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Contents |
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219 a.a.
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212 a.a.
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103 a.a.
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* Residue conservation analysis
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PDB id:
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Membrane protein
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Title:
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Potassium channel kcsa-fab complex in low concentration of k
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Structure:
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Antibody fab fragment heavy chain. Chain: a. Antibody fab fragment light chain. Chain: b. Potassium channel kcsa. Chain: c. Fragment: potassium channel kcsa. Engineered: yes. Mutation: yes
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Source:
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Mus musculus. House mouse. Organism_taxid: 10090. Streptomyces lividans. Organism_taxid: 1916. Expressed in: escherichia coli. Expression_system_taxid: 562
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Biol. unit:
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Dodecamer (from PDB file)
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Resolution:
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2.30Å
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R-factor:
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0.218
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R-free:
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0.235
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Authors:
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Y.Zhou,J.H.Morais-Cabral,A.Kaufman,R.Mackinnon
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Key ref:
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Y.Zhou
et al.
(2001).
Chemistry of ion coordination and hydration revealed by a K+ channel-Fab complex at 2.0 A resolution.
Nature,
414,
43-48.
PubMed id:
DOI:
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Date:
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07-Oct-01
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Release date:
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14-Nov-01
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PROCHECK
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Headers
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References
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No UniProt id for this chain
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Gene Ontology (GO) functional annotation
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Cellular component
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voltage-gated potassium channel complex
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1 term
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Biological process
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potassium ion transport
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1 term
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Biochemical function
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protein binding
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2 terms
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DOI no:
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Nature
414:43-48
(2001)
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PubMed id:
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Chemistry of ion coordination and hydration revealed by a K+ channel-Fab complex at 2.0 A resolution.
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Y.Zhou,
J.H.Morais-Cabral,
A.Kaufman,
R.MacKinnon.
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ABSTRACT
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Ion transport proteins must remove an ion's hydration shell to coordinate the
ion selectively on the basis of its size and charge. To discover how the K+
channel solves this fundamental aspect of ion conduction, we solved the
structure of the KcsA K+ channel in complex with a monoclonal Fab antibody
fragment at 2.0 A resolution. Here we show how the K+ channel displaces water
molecules around an ion at its extracellular entryway, and how it holds a K+ ion
in a square antiprism of water molecules in a cavity near its intracellular
entryway. Carbonyl oxygen atoms within the selectivity filter form a very
similar square antiprism around each K+ binding site, as if to mimic the waters
of hydration. The selectivity filter changes its ion coordination structure in
low K+ solutions. This structural change is crucial to the operation of the
selectivity filter in the cellular context, where the K+ ion concentration near
the selectivity filter varies in response to channel gating.
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Selected figure(s)
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Figure 2.
Figure 2: Stereo view of electron density in the region of the
K+ channel selectivity filter. The 2F[o] - F[c] electron
density map (contoured at 2  )
covers amino acids forming the selectivity filter (two
diagonally opposed subunits are shown), with K+ ions (green
spheres) along the ion pathway, and water molecules (red
spheres) in the vicinity.
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Figure 3.
Figure 3: Stereo view of a hydrated K+ ion in the central
cavity. Eight water molecules (red spheres) surround a single
K+ ion (green sphere) in the cavity. The 2F[o] - F[c] electron
density map is contoured at 2 .
Residues forming the cavity are shown in ball-and-stick
representation. For clarity, only backbone atoms and the side
chains facing the cavity (Thr 75, Ile 100, Phe 103, Gly 104 and
Thr 107) are shown. The subunit closest to the viewer has been
removed.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2001,
414,
43-48)
copyright 2001.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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A.Alam,
and
Y.Jiang
(2011).
Structural studies of ion selectivity in tetrameric cation channels.
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J Gen Physiol, 137,
397-403.
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C.Boiteux,
and
S.Bernèche
(2011).
Absence of ion-binding affinity in the putatively inactivated low-[K+] structure of the KcsA potassium channel.
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Structure, 19,
70-79.
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|
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C.M.Nimigean,
and
T.W.Allen
(2011).
Origins of ion selectivity in potassium channels from the perspective of channel block.
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J Gen Physiol, 137,
405-413.
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I.Waluyo,
C.Huang,
D.Nordlund,
U.Bergmann,
T.M.Weiss,
L.G.Pettersson,
and
A.Nilsson
(2011).
The structure of water in the hydration shell of cations from x-ray Raman and small angle x-ray scattering measurements.
|
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J Chem Phys, 134,
064513.
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J.C.Pai,
J.A.Culver,
J.E.Drury,
R.S.Motani,
R.L.Lieberman,
and
J.A.Maynard
(2011).
Conversion of scFv peptide-binding specificity for crystal chaperone development.
|
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Protein Eng Des Sel, 24,
419-428.
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L.Zúñiga,
V.Márquez,
F.D.González-Nilo,
C.Chipot,
L.P.Cid,
F.V.Sepúlveda,
and
M.I.Niemeyer
(2011).
Gating of a pH-Sensitive K(2P) Potassium Channel by an Electrostatic Effect of Basic Sensor Residues on the Selectivity Filter.
|
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PLoS One, 6,
e16141.
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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.
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Proc Natl Acad Sci U S A, 108,
598-602.
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PDB codes:
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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.
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Proc Natl Acad Sci U S A, 108,
592-597.
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PDB codes:
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N.Monroe,
G.Sennhauser,
M.A.Seeger,
C.Briand,
and
M.G.Grütter
(2011).
Designed ankyrin repeat protein binders for the crystallization of AcrB: Plasticity of the dominant interface.
|
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J Struct Biol, 174,
269-281.
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PDB codes:
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P.D.Dixit,
and
D.Asthagiri
(2011).
Thermodynamics of ion selectivity in the KcsA K+ channel.
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J Gen Physiol, 137,
427-433.
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P.Mitra,
and
D.Pal
(2011).
Combining Bayes classification and point group symmetry under Boolean framework for enhanced protein quaternary structure inference.
|
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Structure, 19,
304-312.
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|
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|
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S.Chakrapani,
J.F.Cordero-Morales,
V.Jogini,
A.C.Pan,
D.M.Cortes,
B.Roux,
and
E.Perozo
(2011).
On the structural basis of modal gating behavior in K(+) channels.
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Nat Struct Mol Biol, 18,
67-74.
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PDB codes:
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T.A.Liu,
H.K.Chang,
and
R.C.Shieh
(2011).
Extracellular K(+) elevates outward currents through Kir2.1 channels by increasing single-channel conductance.
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Biochim Biophys Acta, 1808,
1772-1778.
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V.Babin,
C.Roland,
and
C.Sagui
(2011).
The α-sheet: A missing-in-action secondary structure?
|
| |
Proteins, 79,
937-946.
|
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W.W.Cheng,
J.G.McCoy,
A.N.Thompson,
C.G.Nichols,
and
C.M.Nimigean
(2011).
Mechanism for selectivity-inactivation coupling in KcsA potassium channels.
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Proc Natl Acad Sci U S A, 108,
5272-5277.
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PDB code:
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Y.Cao,
X.Jin,
H.Huang,
M.G.Derebe,
E.J.Levin,
V.Kabaleeswaran,
Y.Pan,
M.Punta,
J.Love,
J.Weng,
M.Quick,
S.Ye,
B.Kloss,
R.Bruni,
E.Martinez-Hackert,
W.A.Hendrickson,
B.Rost,
J.A.Javitch,
K.R.Rajashankar,
Y.Jiang,
and
M.Zhou
(2011).
Crystal structure of a potassium ion transporter, TrkH.
|
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Nature, 471,
336-340.
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PDB code:
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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.
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A.Marsico,
K.Scheubert,
A.Tuukkanen,
A.Henschel,
C.Winter,
R.Winnenburg,
and
M.Schroeder
(2010).
MeMotif: a database of linear motifs in alpha-helical transmembrane proteins.
|
| |
Nucleic Acids Res, 38,
D181-D189.
|
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A.Negoda,
E.Negoda,
and
R.N.Reusch
(2010).
Importance of oligo-R-3-hydroxybutyrates to S. lividans KcsA channel structure and function.
|
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Mol Biosyst, 6,
2249-2255.
|
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A.S.Thomson,
and
B.S.Rothberg
(2010).
Voltage-dependent inactivation gating at the selectivity filter of the MthK K+ channel.
|
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J Gen Physiol, 136,
569-579.
|
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C.Y.Lee,
W.Choi,
J.H.Han,
and
M.S.Strano
(2010).
Coherence resonance in a single-walled carbon nanotube ion channel.
|
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Science, 329,
1320-1324.
|
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|
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D.Rotem,
A.Mason,
and
H.Bayley
(2010).
Inactivation of the KcsA potassium channel explored with heterotetramers.
|
| |
J Gen Physiol, 135,
29-42.
|
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E.D.Burg,
O.Platoshyn,
I.F.Tsigelny,
B.Lozano-Ruiz,
B.K.Rana,
and
J.X.Yuan
(2010).
Tetramerization domain mutations in KCNA5 affect channel kinetics and cause abnormal trafficking patterns.
|
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Am J Physiol Cell Physiol, 298,
C496-C509.
|
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|
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E.J.Denning,
and
T.B.Woolf
(2010).
Cooperative nature of gating transitions in K(+) channels as seen from dynamic importance sampling calculations.
|
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Proteins, 78,
1105-1119.
|
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|
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|
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G.J.Bartlett,
A.Choudhary,
R.T.Raines,
and
D.N.Woolfson
(2010).
n-->pi* interactions in proteins.
|
| |
Nat Chem Biol, 6,
615-620.
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H.Wu,
A.Canfield,
J.Adhikari,
and
S.Huo
(2010).
Quantum mechanical studies on model alpha-pleated sheets.
|
| |
J Comput Chem, 31,
1216-1223.
|
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|
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H.Yu,
S.Y.Noskov,
and
B.Roux
(2010).
Two mechanisms of ion selectivity in protein binding sites.
|
| |
Proc Natl Acad Sci U S A, 107,
20329-20334.
|
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|
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I.Maslennikov,
C.Klammt,
E.Hwang,
G.Kefala,
M.Okamura,
L.Esquivies,
K.Mörs,
C.Glaubitz,
W.Kwiatkowski,
Y.H.Jeon,
and
S.Choe
(2010).
Membrane domain structures of three classes of histidine kinase receptors by cell-free expression and rapid NMR analysis.
|
| |
Proc Natl Acad Sci U S A, 107,
10902-10907.
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J.A.Cieslak,
P.J.Focia,
and
A.Gross
(2010).
Electron spin-echo envelope modulation (ESEEM) reveals water and phosphate interactions with the KcsA potassium channel.
|
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Biochemistry, 49,
1486-1494.
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PDB code:
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J.K.Lee,
and
R.M.Stroud
(2010).
Unlocking the eukaryotic membrane protein structural proteome.
|
| |
Curr Opin Struct Biol, 20,
464-470.
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J.M.Kielec,
K.G.Valentine,
and
A.J.Wand
(2010).
A method for solution NMR structural studies of large integral membrane proteins: reverse micelle encapsulation.
|
| |
Biochim Biophys Acta, 1798,
150-160.
|
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|
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K.M.Thai,
A.Windisch,
D.Stork,
A.Weinzinger,
A.Schiesaro,
R.H.Guy,
E.N.Timin,
S.Hering,
and
G.F.Ecker
(2010).
The hERG potassium channel and drug trapping: insight from docking studies with propafenone derivatives.
|
| |
ChemMedChem, 5,
436-442.
|
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K.McLuskey,
A.W.Roszak,
Y.Zhu,
and
N.W.Isaacs
(2010).
Crystal structures of all-alpha type membrane proteins.
|
| |
Eur Biophys J, 39,
723-755.
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K.R.Vinothkumar,
and
R.Henderson
(2010).
Structures of membrane proteins.
|
| |
Q Rev Biophys, 43,
65.
|
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|
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K.Yoshimura,
and
M.Sokabe
(2010).
Mechanosensitivity of ion channels based on protein-lipid interactions.
|
| |
J R Soc Interface, 7,
S307-S320.
|
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|
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L.Dai,
V.Garg,
and
M.C.Sanguinetti
(2010).
Activation of Slo2.1 channels by niflumic acid.
|
| |
J Gen Physiol, 135,
275-295.
|
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|
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|
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L.G.Cuello,
D.M.Cortes,
V.Jogini,
A.Sompornpisut,
and
E.Perozo
(2010).
A molecular mechanism for proton-dependent gating in KcsA.
|
| |
FEBS Lett, 584,
1126-1132.
|
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|
|
|
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L.G.Cuello,
V.Jogini,
D.M.Cortes,
A.C.Pan,
D.G.Gagnon,
O.Dalmas,
J.F.Cordero-Morales,
S.Chakrapani,
B.Roux,
and
E.Perozo
(2010).
Structural basis for the coupling between activation and inactivation gates in K(+) channels.
|
| |
Nature, 466,
272-275.
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PDB code:
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L.G.Cuello,
V.Jogini,
D.M.Cortes,
A.Sompornpisut,
M.D.Purdy,
M.C.Wiener,
and
E.Perozo
(2010).
Design and characterization of a constitutively open KcsA.
|
| |
FEBS Lett, 584,
1133-1138.
|
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|
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L.G.Cuello,
V.Jogini,
D.M.Cortes,
and
E.Perozo
(2010).
Structural mechanism of C-type inactivation in K(+) channels.
|
| |
Nature, 466,
203-208.
|
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M.Li,
T.Kawate,
S.D.Silberberg,
and
K.J.Swartz
(2010).
Pore-opening mechanism in trimeric P2X receptor channels.
|
| |
Nat Commun, 1,
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M.Mazzolini,
A.Marchesi,
A.Giorgetti,
and
V.Torre
(2010).
Gating in CNGA1 channels.
|
| |
Pflugers Arch, 459,
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Shagufta,
A.P.Ijzerman,
and
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(2010).
Prospective validation of a comprehensive in silico hERG model and its applications to commercial compound and drug databases.
|
| |
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M.P.Eastwood,
R.O.Dror,
and
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(2010).
Principles of conduction and hydrophobic gating in K+ channels.
|
| |
Proc Natl Acad Sci U S A, 107,
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|
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|
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A.T.Caputo,
A.P.Hill,
J.I.Vandenberg,
B.J.Smith,
and
J.M.Gulbis
(2010).
Domain reorientation and rotation of an intracellular assembly regulate conduction in Kir potassium channels.
|
| |
Cell, 141,
1018-1029.
|
|
|
PDB codes:
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|
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|
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P.J.Focke,
and
F.I.Valiyaveetil
(2010).
Studies of ion channels using expressed protein ligation.
|
| |
Curr Opin Chem Biol, 14,
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P.Sundaram,
W.M.Wells,
R.V.Mulkern,
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E.B.Bromfield,
M.Münch,
and
D.B.Orbach
(2010).
Fast human brain magnetic resonance responses associated with epileptiform spikes.
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Magn Reson Med, 64,
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R.Cervenka,
T.Zarrabi,
P.Lukacs,
and
H.Todt
(2010).
The outer vestibule of the Na+ channel-toxin receptor and modulator of permeation as well as gating.
|
| |
Mar Drugs, 8,
1373-1393.
|
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|
|
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|
|
R.S.Norton,
and
J.M.Gulbis
(2010).
Potassium channel gating: not an open and shut case.
|
| |
Proc Natl Acad Sci U S A, 107,
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|
|
|
|
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|
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S.Imai,
M.Osawa,
K.Takeuchi,
and
I.Shimada
(2010).
Structural basis underlying the dual gate properties of KcsA.
|
| |
Proc Natl Acad Sci U S A, 107,
6216-6221.
|
|
|
|
|
|
|
S.J.Stahl,
N.R.Watts,
C.Rader,
M.A.DiMattia,
R.G.Mage,
I.Palmer,
J.D.Kaufman,
J.M.Grimes,
D.I.Stuart,
A.C.Steven,
and
P.T.Wingfield
(2010).
Generation and characterization of a chimeric rabbit/human Fab for co-crystallization of HIV-1 Rev.
|
| |
J Mol Biol, 397,
697-708.
|
|
|
|
|
|
|
S.M.Sine,
H.L.Wang,
S.Hansen,
and
P.Taylor
(2010).
On the origin of ion selectivity in the Cys-loop receptor family.
|
| |
J Mol Neurosci, 40,
70-76.
|
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|
|
|
|
|
S.Weyand,
and
S.Iwata
(2010).
Biochemistry. Old gate gets a new look.
|
| |
Science, 329,
151-152.
|
|
|
|
|
|
|
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:
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|
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T.Zarrabi,
R.Cervenka,
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PDB code:
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PDB codes:
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