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PDBsum entry 3beh

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protein ligands metals Protein-protein interface(s) links
Membrane protein PDB id
3beh
Jmol
Contents
Protein chains
222 a.a. *
Ligands
LDA ×4
Metals
__K ×5
Waters ×23
* Residue conservation analysis
PDB id:
3beh
Name: Membrane protein
Title: Structure of a bacterial cyclic nucleotide regulated ion cha
Structure: Mll3241 protein. Chain: a, b, c, d. Engineered: yes
Source: Mesorhizobium loti. Organism_taxid: 381. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
3.10Å     R-factor:   0.276     R-free:   0.286
Authors: G.M.Clayton,J.H.Morais-Cabral
Key ref:
G.M.Clayton et al. (2008). Structure of the transmembrane regions of a bacterial cyclic nucleotide-regulated channel. Proc Natl Acad Sci U S A, 105, 1511-1515. PubMed id: 18216238 DOI: 10.1073/pnas.0711533105
Date:
18-Nov-07     Release date:   15-Jan-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q98GN8  (CNGK1_RHILO) -  Cyclic nucleotide-gated potassium channel mll3241
Seq:
Struc:
355 a.a.
222 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   4 terms 
  Biological process     potassium ion transmembrane transport   4 terms 
  Biochemical function     nucleotide binding     4 terms  

 

 
DOI no: 10.1073/pnas.0711533105 Proc Natl Acad Sci U S A 105:1511-1515 (2008)
PubMed id: 18216238  
 
 
Structure of the transmembrane regions of a bacterial cyclic nucleotide-regulated channel.
G.M.Clayton, S.Altieri, L.Heginbotham, V.M.Unger, J.H.Morais-Cabral.
 
  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.
 
  Selected figure(s)  
 
Figure 1.
Architecture of 6 TM channel. (A) Illustration of a 6 TM channel. The ion pore regions (S5, Ploop, and S6) are shown in red. Also shown are the S1–S4 domain and a C-terminal cytoplasmic domain [CNB domain (CNBD)]. (B) MlotiK1 structure viewed from the extracellular side. One subunit is shown in red. TMs are labeled S1 to S6. Green spheres in the pore are K^+. (C) Stereo side view of the MlotiK1 channel structure. Extracellular side at the top of figure. Subunits are shown in different colors. Some of the TMs and the S4–S5 linker are labeled. One of the C termini is indicated by C.
Figure 5.
The S4 helix. (A) Stereo side view of MlotiK1 and Kv1.2 S1–S4 domains superposed via S2 and S1. 3[10] regions in S4 of MlotiK1 and Kv1.2 are shown in red and cyan, respectively. Other TMs are represented by brown ribbons. S4 residues discussed in the text are labeled. (B) Extracellular view of S1–S4 domains from MlotiK1 and Kv1.2 superposed via S2 and S1. 3[10] regions in S4 as in A. Other helical regions are in white ribbons. Kv1.2 R1, R2, R3, R4, K5, and R6 and equivalent MlotiK1 Cα atoms are shown as blue and black spheres, respectively. (C) Surface representation of MlotiK1 S1–S4 domain. S4 is shown as a red ribbon, with residues equivalent to R2, R3, R4, K5, and R6 shown as sticks. Protein regions from S1 to S3 are shown as gray surface representations. S1, S2, and S3 helices are shown as green ribbons inside the surface. (D) Same as in C but viewed from the extracellular side.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20729090 A.Cukkemane, R.Seifert, and U.B.Kaupp (2011).
Cooperative and uncooperative cyclic-nucleotide-gated ion channels.
  Trends Biochem Sci, 36, 55-64.  
21135103 F.W.Muskett, S.Thouta, S.J.Thomson, A.Bowen, P.J.Stansfeld, and J.S.Mitcheson (2011).
Mechanistic insight into human ether-à-go-go-related gene (hERG) K+ channel deactivation gating from the solution structure of the EAG domain.
  J Biol Chem, 286, 6184-6191.
PDB code: 2l1m
21430265 S.Schünke, M.Stoldt, J.Lecher, U.B.Kaupp, and D.Willbold (2011).
Structural insights into conformational changes of a cyclic nucleotide-binding domain in solution from Mesorhizobium loti K1 channel.
  Proc Natl Acad Sci U S A, 108, 6121-6126.
PDB code: 2kxl
21296569 W.D.Van Horn, C.G.Vanoye, and C.R.Sanders (2011).
Working model for the structural basis for KCNE1 modulation of the KCNQ1 potassium channel.
  Curr Opin Struct Biol, 21, 283-291.  
19902533 A.Anishkin, A.L.Milac, and H.R.Guy (2010).
Symmetry-restrained molecular dynamics simulations improve homology models of potassium channels.
  Proteins, 78, 932-949.  
20663949 A.M.Powl, A.O.O'Reilly, A.J.Miles, and B.A.Wallace (2010).
Synchrotron radiation circular dichroism spectroscopy-defined structure of the C-terminal domain of NaChBac and its role in channel assembly.
  Proc Natl Acad Sci U S A, 107, 14064-14069.  
20104563 A.Stary, S.J.Wacker, L.Boukharta, U.Zachariae, Y.Karimi-Nejad, J.Aqvist, G.Vriend, and B.L.de Groot (2010).
Toward a consensus model of the HERG potassium channel.
  ChemMedChem, 5, 455-467.  
20502878 D.Balleza, C.Quinto, D.Elias, and F.Gómez-Lagunas (2010).
A high-conductance cation channel from the inner membrane of the free-living soil bacteria Rhizobium etli.
  Arch Microbiol, 192, 595-602.  
19926290 H.X.Zhou, and J.A.McCammon (2010).
The gates of ion channels and enzymes.
  Trends Biochem Sci, 35, 179-185.  
20543828 I.S.Ramsey, Y.Mokrab, I.Carvacho, Z.A.Sands, M.S.Sansom, and D.E.Clapham (2010).
An aqueous H+ permeation pathway in the voltage-gated proton channel Hv1.
  Nat Struct Mol Biol, 17, 869-875.  
20851706 J.A.Butterwick, and R.MacKinnon (2010).
Solution structure and phospholipid interactions of the isolated voltage-sensor domain from KvAP.
  J Mol Biol, 403, 591-606.
PDB code: 2kyh
20667175 K.R.Vinothkumar, and R.Henderson (2010).
Structures of membrane proteins.
  Q Rev Biophys, 43, 65.  
20231479 M...Jensen, D.W.Borhani, K.Lindorff-Larsen, P.Maragakis, V.Jogini, M.P.Eastwood, R.O.Dror, and D.E.Shaw (2010).
Principles of conduction and hydrophobic gating in K+ channels.
  Proc Natl Acad Sci U S A, 107, 5833-5838.  
20723752 R.E.Hulse, Q.Li, and E.Perozo (2010).
Up a hydrophobic creek with a short paddle.
  Cell, 142, 515-516.  
  21115694 R.S.Vieira-Pires, and J.H.Morais-Cabral (2010).
3(10) helices in channels and other membrane proteins.
  J Gen Physiol, 136, 585-592.  
20207950 S.Chakrapani, P.Sompornpisut, P.Intharathep, B.Roux, and E.Perozo (2010).
The activated state of a sodium channel voltage sensor in a membrane environment.
  Proc Natl Acad Sci U S A, 107, 5435-5440.  
19754717 B.Rosati, and D.McKinnon (2009).
Structural and regulatory evolution of cellular electrophysiological systems.
  Evol Dev, 11, 610-618.  
19545635 G.M.Clayton, S.G.Aller, J.Wang, V.Unger, and J.H.Morais-Cabral (2009).
Combining electron crystallography and X-ray crystallography to study the MlotiK1 cyclic nucleotide-regulated potassium channel.
  J Struct Biol, 167, 220-226.  
19718020 L.Wang, and F.J.Sigworth (2009).
Structure of the BK potassium channel in a lipid membrane from electron cryomicroscopy.
  Nature, 461, 292-295.  
19265197 M.Kudrnac, S.Beyl, A.Hohaus, A.Stary, T.Peterbauer, E.Timin, and S.Hering (2009).
Coupled and independent contributions of residues in IS6 and IIS6 to activation gating of CaV1.2.
  J Biol Chem, 284, 12276-12284.  
19508102 S.Choe, and M.Grabe (2009).
Conformational dynamics of the inner pore helix of voltage-gated potassium channels.
  J Chem Phys, 130, 215103.  
19465888 S.Schünke, M.Stoldt, K.Novak, U.B.Kaupp, and D.Willbold (2009).
Solution structure of the Mesorhizobium loti K1 channel cyclic nucleotide-binding domain in complex with cAMP.
  EMBO Rep, 10, 729-735.
PDB code: 2k0g
19260762 S.Y.Lee, A.Banerjee, and R.MacKinnon (2009).
Two separate interfaces between the voltage sensor and pore are required for the function of voltage-dependent K(+) channels.
  PLoS Biol, 7, e47.  
18818307 C.A.Villalba-Galea, W.Sandtner, D.M.Starace, and F.Bezanilla (2008).
S4-based voltage sensors have three major conformations.
  Proc Natl Acad Sci U S A, 105, 17600-17607.  
18614032 D.J.Posson, and P.R.Selvin (2008).
Extent of voltage sensor movement during gating of shaker K+ channels.
  Neuron, 59, 98.  
19092925 K.J.Swartz (2008).
Sensing voltage across lipid membranes.
  Nature, 456, 891-897.  
18989792 S.I.Börjesson, and F.Elinder (2008).
Structure, function, and modification of the voltage sensor in voltage-gated ion channels.
  Cell Biochem Biophys, 52, 149-174.  
18619611 S.L.Altieri, G.M.Clayton, W.R.Silverman, A.O.Olivares, E.M.De la Cruz, L.R.Thomas, and J.H.Morais-Cabral (2008).
Structural and energetic analysis of activation by a cyclic nucleotide binding domain.
  J Mol Biol, 381, 655-669.
PDB codes: 3cl1 3clp 3co2
  18955593 S.L.Wynia-Smith, A.L.Gillian-Daniel, K.A.Satyshur, and G.A.Robertson (2008).
hERG gating microdomains defined by S6 mutagenesis and molecular modeling.
  J Gen Physiol, 132, 507-520.  
18641074 Y.Shafrir, S.R.Durell, and H.R.Guy (2008).
Models of voltage-dependent conformational changes in NaChBac channels.
  Biophys J, 95, 3663-3676.  
18641075 Y.Shafrir, S.R.Durell, and H.R.Guy (2008).
Models of the structure and gating mechanisms of the pore domain of the NaChBac ion channel.
  Biophys J, 95, 3650-3662.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.