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- EMDB-50251: Human choline transporter-like protein 1 (hCTL1/SLC44A1) in peptidisc -

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Basic information

Entry
Database: EMDB / ID: EMD-50251
TitleHuman choline transporter-like protein 1 (hCTL1/SLC44A1) in peptidisc
Map dataNU refinement
Sample
  • Organelle or cellular component: Choline transporter-like protein 1 (hCTL1) in peptidisc
    • Protein or peptide: Choline transporter-like protein 1
KeywordsCholine transporter-like family / CTL / MEMBRANE PROTEIN
Function / homology
Function and homology information


ethanolamine transport / ethanolamine transmembrane transporter activity / Choline catabolism / : / choline catabolic process / choline transmembrane transporter activity / phosphatidylcholine biosynthetic process / choline transport / antiporter activity / Synthesis of PC ...ethanolamine transport / ethanolamine transmembrane transporter activity / Choline catabolism / : / choline catabolic process / choline transmembrane transporter activity / phosphatidylcholine biosynthetic process / choline transport / antiporter activity / Synthesis of PC / transport across blood-brain barrier / transmembrane transport / mitochondrial outer membrane / mitochondrion / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
Choline transporter-like / Plasma-membrane choline transporter
Similarity search - Domain/homology
Choline transporter-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsDriller JH / Pedersen BP
Funding support Denmark, European Union, 2 items
OrganizationGrant numberCountry
LundbeckfondenR380-2021-1207 Denmark
H2020 Marie Curie Actions of the European Commission890822European Union
CitationJournal: To Be Published
Title: To be announced
Authors: Driller JH / Pedersen BP
History
DepositionMay 7, 2024-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateJul 31, 2024-
Current statusJul 31, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50251.png

Downloads & links

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Map

FileDownload / File: emd_50251.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNU refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 400 pix.
= 258.8 Å		0.65 Å/pix.
x 400 pix.
= 258.8 Å		0.65 Å/pix.
x 400 pix.
= 258.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.647 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.5052801 - 0.8460851
Average (Standard dev.)-0.001194088 (±0.019060673)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 258.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: map from local refinement

Fileemd_50251_additional_1.map
Annotationmap from local refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: sharpened map

Fileemd_50251_additional_2.map
Annotationsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_50251_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_50251_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Choline transporter-like protein 1 (hCTL1) in peptidisc

EntireName: Choline transporter-like protein 1 (hCTL1) in peptidisc
Components
  • Organelle or cellular component: Choline transporter-like protein 1 (hCTL1) in peptidisc
    • Protein or peptide: Choline transporter-like protein 1

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Supramolecule #1: Choline transporter-like protein 1 (hCTL1) in peptidisc

SupramoleculeName: Choline transporter-like protein 1 (hCTL1) in peptidisc
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Choline transporter-like protein 1

MacromoleculeName: Choline transporter-like protein 1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGCCSSASSA AQSSKREWKP LEDRSCTDIP WLLLFILFCI GMGFICGFSI ATGAAARLVS GYDSYGNICG QKNTKLEAIP NSGMDHTQRK YVFFLDPCNL DLINRKIKSV ALCVAACPRQ ELKTLSDVQK FAEINGSALC SYNLKPSEYT TSPKSSVLCP KLPVPASAPI ...String:
MGCCSSASSA AQSSKREWKP LEDRSCTDIP WLLLFILFCI GMGFICGFSI ATGAAARLVS GYDSYGNICG QKNTKLEAIP NSGMDHTQRK YVFFLDPCNL DLINRKIKSV ALCVAACPRQ ELKTLSDVQK FAEINGSALC SYNLKPSEYT TSPKSSVLCP KLPVPASAPI PFFHRCAPVN ISCYAKFAEA LITFVSDNSV LHRLISGVMT SKEIILGLCL LSLVLSMILM VIIRYISRVL VWILTILVIL GSLGGTGVLW WLYAKQRRSP KETVTPEQLQ IAEDNLRALL IYAISATVFT VILFLIMLVM RKRVALTIAL FHVAGKVFIH LPLLVFQPFW TFFALVLFWV YWIMTLLFLG TTGSPVQNEQ GFVEFKISGP LQYMWWYHVV GLIWISEFIL ACQQMTVAGA VVTYYFTRDK RNLPFTPILA SVNRLIRYHL GTVAKGSFII TLVKIPRMIL MYIHSQLKGK ENACARCVLK SCICCLWCLE KCLNYLNQNA YTATAINSTN FCTSAKDAFV ILVENALRVA TINTVGDFML FLGKVLIVCS TGLAGIMLLN YQQDYTVWVL PLIIVCLFAF LVAHCFLSIY EMVVDVLFLC FAIDTKYNDG SPGREFYMDK VLMEFVENSR KAMKEAGKGG VADSRELKPM ASGASSALSA LVPR

UniProtKB: Choline transporter-like protein 1

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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

Concentration5.2 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Details: 15mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 6758 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Details: local refinement / Number images used: 64034
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC / Details: Ab initio job
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1) / Details: Non-uniform refinement job
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.4.1) / Details: 3D classification
FSC plot (resolution estimation)

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