PDBsum entry 3b5x

Membrane protein

PDB id: 3b5x

Contents

Protein chains

572 a.a.*

* C-alpha coords only

References listed in PDB file

Key reference

Title

Flexibility in the abc transporter msba: alternating access with a twist.

Authors

A.Ward, C.L.Reyes, J.Yu, C.B.Roth, G.Chang.

Ref.

Proc Natl Acad Sci U S A, 2007, 104, 19005-19010. [DOI no: 10.1073/pnas.0709388104]

PubMed id

18024585

Abstract

ATP-binding cassette (ABC) transporters are integral membrane proteins that translocate a wide variety of substrates across cellular membranes and are conserved from bacteria to humans. Here we compare four x-ray structures of the bacterial ABC lipid flippase, MsbA, trapped in different conformations, two nucleotide-bound structures and two in the absence of nucleotide. Comparison of the nucleotide-free conformations of MsbA reveals a flexible hinge formed by extracellular loops 2 and 3. This hinge allows the nucleotide-binding domains to disassociate while the ATP-binding half sites remain facing each other. The binding of the nucleotide causes a packing rearrangement of the transmembrane helices and changes the accessibility of the transporter from cytoplasmic (inward) facing to extracellular (outward) facing. The inward and outward openings are mediated by two different sets of transmembrane helix interactions. Altogether, the conformational changes between these structures suggest that large ranges of motion may be required for substrate transport.

Figure 1.
Fig. 1. Stereoviews of three conformations of MsbA. (A) Nucleotide bound. (B) Open apo. (C) Closed apo. One monomer in each model is colored with a rainbow gradient (N terminus is blue, C terminus is red), and the other is white. TM helices (TM1–TM6), extracellular loops (EL1–EL3), and intracellular helices (IH1–IH2) are labeled accordingly. AMPPNP molecules are displayed as blue sticks in the nucleotide-bound structure. In all structures, TM4/TM5/IH2 (yellow and orange) associates with the opposite monomer in a conserved manner.

Figure 5.
Fig. 5. Summary of conformational changes in MsbA. (A) Conformational changes within the MsbA dimer alter the accessibility to the internal chamber from inward to outward facing. For clarity, only TM helices (labeled 1–6) of one monomer (cyan) are shown inside a surface rendering of the dimer. The open and closed apo conformations form an inward-facing V between TM4/TM5 and TM3/TM6 (red asterisk). The nucleotide-bound conformation (MsbA-AMPPNP) forms an outward-facing V between TM3/TM6 and TM1/TM2, just above the elbow helix (black asterisk). Upon nucleotide binding, TM4/TM5/IH2 moves, causing TM3/TM6 to split away from TM1/TM2, which results in an outward-facing conformation. Both inward- and outward-facing conformations are mediated by intramolecular interactions within a single monomer, but by different sets of helices. (B) Simplified cartoon model illustrating the points above. The relative position of each TM helix is labeled with a number (one monomer in white and the other in gray). The arrows illustrate the motions required to go to the next state. (C) Top-down view of NBDs (one monomer shown in white and the other in gray). IH1 (green) and IH2 (yellow) from both monomers are shown. In the absence of nucleotide (apo), the NBDs are in similar orientations with the ATP-binding half-sites (LSGGQ and P-loop) facing each other; the P-loops (red) are roughly aligned (dashed lines) with one another across the dimer interface. Upon nucleotide binding (AMPPNP - magenta), the canonical ATP sandwich is formed, aligning the nucleotide between the LSGGQ and P-loop. IH1 tracks with the cis-monomer, whereas IH2 tracks with the trans-monomer. The motion of the NBDs from closed-apo- to nucleotide-bound transmits a structural change (described above) to the TMs via IH1 and IH2, resulting in an outward-facing conformation.