PDBsum entry 3e8b

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Membrane protein PDB id
Protein chains
91 a.a. *
96 a.a. *
MPD ×4
_RB ×11
Waters ×94
* Residue conservation analysis
PDB id:
Name: Membrane protein
Title: Crystal structure of the the open nak channel- rb+ 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.
1.70Å     R-factor:   0.220     R-free:   0.229
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
19-Aug-08     Release date:   23-Dec-08    
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Protein chain
Pfam   ArchSchema ?
Q81HW2  (Q81HW2_BACCR) -  Potassium channel protein
114 a.a.
91 a.a.*
Protein chain
Pfam   ArchSchema ?
Q81HW2  (Q81HW2_BACCR) -  Potassium channel protein
114 a.a.
96 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 7 residue positions (black crosses)


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.
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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21518828 A.Alam, and Y.Jiang (2011).
Structural studies of ion selectivity in tetrameric cation channels.
  J Gen Physiol, 137, 397-403.  
21187421 M.G.Derebe, D.B.Sauer, W.Zeng, A.Alam, N.Shi, and Y.Jiang (2011).
Tuning the ion selectivity of tetrameric cation channels by changing the number of ion binding sites.
  Proc Natl Acad Sci U S A, 108, 598-602.
PDB codes: 3k03 3ouf 3ous
21187429 M.G.Derebe, W.Zeng, Y.Li, A.Alam, and Y.Jiang (2011).
Structural studies of ion permeation and Ca2+ blockage of a bacterial channel mimicking the cyclic nucleotide-gated channel pore.
  Proc Natl Acad Sci U S A, 108, 592-597.
PDB codes: 3k04 3k06 3k08 3k0d 3k0g
19785456 I.Bahar, T.R.Lezon, A.Bakan, and I.H.Shrivastava (2010).
Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins.
  Chem Rev, 110, 1463-1497.  
  20513758 I.Bahar (2010).
On the functional significance of soft modes predicted by coarse-grained models for membrane proteins.
  J Gen Physiol, 135, 563-573.  
20965773 P.J.Focke, and F.I.Valiyaveetil (2010).
Studies of ion channels using expressed protein ligation.
  Curr Opin Chem Biol, 14, 797-802.  
20676101 S.Ye, Y.Li, and Y.Jiang (2010).
Novel insights into K+ selectivity from high-resolution structures of an open K+ channel pore.
  Nat Struct Mol Biol, 17, 1019-1023.
PDB codes: 3ldc 3ldd 3lde
19946269 A.N.Thompson, I.Kim, T.D.Panosian, T.M.Iverson, T.W.Allen, and C.M.Nimigean (2009).
Mechanism of potassium-channel selectivity revealed by Na(+) and Li(+) binding sites within the KcsA pore.
  Nat Struct Mol Biol, 16, 1317-1324.
PDB codes: 3gb7 3iga
19489546 H.Yu, S.Y.Noskov, and B.Roux (2009).
Hydration number, topological control, and ion selectivity.
  J Phys Chem B, 113, 8725-8730.  
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