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- EMDB-32865: Choline transporter-like protein 1 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-32865
TitleCholine transporter-like protein 1
Map data
Sample
  • Cell: Choline transporter-like protein 1 in complex with choline
    • Protein or peptide: Choline transporter-like protein 1
  • Ligand: CHOLINE ION
  • Ligand: CHOLESTEROL
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: 3.86 Å
AuthorsChi XM / Zhou Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971123 China
CitationJournal: 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
DepositionFeb 12, 2022-
Header (metadata) releaseJun 22, 2022-
Map releaseJun 22, 2022-
UpdateSep 14, 2022-
Current statusSep 14, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32865.png

Downloads & links

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Map

FileDownload / File: emd_32865.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.087 Å
Density
Contour LevelBy AUTHOR: 0.537
Minimum - Maximum-2.312985 - 3.4787796
Average (Standard dev.)0.017979296 (±0.09380049)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 234.792 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Choline transporter-like protein 1 in complex with choline

EntireName: Choline transporter-like protein 1 in complex with choline
Components
  • Cell: Choline transporter-like protein 1 in complex with choline
    • Protein or peptide: Choline transporter-like protein 1
  • Ligand: CHOLINE ION
  • Ligand: CHOLESTEROL

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Supramolecule #1: Choline transporter-like protein 1 in complex with choline

SupramoleculeName: Choline transporter-like protein 1 in complex with choline
type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
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 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 73.369844 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #2: CHOLINE ION

MacromoleculeName: CHOLINE ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: CHT
Molecular weightTheoretical: 104.171 Da
Chemical component information

ChemComp-CHT:
CHOLINE ION / Choline

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Macromolecule #3: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 3 / Number of copies: 2 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL / Cholesterol

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 144295
FSC plot (resolution estimation)

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