PDBsum entry 3wmg

Transport protein/inhibitor

PDB id: 3wmg

Contents

Protein chains

589 a.a.

18 a.a.

Ligands

DMU ×5

TRS

Waters ×101

PDB id:

3wmg

Name:

Transport protein/inhibitor

Title:

Crystal structure of an inward-facing eukaryotic abc multidrug transporter g277v/a278v/a279v mutant in complex with an cyclic peptide inhibitor, acap

Structure:

Atp-binding cassette, sub-family b, member 1. Chain: a. Fragment: tmd and nbd domain, unp residues 93-696. Engineered: yes. Mutation: yes. Anti-cmabcb1 peptide. Chain: b. Engineered: yes

Source:

Cyanidioschyzon merolae. Organism_taxid: 45157. Gene: cyme_cmd148c. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932. Synthetic: yes. Other_details: selected by the rapid system protocol

Resolution:

2.40Å R-factor: 0.220 R-free: 0.246

Authors:

A.Kodan,T.Yamaguchi,T.Nakatsu,K.Sakiyama,C.J.Hipolito,A.Fujioka, R.Hirokane,K.Ikeguchi,B.Watanabe,J.Hirtake,Y.Kimura,H.Suga,K.Ueda, H.Kato

Key ref:

A.Kodan et al. (2014). Structural basis for gating mechanisms of a eukaryotic P-glycoprotein homolog. Proc Natl Acad Sci U S A, 111, 4049-4054. PubMed id: 24591620 DOI: 10.1073/pnas.1321562111

Date:

18-Nov-13 Release date: 30-Apr-14

Protein chain

M1VAN7  (M1VAN7_CYAM1) -  Probable ATP-dependent transporter ycf16 from Cyanidioschyzon merolae (strain NIES-3377 / 10D)

Seq: 696 a.a.

Struc: 589 a.a.*

Protein chain

No UniProt id for this chain

Struc: 17 a.a.

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DOI no: 10.1073/pnas.1321562111

Proc Natl Acad Sci U S A 111:4049-4054 (2014)

PubMed id: 24591620

Structural basis for gating mechanisms of a eukaryotic P-glycoprotein homolog.

A.Kodan, T.Yamaguchi, T.Nakatsu, K.Sakiyama, C.J.Hipolito, A.Fujioka, R.Hirokane, K.Ikeguchi, B.Watanabe, J.Hiratake, Y.Kimura, H.Suga, K.Ueda, H.Kato.

ABSTRACT

P-glycoprotein is an ATP-binding cassette multidrug transporter that actively transports chemically diverse substrates across the lipid bilayer. The precise molecular mechanism underlying transport is not fully understood. Here, we present crystal structures of a eukaryotic P-glycoprotein homolog, CmABCB1 from Cyanidioschyzon merolae, in two forms: unbound at 2.6-Å resolution and bound to a unique allosteric inhibitor at 2.4-Å resolution. The inhibitor clamps the transmembrane helices from the outside, fixing the CmABCB1 structure in an inward-open conformation similar to the unbound structure, confirming that an outward-opening motion is required for ATP hydrolysis cycle. These structures, along with site-directed mutagenesis and transporter activity measurements, reveal the detailed architecture of the transporter, including a gate that opens to extracellular side and two gates that open to intramembranous region and the cytosolic side. We propose that the motion of the nucleotide-binding domain drives those gating apparatuses via two short intracellular helices, IH1 and IH2, and two transmembrane helices, TM2 and TM5.