PDBsum entry 3efd

Immune system

PDB id: 3efd

Contents

Protein chains

211 a.a. *

215 a.a. *

30 a.a. *

Waters ×59

* Residue conservation analysis

PDB id:

3efd

Name:

Immune system

Title:

The crystal structure of the cytoplasmic domain of kcsa

Structure:

Fabl. Chain: l. Fabh. Chain: h. Kcsa. Chain: k

Source:

Mus musculus. Organism_taxid: 10090. Escherichia coli. Organism_taxid: 562

Resolution:

2.60Å R-factor: 0.230 R-free: 0.276

Authors:

S.Uysal,V.Vasquez,V.Tereshko,K.Esaki,F.A.Fellouse,S.S.Sidhu,S.Koide, E.Perozo,A.Kossiakoff

Key ref:

S.Uysal et al. (2009). Crystal structure of full-length KcsA in its closed conformation. Proc Natl Acad Sci U S A, 106, 6644-6649. PubMed id: 19346472 DOI: 10.1073/pnas.0810663106

Date:

08-Sep-08 Release date: 14-Apr-09

Protein chain

No UniProt id for this chain

Struc: 211 a.a.

Protein chain

No UniProt id for this chain

Struc: 215 a.a.

Protein chain

No UniProt id for this chain

Struc: 30 a.a.

DOI no: 10.1073/pnas.0810663106

Proc Natl Acad Sci U S A 106:6644-6649 (2009)

PubMed id: 19346472

Crystal structure of full-length KcsA in its closed conformation.

S.Uysal, V.Vásquez, V.Tereshko, K.Esaki, F.A.Fellouse, S.S.Sidhu, S.Koide, E.Perozo, A.Kossiakoff.

ABSTRACT

KcsA is a proton-activated, voltage-modulated K(+) channel that has served as the archetype pore domain in the Kv channel superfamily. Here, we have used synthetic antigen-binding fragments (Fabs) as crystallographic chaperones to determine the structure of full-length KcsA at 3.8 A, as well as that of its isolated C-terminal domain at 2.6 A. The structure of the full-length KcsA-Fab complex reveals a well-defined, 4-helix bundle that projects approximately 70 A toward the cytoplasm. This bundle promotes a approximately 15 degree bending in the inner bundle gate, tightening its diameter and shifting the narrowest point 2 turns of helix below. Functional analysis of the full-length KcsA-Fab complex suggests that the C-terminal bundle remains whole during gating. We suggest that this structure likely represents the physiologically relevant closed conformation of KcsA.

Selected figure(s)

Figure 1.
Crystal structure of FL KcsA in complex with Fab2. (A) CDR sequences of the 3 Fabs selected against FL KcsA from a “reduced genetic code” phage display library. Numbering is according to the Kabat definition (36). Gly is green; Tyr, yellow, Ser, red; and nondiversified positions, gray. (B) Crystal packing of the KcsA–Fab2 complex at 3.8 Å. KcsA is in orange, and the light and heavy chains of the Fab are in cyan (light chain) and magenta (heavy chain). (C) Simulated annealing composite-omit 2Fo-Fc map (contoured at 1σ) of FL KcsA. The red trace shows the fitted model as Cα tracing. (D) The final model of the KcsA–Fab complex. Three regions distinguished by the level of symmetry are highlighted: the fourfold TM segments (blue color; residues 22–117), the twofold bulge helix (red color; residues 118–135), and the fourfold distal C-terminal bundle (gray color; residues 136–158). (E and F) Experimental (E) EPR mobility and (F) NiEdda accessibility parameters (11) from membrane-reconstituted FL KcsA, mapped on the crystal model of FL KcsA. The scales represent a linear increase in local dynamics (E) and accessibility to the aqueous media (F).

Figure 2.
Influence of the C-terminal truncation on the conformation of the inner helix bundle gate. (A) Cα superposition of the high-resolution truncated KcsA structure (1K4C; red ribbons) with FL KcsA (blue ribbons). Inset highlights the splaying out of the inner helix bundle gate between residues 110 and 115, resulting in a 15° outward tilting. (B) Radius profile (calculated with the program HOLE; ref. 29) of truncated (red) and FL KcsA (blue).

Figures were selected by the author.