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Yorodumi- EMDB-50251: Human choline transporter-like protein 1 (hCTL1/SLC44A1) in peptidisc -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-50251 | |||||||||
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Title | Human choline transporter-like protein 1 (hCTL1/SLC44A1) in peptidisc | |||||||||
Map data | NU refinement | |||||||||
Sample |
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Keywords | Choline transporter-like family / CTL / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information ethanolamine transport / Transport of bile salts and organic acids, metal ions and amine compounds / ethanolamine transmembrane transporter activity / choline transmembrane transporter activity / Choline catabolism / choline catabolic process / choline transport / phosphatidylcholine biosynthetic process / antiporter activity / Synthesis of PC ...ethanolamine transport / Transport of bile salts and organic acids, metal ions and amine compounds / ethanolamine transmembrane transporter activity / choline transmembrane transporter activity / Choline catabolism / choline catabolic process / choline transport / phosphatidylcholine biosynthetic process / 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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Driller JH / Pedersen BP | |||||||||
Funding support | Denmark, European Union, 2 items
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Citation | Journal: To Be Published Title: To be announced Authors: Driller JH / Pedersen BP | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_50251.map.gz | 120.7 MB | EMDB map data format | |
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Header (meta data) | emd-50251-v30.xml emd-50251.xml | 19.9 KB 19.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_50251_fsc.xml | 18.4 KB | Display | FSC data file |
Images | emd_50251.png | 65 KB | ||
Filedesc metadata | emd-50251.cif.gz | 5.2 KB | ||
Others | emd_50251_additional_1.map.gz emd_50251_additional_2.map.gz emd_50251_half_map_1.map.gz emd_50251_half_map_2.map.gz | 121.1 MB 230.1 MB 226.4 MB 226.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-50251 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-50251 | HTTPS FTP |
-Validation report
Summary document | emd_50251_validation.pdf.gz | 958.1 KB | Display | EMDB validaton report |
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Full document | emd_50251_full_validation.pdf.gz | 957.7 KB | Display | |
Data in XML | emd_50251_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | emd_50251_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50251 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50251 | HTTPS FTP |
-Related structure data
Related structure data | 5o7zC 5o80C 5o81C 5o82C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_50251.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | NU refinement | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.647 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: map from local refinement
File | emd_50251_additional_1.map | ||||||||||||
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Annotation | map from local refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: sharpened map
File | emd_50251_additional_2.map | ||||||||||||
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Annotation | sharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_50251_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_50251_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Choline transporter-like protein 1 (hCTL1) in peptidisc
Entire | Name: Choline transporter-like protein 1 (hCTL1) in peptidisc |
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Components |
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-Supramolecule #1: Choline transporter-like protein 1 (hCTL1) in peptidisc
Supramolecule | Name: Choline transporter-like protein 1 (hCTL1) in peptidisc type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Choline transporter-like protein 1
Macromolecule | Name: Choline transporter-like protein 1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5.2 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: 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 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 6758 / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |