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- EMDB-1098: Three-dimensional structure of a bacterial oxalate transporter. -

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Basic information

Entry
Database: EMDB / ID: EMD-1098
TitleThree-dimensional structure of a bacterial oxalate transporter.
Map dataThis is an image of the bacterial oxalate transporter(OxlT)in the oxalate-bound, "closed" state. OxlT is a representative member of the Major Facilitator Superfamily (MFS).
Sample
  • Sample: Oxalate Transporter
  • Protein or peptide: oxalate transporter
Biological speciesOxalobacter formigenes (bacteria)
Methodelectron crystallography / cryo EM / Resolution: 6.5 Å
AuthorsHirai T / Heymann JAW / Shi D / Sarker R / Maloney PC / Subramaniam S
CitationJournal: Nat Struct Biol / Year: 2002
Title: Three-dimensional structure of a bacterial oxalate transporter.
Authors: Teruhisa Hirai / Jürgen A W Heymann / Dan Shi / Rafiquel Sarker / Peter C Maloney / Sriram Subramaniam /
Abstract: The major facilitator superfamily (MFS) represents one of the largest classes of evolutionarily related membrane transporter proteins. Here we present the three-dimensional structure at 6.5 A ...The major facilitator superfamily (MFS) represents one of the largest classes of evolutionarily related membrane transporter proteins. Here we present the three-dimensional structure at 6.5 A resolution of a bacterial member of this superfamily, OxlT. The structure, derived from an electron crystallographic analysis of two-dimensional crystals, reveals that the 12 helices in the OxlT molecule are arranged around a central cavity, which is widest at the center of the membrane. The helices divide naturally into three groups: a peripheral set comprising helices 3, 6, 9 and 12; a second set comprising helices 2, 5, 8 and 11 that faces the central substrate transport pathway across most of the length of the membrane; and a third set comprising helices 1, 4, 7 and 10 that participate in the pathway either on the cytoplasmic side (4 and 10) or on the periplasmic side (1 and 7). Overall, the architecture of the protein is remarkably symmetric, providing a compelling molecular explanation for the ability of such transporters to carry out bi-directional substrate transport.
History
DepositionAug 23, 2004-
Header (metadata) releaseOct 6, 2004-
Map releaseOct 6, 2004-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 66
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 66
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1098.gif

Downloads & links

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Map

FileDownload / File: emd_1098.map.gz / Format: CCP4 / Size: 3.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is an image of the bacterial oxalate transporter(OxlT)in the oxalate-bound, "closed" state. OxlT is a representative member of the Major Facilitator Superfamily (MFS).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.55 Å/pix.
x 157 pix.
= 100. Å		0.53 Å/pix.
x 65 pix.
= 79. Å		0.55 Å/pix.
x 86 pix.
= 100.3 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 0.5511 Å / Y: 0.52667 Å / Z: 0.54945 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 54.0 / Movie #1: 66
Minimum - Maximum-162.380218509999992 - 256.0
Average (Standard dev.)5.49867582 (±48.494132999999998)
SymmetrySpace group: 18
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin1481-78
Dimensions6586157
Spacing150182182
CellA: 100.30002 Å / B: 79.00005 Å / C: 100.000084 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.55109890109890.526666666666670.54945054945055
M x/y/z182150182
origin x/y/z0.0000.0000.000
length x/y/z100.30079.000100.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-96-56-288
NX/NY/NZ192112576
MAP C/R/S123
start NC/NR/NS8114-78
NC/NR/NS8665157
D min/max/mean-162.380256.0005.499

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Supplemental data

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Sample components

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Entire : Oxalate Transporter

EntireName: Oxalate Transporter
Components
  • Sample: Oxalate Transporter
  • Protein or peptide: oxalate transporter

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Supramolecule #1000: Oxalate Transporter

SupramoleculeName: Oxalate Transporter / type: sample / ID: 1000 / Number unique components: 1

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Macromolecule #1: oxalate transporter

MacromoleculeName: oxalate transporter / type: protein_or_peptide / ID: 1 / Name.synonym: OxlT
Details: Oxalate(-ooc-coo-) is believed to be bound in the central cavity of OxlT in this crystal form. Endogenous E.coli lipids and added synthetic lipids are expected to be present in this two ...Details: Oxalate(-ooc-coo-) is believed to be bound in the central cavity of OxlT in this crystal form. Endogenous E.coli lipids and added synthetic lipids are expected to be present in this two dimensional crystal. No detectable density for lipid or oxalate is observed at current resolution.
Recombinant expression: Yes
Source (natural)Organism: Oxalobacter formigenes (bacteria) / Location in cell: cell membrane
Molecular weightExperimental: 44 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pBluescript II SKplus and pMS421

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state2D array

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Sample preparation

GridDetails: 400 mesh Cu grid
VitrificationCryogen name: NITROGEN / Chamber temperature: 77 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: MRC plunger

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Electron microscopy

MicroscopeFEI TECNAI F30
TemperatureMin: 90 K / Max: 95 K
Alignment procedureLegacy - Astigmatism: astigmatism was corrected at 200,000 times magnification
DetailsTecnai12, 120KV with tungsten filament was also used at early stage. Floodbeam was also used for some images as illumination mode.
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 47 / Average electron dose: 10 e/Å2
Details: The best images were selected by optical diffraction.
Od range: 0.5 / Bits/pixel: 10
Tilt angle min0
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 57000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.1 µm / Nominal magnification: 59000
Sample stageSpecimen holder: side entry / Specimen holder model: GATAN LIQUID NITROGEN / Tilt angle max: 45 / Tilt series - Axis1 - Min angle: 0 ° / Tilt series - Axis1 - Max angle: 45 °
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

DetailsSpecimens were either embedded in 3.5% trehalose or prepared as frozen-hydrated specimens.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: OTHER / Software - Name: MRC
Details: Amplitudes were scaled with respect to reference amplitudes from the helix model.
Crystal parametersUnit cell - A: 100.3 Å / Unit cell - B: 79 Å / Unit cell - C: 100 Å / Unit cell - γ: 90 ° / Unit cell - α: 90 ° / Unit cell - β: 90 ° / Plane group: P 2 21 21
CTF correctionDetails: ctfsearch or ttrefine on each image

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