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- EMDB-62528: human creatine transporter -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-62528
Titlehuman creatine transporter
Map data
Sample
  • Complex: Creatine transporter
    • Protein or peptide: Sodium- and chloride-dependent creatine transporter 1
  • Ligand: 3-carbamimidamidopropanoic acid
  • Ligand: CHLORIDE ION
  • Ligand: SODIUM ION
Keywordscreatine / transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


creatine transmembrane transporter activity / creatine:sodium symporter activity / creatine transmembrane transport / creatine metabolic process / nitrogen compound transport / gamma-aminobutyric acid:sodium:chloride symporter activity / Creatine metabolism / neurotransmitter transport / amino acid transport / muscle contraction ...creatine transmembrane transporter activity / creatine:sodium symporter activity / creatine transmembrane transport / creatine metabolic process / nitrogen compound transport / gamma-aminobutyric acid:sodium:chloride symporter activity / Creatine metabolism / neurotransmitter transport / amino acid transport / muscle contraction / sodium ion transmembrane transport / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsYu J / Ge JP / Chen JH
Funding support China, 1 items
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, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62528.png

Downloads & links

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Map

FileDownload / File: emd_62528.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 240 pix.
= 253.2 Å		1.06 Å/pix.
x 240 pix.
= 253.2 Å		1.06 Å/pix.
x 240 pix.
= 253.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.3584437 - 2.0975833
Average (Standard dev.)-0.000349295 (±0.037181035)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 253.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62528_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62528_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_62528_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 : Creatine transporter

EntireName: Creatine transporter
Components
  • Complex: Creatine transporter
    • Protein or peptide: Sodium- and chloride-dependent creatine transporter 1
  • Ligand: 3-carbamimidamidopropanoic acid
  • Ligand: CHLORIDE ION
  • Ligand: SODIUM ION

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Supramolecule #1: Creatine transporter

SupramoleculeName: Creatine transporter / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Sodium- and chloride-dependent creatine transporter 1

MacromoleculeName: Sodium- and chloride-dependent creatine transporter 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70.568336 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAKKSAENGI YSVSGDEKKG PLIAPGPDGA PAKGDGPVGL GTPGGRLAVP PRETWTRQMD FIMSCVGFAV GLGNVWRFPY LCYKNGGGV FLIPYVLIAL VGGIPIFFLE ISLGQFMKAG SINVWNICPL FKGLGYASMV IVFYCNTYYI MVLAWGFYYL V KSFTTTLP ...String:
MAKKSAENGI YSVSGDEKKG PLIAPGPDGA PAKGDGPVGL GTPGGRLAVP PRETWTRQMD FIMSCVGFAV GLGNVWRFPY LCYKNGGGV FLIPYVLIAL VGGIPIFFLE ISLGQFMKAG SINVWNICPL FKGLGYASMV IVFYCNTYYI MVLAWGFYYL V KSFTTTLP WATCGHTWNT PDCVEIFRHE DCANASLANL TCDQLADRRS PVIEFWENKV LRLSGGLEVP GALNWEVTLC LL ACWVLVY FCVWKGVKST GKIVYFTATF PYVVLVVLLV RGVLLPGALD GIIYYLKPDW SKLGSPQVWI DAGTQIFFSY AIG LGALTA LGSYNRFNNN CYKDAIILAL INSGTSFFAG FVVFSILGFM AAEQGVHISK VAESGPGLAF IAYPRAVTLM PVAP LWAAL FFFMLLLLGL DSQFVGVEGF ITGLLDLLPA SYYFRFQREI SVALCCALCF VIDLSMVTDG GMYVFQLFDY YSASG TTLL WQAFWECVVV AWVYGADRFM DDIACMIGYR PCPWMKWCWS FFTPLVCMGI FIFNVVYYEP LVYNNTYVYP WWGEAM GWA FALSSMLCVP LHLLGCLLRA KGTMAERWQH LTQPIWGLHH LEYRAQDADV RGLTTLTPVS ESSKVVVVES VM

UniProtKB: Sodium- and chloride-dependent creatine transporter 1

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Macromolecule #2: 3-carbamimidamidopropanoic acid

MacromoleculeName: 3-carbamimidamidopropanoic acid / type: ligand / ID: 2 / Number of copies: 1 / Formula: A1D9S
Molecular weightTheoretical: 131.133 Da

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Macromolecule #3: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #4: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 4 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 262011
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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