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- EMDB-6087: Single particle cryo-EM reconstruction of ABC transporter TmrAB -

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Basic information

Entry
Database: EMDB / ID: EMD-6087
TitleSingle particle cryo-EM reconstruction of ABC transporter TmrAB
Map data3D reconstruction of TmrAB
Sample
  • Sample: TmrAB
  • Protein or peptide: ABC exporter
KeywordsABC transporter / TmrAB
Function / homology
Function and homology information


ABC-type transporter activity / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Multidrug resistance ABC transporter ATP-binding and permease protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.0 Å
AuthorsKim JM / Wu S / Tomasiak T / Mergel C / Winter MB / Stiller S / Robles-Colmanares Y / Stroud RM / Tampe R / Craik CS / Cheng Y
CitationJournal: Nature / Year: 2015
Title: Subnanometre-resolution electron cryomicroscopy structure of a heterodimeric ABC exporter.
Authors: JungMin Kim / Shenping Wu / Thomas M Tomasiak / Claudia Mergel / Michael B Winter / Sebastian B Stiller / Yaneth Robles-Colmanares / Robert M Stroud / Robert Tampé / Charles S Craik / Yifan Cheng /
Abstract: ATP-binding cassette (ABC) transporters translocate substrates across cell membranes, using energy harnessed from ATP binding and hydrolysis at their nucleotide-binding domains. ABC exporters are ...ATP-binding cassette (ABC) transporters translocate substrates across cell membranes, using energy harnessed from ATP binding and hydrolysis at their nucleotide-binding domains. ABC exporters are present both in prokaryotes and eukaryotes, with examples implicated in multidrug resistance of pathogens and cancer cells, as well as in many human diseases. TmrAB is a heterodimeric ABC exporter from the thermophilic Gram-negative eubacterium Thermus thermophilus; it is homologous to various multidrug transporters and contains one degenerate site with a non-catalytic residue next to the Walker B motif. Here we report a subnanometre-resolution structure of detergent-solubilized TmrAB in a nucleotide-free, inward-facing conformation by single-particle electron cryomicroscopy. The reconstructions clearly resolve characteristic features of ABC transporters, including helices in the transmembrane domain and nucleotide-binding domains. A cavity in the transmembrane domain is accessible laterally from the cytoplasmic side of the membrane as well as from the cytoplasm, indicating that the transporter lies in an inward-facing open conformation. The two nucleotide-binding domains remain in contact via their carboxy-terminal helices. Furthermore, comparison between our structure and the crystal structures of other ABC transporters suggests a possible trajectory of conformational changes that involves a sliding and rotating motion between the two nucleotide-binding domains during the transition from the inward-facing to outward-facing conformations.
History
DepositionSep 7, 2014-
Header (metadata) releaseOct 8, 2014-
Map releaseNov 5, 2014-
UpdateJan 21, 2015-
Current statusJan 21, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.5
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 5.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_6087.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D reconstruction of TmrAB
Voxel sizeX=Y=Z: 3.74 Å
Density
Contour LevelBy AUTHOR: 5.5 / Movie #1: 5.5
Minimum - Maximum-4.54654741 - 15.486992839999999
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-32-32-32
Dimensions646464
Spacing646464
CellA=B=C: 239.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.743.743.74
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z239.360239.360239.360
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ969680
MAP C/R/S123
start NC/NR/NS-32-32-32
NC/NR/NS646464
D min/max/mean-4.54715.4870.000

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Supplemental data

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Sample components

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Entire : TmrAB

EntireName: TmrAB
Components
  • Sample: TmrAB
  • Protein or peptide: ABC exporter

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Supramolecule #1000: TmrAB

SupramoleculeName: TmrAB / type: sample / ID: 1000 / Details: single particle; sample was monodisperse / Oligomeric state: heterodimer / Number unique components: 1
Molecular weightExperimental: 135 KDa / Theoretical: 135 KDa

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Macromolecule #1: ABC exporter

MacromoleculeName: ABC exporter / type: protein_or_peptide / ID: 1 / Name.synonym: TmrAB / Number of copies: 1 / Oligomeric state: heterodimer / Recombinant expression: Yes
Source (natural)Organism: Thermus thermophilus (bacteria) / synonym: thermophilic Gram-negative eubacterium
Molecular weightExperimental: 135 KDa / Theoretical: 135 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Multidrug resistance ABC transporter ATP-binding and permease protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

GridDetails: Quantifoil grid
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.12 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 80000
Sample stageSpecimen holder: CT3500 / Specimen holder model: GATAN LIQUID NITROGEN
DateJan 1, 2012
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k)
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: each particle
Final reconstructionResolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 36000

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