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PDBsum entry 2r9r
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Membrane protein, transport protein
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PDB id
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2r9r
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Contents |
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326 a.a.
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386 a.a.
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363 a.a.
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References listed in PDB file
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Key reference
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Title
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Atomic structure of a voltage-Dependent k+ channel in a lipid membrane-Like environment.
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Authors
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S.B.Long,
X.Tao,
E.B.Campbell,
R.Mackinnon.
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Ref.
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Nature, 2007,
450,
376-382.
[DOI no: ]
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PubMed id
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Abstract
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Voltage-dependent K+ (Kv) channels repolarize the action potential in neurons
and muscle. This type of channel is gated directly by membrane voltage through
protein domains known as voltage sensors, which are molecular voltmeters that
read the membrane voltage and regulate the pore. Here we describe the structure
of a chimaeric voltage-dependent K+ channel, which we call the 'paddle-chimaera
channel', in which the voltage-sensor paddle has been transferred from Kv2.1 to
Kv1.2. Crystallized in complex with lipids, the complete structure at 2.4
ångström resolution reveals the pore and voltage sensors embedded in a
membrane-like arrangement of lipid molecules. The detailed structure, which can
be compared directly to a large body of functional data, explains charge
stabilization within the membrane and suggests a mechanism for voltage-sensor
movements and pore gating.
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Figure 4.
Figure 4: Details of the voltage sensor. a, Stereo
representation of a voltage sensor and the S4–S5 linker helix
(white  -carbon
trace) in relation to the pore (cyan -carbon
trace). The view is from the side (extracellular solution
'above' and intracellular solution 'below'). Select residues are
shown as sticks and are coloured as indicated in the text. b,
Voltage sensor and S4–S5 linker helix (white -carbon
trace) viewed from the pore. Yellow side chains from a and water
molecules are now coloured according to atom type (yellow,
carbon; blue, nitrogen; red, oxygen; green, phenylalanine 233;
cyan, water). Ionized hydrogen bonds between basic and acidic
residues are indicated by dashed yellow lines.
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Figure 6.
Figure 6: Hypothetical mechanism of voltage-dependent gating.
a, Representation of the voltage sensor and S4–S5 linker helix
from the crystal structure (open conformation). Helices are
drawn as ribbons. The view is from the pore, as in Fig. 5, with
the extracellular solution 'above' and the intracellular
solution 'below'. The gating charges (R1 to K5) are shown as
blue sticks. Negatively charged residues in the external and
internal clusters are red; the phenylalanine in the middle is
green. The positively charged residues reach 'outward' towards
the extracellular solution. b, Depiction of a hypothetical
closed conformation of the voltage sensor. The S1 and S2 helices
are hypothesized to maintain their position, whereas the S3–S4
paddle has moved inward. The positive charges on S4 now reach
towards the intracellular solution, and are stabilized through
interactions with the internal negative cluster. The -carbon
position of R1 is adjacent to the phenylalanine, representing a
displacement perpendicular to the plane of the membrane of
approximately 15 Å relative to its location in the open
structure (a). The inward displacement of the S4 helix pushes
down on the N-terminal end of the S4–S5 linker helix, causing
it to tilt towards the intracellular side and to close the pore.
c, Depiction of the open conformation of the S4–S5 linker
helices and pore from the crystal structure. The S4–S5 linker
helices (orange) rest on the S6 helices (blue ribbons) near the
intracellular side. d, A hypothetical model of the S4–S5
linker helices and pore in a closed conformation based on the
crystal structure of a closed potassium channel pore (KcsA, PDB
accession number, 1K4C)^18.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2007,
450,
376-382)
copyright 2007.
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Secondary reference #1
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Title
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Crystal structure of a mammalian voltage-Dependent shaker family k+ channel.
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Authors
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S.B.Long,
E.B.Campbell,
R.Mackinnon.
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Ref.
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Science, 2005,
309,
897-903.
[DOI no: ]
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PubMed id
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Figure 3.
Fig. 3. Comparison of the pore of three K+ channels.
Stereoviews of the Kv1.2 K+ channel (red, residues 325 to 418),
the KcsA K+ channel (gray, PDB ID 1K4C [PDB]
, residues 26 to 119), and the KvAP K+ channel (blue, PDB ID
1ORQ [PDB]
, residues 147 to 240) are shown in (A), with two subunits
viewed from the side and in (B), with four subunits viewed along
the pore axis from the intracellular solution. Channels were
superimposed by aligning main-chain atoms of the selectivity
filter and pore helices. Outer and inner helices refer to S5 and
S6 in Kv1.2. The inner helices form the bundle crossing at the
narrowest point, as shown in (B). An asterisk indicates the
position of the Pro-Val-Pro sequence on the inner (S6) helix of
Kv1.2 and also corresponds to the position of Gly 229 in KvAP.
The figure was generated with Molscript (54).
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Figure 5.
Fig. 5. Electron density of the ß subunit NADP+ cofactor
and active-site cleft. (A) The omit electron density for the
NADP+ cofactor bound at the active site of the ß subunit.
The F[o] - F[c] simulated annealing omit electron density at 2.9
Å resolution is contoured at 4  (blue mesh) and
shown with the NADP+ molecule drawn as red sticks. (B) "Extra"
density in the active-site cleft of the ß subunit. A 2F[o]
- F[c] electron density map to 2.9 Å resolution and
contoured at 0.8 is drawn in a
pocket above the catalytic residues. The NADP+ cofactor is shown
as red sticks.
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The above figures are
reproduced from the cited reference
with permission from the AAAs
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