+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32865 | |||||||||
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Title | Choline transporter-like protein 1 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | choline binding / cholesterol binding / transporter / TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information ethanolamine transmembrane transporter activity / ethanolamine 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 / antiporter activity / Synthesis of PC ...ethanolamine transmembrane transporter activity / ethanolamine 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 / 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: 3.86 Å | |||||||||
Authors | Chi XM / Zhou Q | |||||||||
Funding support | China, 1 items
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Citation | Journal: Structure / Year: 2022 Title: Rational exploration of fold atlas for human solute carrier proteins. Authors: Tengyu Xie / Ximin Chi / Bangdong Huang / Fangfei Ye / Qiang Zhou / Jing Huang / Abstract: The solute carrier (SLC) superfamily is the largest group of proteins responsible for the transmembrane transport of substances in human cells. It includes more than 400 members that are organized ...The solute carrier (SLC) superfamily is the largest group of proteins responsible for the transmembrane transport of substances in human cells. It includes more than 400 members that are organized into 65 families according to their physiological function and sequence similarity. Different families of SLCs can adopt the same or different folds that determine the mechanism and reflect the evolutionary relationship between SLC members. Analysis of structural data in the literature before this work showed 13 different folds in the SLC superfamily covering 40 families and 343 members. To further study their mechanism, we systematically explored the SLC superfamily to look for more folds. Based on our results, at least three new folds are found for the SLC superfamily, one of which is in the choline-like transporter family (SLC44) and has been experimentally verified. Our work has laid a foundation and provided important insights for the systematic and comprehensive study of the structure and function of SLC. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32865.map.gz | 36.2 MB | EMDB map data format | |
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Header (meta data) | emd-32865-v30.xml emd-32865.xml | 10.1 KB 10.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_32865_fsc.xml | 9.9 KB | Display | FSC data file |
Images | emd_32865.png | 80.8 KB | ||
Filedesc metadata | emd-32865.cif.gz | 5.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32865 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32865 | HTTPS FTP |
-Validation report
Summary document | emd_32865_validation.pdf.gz | 511.5 KB | Display | EMDB validaton report |
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Full document | emd_32865_full_validation.pdf.gz | 511 KB | Display | |
Data in XML | emd_32865_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | emd_32865_validation.cif.gz | 13.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32865 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32865 | HTTPS FTP |
-Related structure data
Related structure data | 7wwbMC M: atomic model generated by this map 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_32865.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.087 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Choline transporter-like protein 1 in complex with choline
Entire | Name: Choline transporter-like protein 1 in complex with choline |
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Components |
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-Supramolecule #1: Choline transporter-like protein 1 in complex with choline
Supramolecule | Name: Choline transporter-like protein 1 in complex with choline type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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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 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 73.369844 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGCCSSASSA AQSSKREWKP LEDRSCTDIP WLLLFILFCI GMGFICGFSI ATGAAARLVS GYDSYGNICG QKNTKLEAIP NSGMDHTQR KYVFFLDPCN LDLINRKIKS VALCVAACPR QELKTLSDVQ KFAEINGSAL CSYNLKPSEY TTSPKSSVLC P KLPVPASA ...String: MGCCSSASSA AQSSKREWKP LEDRSCTDIP WLLLFILFCI GMGFICGFSI ATGAAARLVS GYDSYGNICG QKNTKLEAIP NSGMDHTQR KYVFFLDPCN LDLINRKIKS VALCVAACPR QELKTLSDVQ KFAEINGSAL CSYNLKPSEY TTSPKSSVLC P KLPVPASA PIPFFHRCAP VNISCYAKFA EALITFVSDN SVLHRLISGV MTSKEIILGL CLLSLVLSMI LMVIIRYISR VL VWILTIL VILGSLGGTG VLWWLYAKQR RSPKETVTPE QLQIAEDNLR ALLIYAISAT VFTVILFLIM LVMRKRVALT IAL FHVAGK VFIHLPLLVF QPFWTFFALV LFWVYWIMTL LFLGTTGSPV QNEQGFVEFK ISGPLQYMWW YHVVGLIWIS EFIL ACQQM TVAGAVVTYY FTRDKRNLPF TPILASVNRL IRYHLGTVAK GSFIITLVKI PRMILMYIHS QLKGKENACA RCVLK SCIC CLWCLEKCLN YLNQNAYTAT AINSTNFCTS AKDAFVILVE NALRVATINT VGDFMLFLGK VLIVCSTGLA GIMLLN YQQ DYTVWVLPLI IVCLFAFLVA HCFLSIYEMV VDVLFLCFAI DTKYNDGSPG REFYMDKVLM EFVENSRKAM KEAGKGG VA DSRELKPMAS GASSA UniProtKB: Choline transporter-like protein 1 |
-Macromolecule #2: CHOLINE ION
Macromolecule | Name: CHOLINE ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: CHT |
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Molecular weight | Theoretical: 104.171 Da |
Chemical component information | ChemComp-CHT: |
-Macromolecule #3: CHOLESTEROL
Macromolecule | Name: CHOLESTEROL / type: ligand / ID: 3 / Number of copies: 2 / Formula: CLR |
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Molecular weight | Theoretical: 386.654 Da |
Chemical component information | ChemComp-CLR: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |