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- PDB-9qu3: Cryo-EM structure of the human choline transporter-like protein h... -

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Basic information

Entry
Database: PDB / ID: 9qu3
TitleCryo-EM structure of the human choline transporter-like protein hCTL1 in LMNG
ComponentsCholine transporter-like protein 1
KeywordsMEMBRANE PROTEIN / SLC44
Function / homology
Function and homology information


ethanolamine transport / ethanolamine transmembrane transporter activity / Transport of bile salts and organic acids, metal ions and amine compounds / 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 / Transport of bile salts and organic acids, metal ions and amine compounds / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsDriller, J.H. / Nel, L. / Pedersen, B.P.
Funding support Denmark, European Union, 4items
OrganizationGrant numberCountry
LundbeckfondenR380-2021-1207 Denmark
H2020 Marie Curie Actions of the European Commission890822European Union
Danish National Research Foundation0135-00032B Denmark
The Carlsberg FoundationCF19-0127 Denmark
CitationJournal: To Be Published
Title: Comparative and structural analysis of choline transport between eukaryotic choline transport protein families FLVCR and CTL
Authors: Nel, L. / Driller, J.H. / Driller, R. / Frain, K.M. / Pedersen, B.P.
History
DepositionApr 10, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Choline transporter-like protein 1


Theoretical massNumber of molelcules
Total (without water)73,8941
Polymers73,8941
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Choline transporter-like protein 1 / CDw92 / Solute carrier family 44 member 1


Mass: 73893.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC44A1, CD92, CDW92, CTL1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8WWI5
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Choline transporter-like protein 1 in LMNG detergent / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15 mA / Grid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115320 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 78.08 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00212960
ELECTRON MICROSCOPYf_angle_d0.43354021
ELECTRON MICROSCOPYf_chiral_restr0.0319488
ELECTRON MICROSCOPYf_plane_restr0.0039468
ELECTRON MICROSCOPYf_dihedral_angle_d3.8733385

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