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- EMDB-36025: Human high-affinity choline transporter CHT1 in the HC-3-bound ou... -

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Basic information

Entry
Database: EMDB / ID: EMD-36025
TitleHuman high-affinity choline transporter CHT1 in the HC-3-bound outward-facing open conformation, dimeric state
Map data
Sample
  • Complex: Human high-affinity choline transporter 1
    • Protein or peptide: High affinity choline transporter 1
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: HEXADECANE
  • Ligand: (2S,2'S)-2,2'-biphenyl-4,4'-diylbis(2-hydroxy-4,4-dimethylmorpholin-4-ium)
KeywordsCHT1 / SLC5A7 / high affinity choline transporter / choline transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


choline:sodium symporter activity / Defective SLC5A7 causes distal hereditary motor neuronopathy 7A (HMN7A) / Defective SLC5A7 causes distal hereditary motor neuronopathy 7A (HMN7A) / acetylcholine biosynthetic process / Transport of bile salts and organic acids, metal ions and amine compounds / choline transmembrane transporter activity / Acetylcholine Neurotransmitter Release Cycle / neuromuscular synaptic transmission / choline transport / choline binding ...choline:sodium symporter activity / Defective SLC5A7 causes distal hereditary motor neuronopathy 7A (HMN7A) / Defective SLC5A7 causes distal hereditary motor neuronopathy 7A (HMN7A) / acetylcholine biosynthetic process / Transport of bile salts and organic acids, metal ions and amine compounds / choline transmembrane transporter activity / Acetylcholine Neurotransmitter Release Cycle / neuromuscular synaptic transmission / choline transport / choline binding / synaptic transmission, cholinergic / neurotransmitter transport / neuromuscular junction / transmembrane transport / synaptic vesicle membrane / presynaptic membrane / early endosome membrane / perikaryon / in utero embryonic development / axon / dendrite / synapse / membrane / plasma membrane
Similarity search - Function
: / Sodium/solute symporter / Sodium/glucose symporter superfamily / Sodium:solute symporter family / Sodium:solute symporter family profile.
Similarity search - Domain/homology
High affinity choline transporter 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsGao Y / Qiu Y / Zhao Y
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37030304 China
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Transport mechanism of presynaptic high-affinity choline uptake by CHT1.
Authors: Yunlong Qiu / Yiwei Gao / Bo Huang / Qinru Bai / Yan Zhao /
Abstract: Choline is a vital nutrient and a precursor for the biosynthesis of essential metabolites, including acetylcholine (ACh), that play a central role in fetal development, especially in the brain. In ...Choline is a vital nutrient and a precursor for the biosynthesis of essential metabolites, including acetylcholine (ACh), that play a central role in fetal development, especially in the brain. In cholinergic neurons, the high-affinity choline transporter (CHT1) provides an extraordinarily efficient reuptake mechanism to reutilize choline derived from intrasynaptical ACh hydrolysis and maintain ACh synthesis in the presynapse. Here, we determined structures of human CHT1 in three discrete states: the outward-facing state bound with the competitive inhibitor hemicholinium-3 (HC-3); the inward-facing occluded state bound with the substrate choline; and the inward-facing apo open state. Our structures and functional characterizations elucidate how the inhibitor and substrate are recognized. Moreover, our findings shed light on conformational changes when transitioning from an outward-facing to an inward-facing state and establish a framework for understanding the transport cycle, which relies on the stabilization of the outward-facing state by a short intracellular helix, IH1.
History
DepositionApr 27, 2023-
Header (metadata) releaseApr 3, 2024-
Map releaseApr 3, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36025.png

Downloads & links

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Map

FileDownload / File: emd_36025.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 300 pix.
= 246. Å		0.82 Å/pix.
x 300 pix.
= 246. Å		0.82 Å/pix.
x 300 pix.
= 246. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.418
Minimum - Maximum-1.0665987 - 1.7774464
Average (Standard dev.)0.0038182884 (±0.060963675)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 246.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36025_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36025_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human high-affinity choline transporter 1

EntireName: Human high-affinity choline transporter 1
Components
  • Complex: Human high-affinity choline transporter 1
    • Protein or peptide: High affinity choline transporter 1
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: HEXADECANE
  • Ligand: (2S,2'S)-2,2'-biphenyl-4,4'-diylbis(2-hydroxy-4,4-dimethylmorpholin-4-ium)

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Supramolecule #1: Human high-affinity choline transporter 1

SupramoleculeName: Human high-affinity choline transporter 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: High affinity choline transporter 1

MacromoleculeName: High affinity choline transporter 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 63.239145 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAFHVEGLIA IIVFYLLILL VGIWAAWRTK NSGSAEERSE AIIVGGRDIG LLVGGFTMTA TWVGGGYING TAEAVYVPGY GLAWAQAPI GYSLSLILGG LFFAKPMRSK GYVTMLDPFQ QIYGKRMGGL LFIPALMGEM FWAAAIFSAL GATISVIIDV D MHISVIIS ...String:
MAFHVEGLIA IIVFYLLILL VGIWAAWRTK NSGSAEERSE AIIVGGRDIG LLVGGFTMTA TWVGGGYING TAEAVYVPGY GLAWAQAPI GYSLSLILGG LFFAKPMRSK GYVTMLDPFQ QIYGKRMGGL LFIPALMGEM FWAAAIFSAL GATISVIIDV D MHISVIIS ALIATLYTLV GGLYSVAYTD VVQLFCIFVG LWISVPFALS HPAVADIGFT AVHAKYQKPW LGTVDSSEVY SW LDSFLLL MLGGIPWQAY FQRVLSSSSA TYAQVLSFLA AFGCLVMAIP AILIGAIGAS TDWNQTAYGL PDPKTTEEAD MIL PIVLQY LCPVYISFFG LGAVSAAVMS SADSSILSAS SMFARNIYQL SFRQNASDKE IVWVMRITVF VFGASATAMA LLTK TVYGL WYLSSDLVYI VIFPQLLCVL FVKGTNTYGA VAGYVSGLFL RITGGEPYLY LQPLIFYPGY YPDDNGIYNQ KFPFK TLAM VTSFLTNICI SYLAKYLFES GTLPPKLDVF DAVVARHSEE NMDKTILVKN ENIKLDELAL VKPRQSMTLS STFTNK EAF LDVDSSPEGS GTEDNLQ

UniProtKB: High affinity choline transporter 1

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Macromolecule #3: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #4: Lauryl Maltose Neopentyl Glycol

MacromoleculeName: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 4 / Number of copies: 2 / Formula: AV0
Molecular weightTheoretical: 1.005188 KDa
Chemical component information

ChemComp-AV0:
Lauryl Maltose Neopentyl Glycol

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Macromolecule #5: HEXADECANE

MacromoleculeName: HEXADECANE / type: ligand / ID: 5 / Number of copies: 2 / Formula: R16
Molecular weightTheoretical: 226.441 Da
Chemical component information

ChemComp-R16:
HEXADECANE

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Macromolecule #6: (2S,2'S)-2,2'-biphenyl-4,4'-diylbis(2-hydroxy-4,4-dimethylmorphol...

MacromoleculeName: (2S,2'S)-2,2'-biphenyl-4,4'-diylbis(2-hydroxy-4,4-dimethylmorpholin-4-ium)
type: ligand / ID: 6 / Number of copies: 2 / Formula: HC6
Molecular weightTheoretical: 414.538 Da
Chemical component information

ChemComp-HC6:
(2S,2'S)-2,2'-biphenyl-4,4'-diylbis(2-hydroxy-4,4-dimethylmorpholin-4-ium)

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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

Concentration10 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was obtained from the monodispersed peak fractions of the size-exclusion chromatography.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / 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: 2.2 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 165000
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

Particle selectionNumber selected: 827001
Startup modelType of model: INSILICO MODEL
In silico model: The insilico model was generated using the ab-initio reconstruction in cryoSPARC.
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 12269
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final 3D classificationNumber classes: 6 / Software - Name: cryoSPARC (ver. 3.3.1)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-8j74:
Human high-affinity choline transporter CHT1 in the HC-3-bound outward-facing open conformation, dimeric state

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