H [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.202α = 90
b = 79.594β = 99.11
c = 49.984γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOLREPphasing
CNSrefinement
MOSFLMdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations, Refinement description