3BEH | pdb_00003beh

Structure of a Bacterial Cyclic Nucleotide Regulated Ion Channel

PDB DOI: https://doi.org/10.2210/pdb3BEH/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Mesorhizobium loti
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2007-11-18 Released: 2008-01-15
Deposition Author(s): Clayton, G.M., Morais-Cabral, J.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.286 (Depositor), 0.282 (DCC)
R-Value Work:
0.276 (Depositor), 0.273 (DCC)
R-Value Observed:
0.276 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure of the transmembrane regions of a bacterial cyclic nucleotide-regulated channel.

Clayton, G.M., Altieri, S., Heginbotham, L., Unger, V.M., Morais-Cabral, J.H.

(2008) Proc Natl Acad Sci U S A 105: 1511-1515

PubMed: 18216238 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.0711533105
Primary Citation Related Structures:
2ZD9, 3BEH

PubMed Abstract:
The six-transmembrane helix (6 TM) tetrameric cation channels form the largest ion channel family, some members of which are voltage-gated and others are not. There are no reported channel structures to match the wealth of functional data on the non-voltage-gated members. We determined the structure of the transmembrane regions of the bacterial cyclic nucleotide-regulated channel MlotiK1, a non-voltage-gated 6 TM channel. The structure showed how the S1-S4 domain and its associated linker can serve as a clamp to constrain the gate of the pore and possibly function in concert with ligand-binding domains to regulate the opening of the pore. The structure also led us to hypothesize a new mechanism by which motions of the S6 inner helices can gate the ion conduction pathway at a position along the pore closer to the selectivity filter than the canonical helix bundle crossing.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 152.18 kDa
Atom Count: 6,673
Modeled Residue Count: 895
Deposited Residue Count: 1,420
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mll3241 protein	A, B, C, D	355	Mesorhizobium loti	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q98GN8 (Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)) Explore Q98GN8 Go to UniProtKB: Q98GN8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q98GN8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LDA Query on LDA Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth D] SDF format, chain M [auth D] SDF format, chain K [auth C] MOL2 format, chain I [auth A] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] mmCIF format, chain I [auth A] mmCIF format, chain L [auth D] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C]	I [auth A], K [auth C], L [auth D], M [auth D]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D] Interactions & Density Focus chain I [auth A] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain H [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A]	E [auth A], F [auth A], G [auth A], H [auth A], J [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.286 (Depositor), 0.282 (DCC)
R-Value Work: 0.276 (Depositor), 0.273 (DCC)
R-Value Observed: 0.276 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 282.73	α = 90
b = 282.73	β = 90
c = 105.46	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-01-15

Deposition Author(s):

Clayton, G.M.

Morais-Cabral, J.H.

Revision History (Full details and data files)

Version 1.0: 2008-01-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations