PDBsum entry 3lut

Membrane protein

PDB id: 3lut

Contents

Protein chains

326 a.a.

390 a.a.

Ligands

NAP

Metals

__K ×6

Waters ×86

References listed in PDB file

Key reference

Title

Structure of the full-Length shaker potassium channel kv1.2 by normal-Mode-Based X-Ray crystallographic refinement.

Authors

X.Chen, Q.Wang, F.Ni, J.Ma.

Ref.

Proc Natl Acad Sci U S A, 2010, 107, 11352-11357.

PubMed id

20534430

Abstract

Voltage-dependent potassium channels (Kv) are homotetramers composed of four voltage sensors and one pore domain. Because of high-level structural flexibility, the first mammalian Kv structure, Kv1.2 at 2.9 A, has about 37% molecular mass of the transmembrane portion not resolved. In this study, by applying a novel normal-mode-based X-ray crystallographic refinement method to the original diffraction data and structural model, we established the structure of full-length Kv1.2 in its native form. This structure offers mechanistic insights into voltage sensing. Particularly, it shows a hydrophobic layer of about 10 A at the midpoint of the membrane bilayer, which is likely the molecular basis for the observed "focused electric field" of Kv1.2 between the internal and external solutions. This work also demonstrated the potential of the refinement method in bringing up large chunks of missing densities, thus beneficial to structural refinement of many difficult systems.

Secondary reference #1

Title

Crystal structure of a mammalian voltage-Dependent shaker family k+ channel.

Authors

S.B.Long, E.B.Campbell, R.Mackinnon.

Ref.

Science, 2005, 309, 897-903. [DOI no: 10.1126/science.1116269]

PubMed id

16002581

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).

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.

The above figures are reproduced from the cited reference with permission from the AAAs

Secondary reference #2

Title

Atomic structure of a voltage-Dependent k+ channel in a lipid membrane-Like environment.

Authors

S.B.Long, X.Tao, E.B.Campbell, R.Mackinnon.

Ref.

Nature, 2007, 450, 376-382. [DOI no: 10.1038/nature06265]

PubMed id

18004376

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.

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.

The above figures are reproduced from the cited reference with permission from Macmillan Publishers Ltd