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- EMDB-5498: Structure of ABCA4, the photoreceptor-specific ATP-binding casset... -

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Basic information

Entry
Database: EMDB / ID: EMD-5498
TitleStructure of ABCA4, the photoreceptor-specific ATP-binding cassette transporter, in complex with AMPPNP
Map dataReconstruction of the ABCA4-AMPPNP complex
Sample
  • Sample: ABCA4 purified from bovine rod outer segments and supplemented with AMPPNP, a non-hydrolyzable ATP analogue
  • Protein or peptide: ABCA4
KeywordsABC transporter / ABCA subfamily / vision / photoreceptor / retinoids
Biological speciesBos taurus (cattle)
Methodsingle particle reconstruction / negative staining / Resolution: 18.9 Å
AuthorsTsybovsky Y / Orban T / Molday RS / Taylor D / Palczewski K
CitationJournal: Structure / Year: 2013
Title: Molecular organization and ATP-induced conformational changes of ABCA4, the photoreceptor-specific ABC transporter.
Authors: Yaroslav Tsybovsky / Tivadar Orban / Robert S Molday / Derek Taylor / Krzysztof Palczewski /
Abstract: ATP-binding cassette (ABC) transporters use ATP to translocate various substrates across cellular membranes. Several members of subfamily A of mammalian ABC transporters are associated with severe ...ATP-binding cassette (ABC) transporters use ATP to translocate various substrates across cellular membranes. Several members of subfamily A of mammalian ABC transporters are associated with severe health disorders, but their unusual complexity and large size have so far precluded structural characterization. ABCA4 is localized to the discs of vertebrate photoreceptor outer segments. This protein transports N-retinylidene-phosphatidylethanolamine to the outer side of disc membranes to prevent formation of toxic compounds causing macular degeneration. An 18 Å-resolution structure of ABCA4 isolated from bovine rod outer segments was determined using electron microscopy and single-particle reconstruction. Significant conformational changes in the cytoplasmic and transmembrane regions were observed upon binding of a nonhydrolyzable ATP analog and accompanied by altered hydrogen/deuterium exchange in the Walker A motif of one of the nucleotide-binding domains. These findings provide an initial view of the molecular organization and functional rearrangements for any member of the ABCA subfamily of ABC transporters.
History
DepositionSep 12, 2012-
Header (metadata) releaseSep 26, 2012-
Map releaseApr 17, 2013-
UpdateMay 22, 2013-
Current statusMay 22, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0363
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0363
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

FileDownload / File: emd_5498.map.gz / Format: CCP4 / Size: 11.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the ABCA4-AMPPNP complex
Voxel sizeX=Y=Z: 2.13 Å
Density
Contour LevelBy AUTHOR: 0.0363 / Movie #1: 0.0363
Minimum - Maximum-0.07316811 - 0.11665386
Average (Standard dev.)-0.00164775 (±0.010085)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions144144144
Spacing144144144
CellA=B=C: 306.72003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.132.132.13
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z306.720306.720306.720
α/β/γ90.00090.00090.000
start NX/NY/NZ-5029166
NX/NY/NZ106122134
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS144144144
D min/max/mean-0.0730.117-0.002

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Supplemental data

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Sample components

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Entire : ABCA4 purified from bovine rod outer segments and supplemented wi...

EntireName: ABCA4 purified from bovine rod outer segments and supplemented with AMPPNP, a non-hydrolyzable ATP analogue
Components
  • Sample: ABCA4 purified from bovine rod outer segments and supplemented with AMPPNP, a non-hydrolyzable ATP analogue
  • Protein or peptide: ABCA4

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Supramolecule #1000: ABCA4 purified from bovine rod outer segments and supplemented wi...

SupramoleculeName: ABCA4 purified from bovine rod outer segments and supplemented with AMPPNP, a non-hydrolyzable ATP analogue
type: sample / ID: 1000
Details: The total molecular weight includes estimated MW of Amphipol 8-35 bound to the protein
Oligomeric state: monomer / Number unique components: 1
Molecular weightExperimental: 400 KDa / Theoretical: 360 KDa / Method: Size exclusion chromatography

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Macromolecule #1: ABCA4

MacromoleculeName: ABCA4 / type: protein_or_peptide / ID: 1 / Name.synonym: ABCR, rim protein
Details: The total molecular weight includes estimated MW of Amphipol 8-35 bound to the protein
Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Bos taurus (cattle) / synonym: bovine / Tissue: Retina / Cell: Rod photoreceptor / Organelle: outer segment / Location in cell: outer segment disk membrane
Molecular weightExperimental: 400 KDa / Theoretical: 360 KDa

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.5
Details: 20 mM BTP, pH 7.5, 150 mM NaCl, 10% glycerol, 1 mM DTT, 1 mM AMPPNP
StainingType: NEGATIVE
Details: Grids with adsorbed protein were stained with 1% w/v uranyl acetate for 10 seconds
GridDetails: Glow discharged Cu/Pd 400 mesh grids with thin carbon support.
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 70373 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: OTHER / Tilt angle max: 45
DateApr 21, 2012
Image recordingNumber real images: 200
Tilt angle min0
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each defocus group
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 18.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider / Number images used: 38090
DetailsThe particles were selected manually

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