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- EMDB-1593: Electron crystallographic reconstruction of human copper transpor... -

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Basic information

Entry
Database: EMDB / ID: EMD-1593
TitleElectron crystallographic reconstruction of human copper transporter (hCTR1).
Map dataVolume map of human copper transporter (hCTR1) metal free.
Sample
  • Sample: human copper transporter hCTR1
  • Protein or peptide: hCTR1
KeywordsCryo-EM / electron crystallography / 2D-crystal / membrane protein / copper
Function / homology
Function and homology information


silver ion transmembrane transporter activity / plasma membrane copper ion transport / Metal ion SLC transporters / silver ion transmembrane transport / copper ion transmembrane transporter activity / copper ion import / vascular endothelial growth factor receptor-2 signaling pathway / copper ion transport / xenobiotic transport / xenobiotic transmembrane transporter activity ...silver ion transmembrane transporter activity / plasma membrane copper ion transport / Metal ion SLC transporters / silver ion transmembrane transport / copper ion transmembrane transporter activity / copper ion import / vascular endothelial growth factor receptor-2 signaling pathway / copper ion transport / xenobiotic transport / xenobiotic transmembrane transporter activity / intercalated disc / intracellular copper ion homeostasis / establishment of localization in cell / recycling endosome membrane / protein complex oligomerization / late endosome membrane / early endosome membrane / basolateral plasma membrane / angiogenesis / apical plasma membrane / copper ion binding / identical protein binding / plasma membrane
Similarity search - Function
Ctr copper transporter / Ctr copper transporter family
Similarity search - Domain/homology
High affinity copper uptake protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodelectron crystallography / cryo EM / negative staining / Resolution: 7.0 Å
AuthorsDeFeo CJ / Aller SG / Siluvai GS / Blackburn NJ / Unger VM
CitationJournal: Proc Natl Acad Sci U S A / Year: 2009
Title: Three-dimensional structure of the human copper transporter hCTR1.
Authors: Christopher J De Feo / Stephen G Aller / Gnana S Siluvai / Ninian J Blackburn / Vinzenz M Unger /
Abstract: Copper uptake proteins (CTRs), mediate cellular acquisition of the essential metal copper in all eukaryotes. Here, we report the structure of the human CTR1 protein solved by electron crystallography ...Copper uptake proteins (CTRs), mediate cellular acquisition of the essential metal copper in all eukaryotes. Here, we report the structure of the human CTR1 protein solved by electron crystallography to an in plane resolution of 7 A. Reminiscent of the design of traditional ion channels, trimeric hCTR1 creates a pore that stretches across the membrane bilayer at the interface between the subunits. Assignment of the helices identifies the second transmembrane helix as the key element lining the pore, and reveals how functionally important residues on this helix could participate in Cu(I)-coordination during transport. Aligned with and sealing both ends of the pore, extracellular and intracellular domains of hCTR1 appear to provide additional metal binding sites. Consistent with the existence of distinct metal binding sites, we demonstrate that hCTR1 stably binds 2 Cu(I)-ions through 3-coordinate Cu-S bonds, and that mutations in one of these putative binding sites results in a change of coordination chemistry.
History
DepositionJan 23, 2009-
Header (metadata) releaseFeb 25, 2009-
Map releaseApr 1, 2009-
UpdateSep 25, 2013-
Current statusSep 25, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 70
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 70
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 95
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1593.gif

Downloads & links

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Map

FileDownload / File: emd_1593.map.gz / Format: CCP4 / Size: 22.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVolume map of human copper transporter (hCTR1) metal free.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1 Å/pix.
x 401 pix.
= 400. Å		1.01 Å/pix.
x 123 pix.
= 89. Å		1.01 Å/pix.
x 123 pix.
= 89. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 1.01136 Å / Y: 1.01136 Å / Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 75.0 / Movie #1: 70
Minimum - Maximum-211.531204220000006 - 250.0
Average (Standard dev.)-2.75661373 (±31.055322650000001)
SymmetrySpace group: 177
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-17-17-200
Dimensions123123401
Spacing8888400
CellA: 88.99969 Å / B: 88.99969 Å / C: 400.0 Å
α: 90.0 ° / β: 90.0 ° / γ: 120.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.01136363636361.01136363636361
M x/y/z8888400
origin x/y/z0.0000.0000.000
length x/y/z89.00089.000400.000
α/β/γ90.00090.000120.000
start NX/NY/NZ-17-17-200
NX/NY/NZ123123401
MAP C/R/S213
start NC/NR/NS-17-17-200
NC/NR/NS123123401
D min/max/mean-211.531250.000-2.757

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Supplemental data

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Sample components

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Entire : human copper transporter hCTR1

EntireName: human copper transporter hCTR1
Components
  • Sample: human copper transporter hCTR1
  • Protein or peptide: hCTR1

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Supramolecule #1000: human copper transporter hCTR1

SupramoleculeName: human copper transporter hCTR1 / type: sample / ID: 1000 / Oligomeric state: trimer / Number unique components: 1
Molecular weightTheoretical: 66 KDa

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Macromolecule #1: hCTR1

MacromoleculeName: hCTR1 / type: protein_or_peptide / ID: 1 / Name.synonym: copper transporter / Number of copies: 3 / Oligomeric state: trimer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Location in cell: Plasma Membrane
Molecular weightTheoretical: 66 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus) / Recombinant plasmid: pPic3.5
SequenceUniProtKB: High affinity copper uptake protein 1

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingelectron crystallography
Aggregation state2D array

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Sample preparation

Concentration0.37 mg/mL
BufferpH: 7.4 / Details: 10mM MOPS, 280mM NaCl, 2.0 mM EDTA
StainingType: NEGATIVE / Details: none
GridDetails: 300 mesh molybdenum grids
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 93 K / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: Home built plunger. no special treatment
Method: Blot for 5 seconds before plunging
Detailsgrown by dialysis
Crystal formationDetails: grown by dialysis

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureMin: 93 K / Max: 93 K / Average: 93 K
Alignment procedureLegacy - Astigmatism: 230,000 times magnification
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7.0 µm / Number real images: 58 / Average electron dose: 10 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Gatan Side Entry / Specimen holder model: GATAN LIQUID NITROGEN / Tilt angle min: 1.2 / Tilt angle max: 46.2 / Tilt series - Axis1 - Min angle: 1.2 ° / Tilt series - Axis1 - Max angle: 46.2 °
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: OTHER / Software - Name: MRC
Crystal parametersUnit cell - A: 89 Å / Unit cell - B: 89 Å / Unit cell - C: 400 Å / Unit cell - γ: 120 ° / Unit cell - α: 90 ° / Unit cell - β: 90 ° / Plane group: P 6 2 2
CTF correctionDetails: Each image

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