PDBsum entry 3e8h

Membrane protein

PDB id: 3e8h

Contents

Protein chains

91 a.a. *

96 a.a. *

Ligands

MPD ×4

Metals

__K ×10

Waters ×96

* Residue conservation analysis

PDB id:

3e8h

Name:

Membrane protein

Title:

Crystal structure of the the open nak channel-k+ complex

Structure:

Potassium channel protein. Chain: a, b. Fragment: transmembrane domain, residues 19-110. Engineered: yes

Source:

Bacillus cereus. Organism_taxid: 1396. Atcc: 14579. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.80Å R-factor: 0.212 R-free: 0.234

Authors:

Y.Jiang,A.Alam

Key ref:

A.Alam and Y.Jiang (2009). Structural analysis of ion selectivity in the NaK channel. Nat Struct Biol, 16, 35-41. PubMed id: 19098915 DOI: 10.1038/nsmb.1537

Date:

19-Aug-08 Release date: 23-Dec-08

Protein chain

Q81HW2  (Q81HW2_BACCR) -  Potassium channel protein from Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)

Seq: 114 a.a.

Struc: 91 a.a.*

Protein chain

Q81HW2  (Q81HW2_BACCR) -  Potassium channel protein from Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)

Seq: 114 a.a.

Struc: 96 a.a.*

* PDB and UniProt seqs differ at 7 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B: E.C.?

DOI no: 10.1038/nsmb.1537

Nat Struct Biol 16:35-41 (2009)

PubMed id: 19098915

Structural analysis of ion selectivity in the NaK channel.

A.Alam, Y.Jiang.

ABSTRACT

Here we present a detailed characterization of ion binding in the NaK pore using the high-resolution structures of NaK in complex with various cations. These structures reveal four ion binding sites with similar chemical environments but vastly different ion preference. The most nonselective of all is site 3, which is formed exclusively by backbone carbonyl oxygen atoms and resides deep within the selectivity filter. Additionally, four water molecules in combination with four backbone carbonyl oxygen atoms are seen to participate in K(+) and Rb(+) ion chelation, at both the external entrance and the vestibule of the NaK filter, confirming the channel's preference for an octahedral ligand configuration for K(+) and Rb(+) binding. In contrast, Na(+) binding in the NaK filter, particularly at site 4, utilizes a pyramidal ligand configuration that requires the participation of a water molecule in the cavity. Therefore, the ability of the NaK filter to bind both Na(+) and K(+) ions seemingly arises from the ions' ability to use the existing environment in unique ways, rather than from any structural rearrangements of the filter itself.

Selected figure(s)

Figure 2.
(a,b) The 2F[o] – F[c] ion omit maps (1.5 ) show electron density of ion binding in the K^+ complex (a) and Rb^+ complex (b) of NaKN 19. K^+ and Rb^+ ions are colored green, with water molecules represented as red spheres. (c) The maintenance of an octahedral ligand arrangement in the K^+ complex, which also holds true for the Rb^+ complex. Oxygen atoms from the front and back subunits chelating the ions are shown as red spheres. (d) F[Cs soak] – F[K] difference map contoured at 10 , showing Cs^+ binding at site 3.

Figure 4.
(a) F[Ba soak] – F[K] difference map (blue mesh) contoured at 10 showing the two Ba^2+ binding sites. (b) 2F[o] – F[c] ion omit maps of a Ba^2+-soaked crystal contoured at 1.5 . The electron density at the external entrance and site 3 was modeled as Ba^2+ (orange spheres), and water molecules are modeled as red spheres. (c) Ba^2+ (left) and Ca^2+ (right) blocking of ^86Rb influx in liposomes loaded with NaCl.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: Nat Struct Biol (2009, 16, 35-41) copyright 2009.

Figures were selected by an automated process.