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- EMDB-50252: Human choline transporter-like protein 1 (hCTL1/SLC44A1) in LMNG -

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Basic information

Entry
Database: EMDB / ID: EMD-50252
TitleHuman choline transporter-like protein 1 (hCTL1/SLC44A1) in LMNG
Map datalocal refinement
Sample
  • Organelle or cellular component: Choline transporter-like protein 1 in LMNG
    • Protein or peptide: human choline transporter-like protein 1
KeywordsCholine transporter-like family / CTL / MEMBRANE PROTEIN
Function / homology
Function and homology information


Transport of bile salts and organic acids, metal ions and amine compounds / choline transmembrane transporter activity / Choline catabolism / choline catabolic process / choline transport / phosphatidylcholine biosynthetic process / Synthesis of PC / transmembrane transporter activity / transport across blood-brain barrier / transmembrane transport ...Transport of bile salts and organic acids, metal ions and amine compounds / choline transmembrane transporter activity / Choline catabolism / choline catabolic process / choline transport / phosphatidylcholine biosynthetic process / Synthesis of PC / transmembrane transporter activity / transport across blood-brain barrier / transmembrane transport / mitochondrial outer membrane / membrane => GO:0016020 / 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_50252.png

Downloads & links

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Map

FileDownload / File: emd_50252.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocal refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 240 pix.
= 232.92 Å		0.97 Å/pix.
x 240 pix.
= 232.92 Å		0.97 Å/pix.
x 240 pix.
= 232.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9705 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.24440707 - 0.46008757
Average (Standard dev.)-0.0007668122 (±0.013094537)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 232.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50252_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: sharpened map

Fileemd_50252_additional_1.map
Annotationsharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: local refinement map with improved density for the...

Fileemd_50252_additional_2.map
Annotationlocal refinement map with improved density for the extracellular domain
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_50252_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_50252_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Choline transporter-like protein 1 in LMNG

EntireName: Choline transporter-like protein 1 in LMNG
Components
  • Organelle or cellular component: Choline transporter-like protein 1 in LMNG
    • Protein or peptide: human choline transporter-like protein 1

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Supramolecule #1: Choline transporter-like protein 1 in LMNG

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

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Macromolecule #1: human choline transporter-like protein 1

MacromoleculeName: human 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

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.
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: 115320
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4.4.1) / Details: Ab initio job
Final angle assignmentType: MAXIMUM LIKELIHOOD / Details: Non-uniform refinement job
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 4.4.1) / Details: 3D classification
FSC plot (resolution estimation)

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