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- PDB-9kr7: human creatine transporter -

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Basic information

Entry
Database: PDB / ID: 9kr7
Titlehuman creatine transporter
ComponentsSodium- and chloride-dependent creatine transporter 1
KeywordsMEMBRANE PROTEIN / creatine / transporter
Function / homology
Function and homology information


creatine transmembrane transporter activity / creatine:sodium symporter activity / creatine transmembrane transport / nitrogen compound transport / creatine metabolic process / Creatine metabolism / gamma-aminobutyric acid:sodium:chloride symporter activity / neurotransmitter transport / amino acid transport / sodium ion transmembrane transport ...creatine transmembrane transporter activity / creatine:sodium symporter activity / creatine transmembrane transport / nitrogen compound transport / creatine metabolic process / Creatine metabolism / gamma-aminobutyric acid:sodium:chloride symporter activity / neurotransmitter transport / amino acid transport / sodium ion transmembrane transport / muscle contraction / apical plasma membrane / membrane / plasma membrane
Similarity search - Function
Sodium:neurotransmitter symporter, creatine / Sodium:neurotransmitter symporter family signature 2. / Sodium:neurotransmitter symporter family signature 1. / Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile.
Similarity search - Domain/homology
Sodium- and chloride-dependent creatine transporter 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsYu, J. / Ge, J.P. / Chen, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Cell Discov / Year: 2025
Title: Transport and inhibition mechanisms of human creatine transporter.
Authors: Jiahui Chen / Yimin Zhang / Nanhao Chen / Jingpeng Ge / Jie Yu /
History
DepositionNov 27, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
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Revision 1.0May 21, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.1Jun 25, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 25, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sodium- and chloride-dependent creatine transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6042
Polymers70,5681
Non-polymers351
Water1267
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 Sodium- and chloride-dependent creatine transporter 1 / CT1 / Creatine transporter 1 / Solute carrier family 6 member 8


Mass: 70568.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC6A8 / Production host: Homo sapiens (human) / References: UniProt: P48029
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: Creatine transporter / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Strain: Human Embryonic Kidney Cells 293
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 261670 / Symmetry type: POINT
RefinementHighest resolution: 3.29 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0044400
ELECTRON MICROSCOPYf_angle_d0.5226010
ELECTRON MICROSCOPYf_dihedral_angle_d3.83577
ELECTRON MICROSCOPYf_chiral_restr0.039657
ELECTRON MICROSCOPYf_plane_restr0.004730

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