[English] 日本語
Yorodumi- PDB-7qks: Cryo-EM structure of ABC transporter STE6-2p from Pichia pastoris... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qks | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of ABC transporter STE6-2p from Pichia pastoris in apo conformation at 3.1 A resolution | ||||||
Components | Plasma membrane ATP-binding cassette transporter required for the export of a-factor | ||||||
Keywords | TRANSPORT PROTEIN / ABC transporter / ABCB / MDR / membrane protein / Pichia pastoris | ||||||
Function / homology | Function and homology information ABC-type transporter activity / ATP hydrolysis activity / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Komagataella phaffii CBS 7435 (fungus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
Authors | Schleker, E.S.M. / Reinhart, C. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2022 Title: Structural and functional investigation of ABC transporter STE6-2p from reveals unexpected interaction with sterol molecules. Authors: E Sabine M Schleker / Sabine Buschmann / Hao Xie / Sonja Welsch / Hartmut Michel / Christoph Reinhart / Abstract: Adenosine triphosphate (ATP)-binding cassette (ABC) transporters are multidomain transmembrane proteins, which facilitate the transport of various substances across cell membranes using energy ...Adenosine triphosphate (ATP)-binding cassette (ABC) transporters are multidomain transmembrane proteins, which facilitate the transport of various substances across cell membranes using energy derived from ATP hydrolysis. They are important drug targets since they mediate decreased drug susceptibility during pharmacological treatments. For the methylotrophic yeast , a model organism that is a widely used host for protein expression, the role and function of its ABC transporters is unexplored. In this work, we investigated the ABC-B transporter STE6-2p. Functional investigations revealed that STE6-2p is capable of transporting rhodamines in vivo and is active in the presence of verapamil and triazoles in vitro. A phylogenetic analysis displays homology among multidrug resistance (MDR) transporters from pathogenic fungi to human ABC-B transporters. Further, we present high-resolution single-particle electron cryomicroscopy structures of an ABC transporter from in the apo conformation (3.1 Å) and in complex with verapamil and adenylyl imidodiphosphate (AMP-PNP) (3.2 Å). An unknown density between transmembrane helices 4, 5, and 6 in both structures suggests the presence of a sterol-binding site of unknown function. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7qks.cif.gz | 220.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7qks.ent.gz | 170.1 KB | Display | PDB format |
PDBx/mmJSON format | 7qks.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qks_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7qks_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7qks_validation.xml.gz | 45.9 KB | Display | |
Data in CIF | 7qks_validation.cif.gz | 69 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qk/7qks ftp://data.pdbj.org/pub/pdb/validation_reports/qk/7qks | HTTPS FTP |
-Related structure data
Related structure data | 14050MC 7qkrC C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 144974.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Komagataella phaffii CBS 7435 (fungus) Strain: ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1 Gene: STE6-2, PP7435_Chr1-1574 / Production host: Komagataella phaffii CBS 7435 (fungus) / Strain (production host): X-33 / References: UniProt: F2QQK6 |
---|---|
#2: Chemical | ChemComp-9Z9 / ( |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: STE6-2p / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: Komagataella phaffii CBS 7435 (fungus) / Strain: X33 |
Source (recombinant) | Organism: Komagataella phaffii CBS 7435 (fungus) / Strain: X33 |
Buffer solution | pH: 8 |
Specimen | Conc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2.1 nm / Nominal defocus min: 1.1 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
---|---|
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 89358 / Symmetry type: POINT |