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- EMDB-66096: Structural mechanism of substrate binding of the human Proline Tr... -

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Basic information

Entry
Database: EMDB / ID: EMD-66096
TitleStructural mechanism of substrate binding of the human Proline Transporter
Map data
Sample
  • Complex: PROT
    • Protein or peptide: Sodium-dependent proline transporter
  • Ligand: SODIUM ION
  • Ligand: CHLORIDE ION
  • Ligand: (2S)-2,3-dihydro-1H-pyrrole-2-carboxylic acid
  • Ligand: CHOLESTEROL
  • Ligand: CHOLESTEROL HEMISUCCINATE
KeywordsTRANSPORT PROTEIN / L-PROLINE
Function / homology
Function and homology information


proline:sodium symporter activity / L-proline transmembrane transporter activity / glycine import across plasma membrane / Creatine metabolism / proline transport / SLC-mediated transport of neurotransmitters / neurotransmitter transport / sodium ion transmembrane transport / protein catabolic process / synaptic membrane ...proline:sodium symporter activity / L-proline transmembrane transporter activity / glycine import across plasma membrane / Creatine metabolism / proline transport / SLC-mediated transport of neurotransmitters / neurotransmitter transport / sodium ion transmembrane transport / protein catabolic process / synaptic membrane / synapse / membrane / plasma membrane
Similarity search - Function
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-dependent proline transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsZhou Y / Wu JX / Wang JQ / Wang NQ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371266 China
CitationJournal: To Be Published
Title: Structural insights into transport mechanism of proline transporter
Authors: Zhou Y / Wu JX
History
DepositionSep 3, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66096.png

Downloads & links

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Map

FileDownload / File: emd_66096.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-5.181934 - 7.440395
Average (Standard dev.)-0.0030604296 (±0.13190931)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 276.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66096_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_66096_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_66096_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 : PROT

EntireName: PROT
Components
  • Complex: PROT
    • Protein or peptide: Sodium-dependent proline transporter
  • Ligand: SODIUM ION
  • Ligand: CHLORIDE ION
  • Ligand: (2S)-2,3-dihydro-1H-pyrrole-2-carboxylic acid
  • Ligand: CHOLESTEROL
  • Ligand: CHOLESTEROL HEMISUCCINATE

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Supramolecule #1: PROT

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

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Macromolecule #1: Sodium-dependent proline transporter

MacromoleculeName: Sodium-dependent proline transporter / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70.960219 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKKLQGAHLR KPVTPDLLMT PSDQGDVDLD VDFAAHRGNW TGKLDFLLSC IGYCVGLGNV WRFPYRAYTN GGGAFLVPYF LMLAICGIP LFFLELSLGQ FSSLGPLAVW KISPLFKGAG AAMLLIVGLV AIYYNMIIAY VLFYLFASLT SDLPWEHCGN W WNTELCLE ...String:
MKKLQGAHLR KPVTPDLLMT PSDQGDVDLD VDFAAHRGNW TGKLDFLLSC IGYCVGLGNV WRFPYRAYTN GGGAFLVPYF LMLAICGIP LFFLELSLGQ FSSLGPLAVW KISPLFKGAG AAMLLIVGLV AIYYNMIIAY VLFYLFASLT SDLPWEHCGN W WNTELCLE HRVSKDGNGA LPLNLTCTVS PSEEYWSRYV LHIQGSQGIG SPGEIRWNLC LCLLLAWVIV FLCILKGVKS SG KVVYFTA TFPYLILLML LVRGVTLPGA WKGIQFYLTP QFHHLLSSKV WIEAALQIFY SLGVGFGGLL TFASYNTFHQ NIY RDTFIV TLGNAITSIL AGFAIFSVLG YMSQELGVPV DQVAKAGPGL AFVVYPQAMT MLPLSPFWSF LFFFMLLTLG LDSQ FAFLE TIVTAVTDEF PYYLRPKKAV FSGLICVAMY LMGLILTTDG GMYWLVLLDD YSASFGLMVV VITTCLAVTR VYGIQ RFCR DIHMMLGFKP GLYFRACWLF LSPATLLALM VYSIVKYQPS EYGSYRFPPW AELLGILMGL LSCLMIPAGM LVAVLR EEG SLWERLQQAS RPAMDWGPSL EENRTGMYVA TLAGSQSPKP LMVHMRKYGG ITSFENTAIE VDREIAEEEE SMM

UniProtKB: Sodium-dependent proline transporter

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Macromolecule #2: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 2 / Number of copies: 2
Molecular weightTheoretical: 22.99 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: (2S)-2,3-dihydro-1H-pyrrole-2-carboxylic acid

MacromoleculeName: (2S)-2,3-dihydro-1H-pyrrole-2-carboxylic acid / type: ligand / ID: 4 / Number of copies: 1 / Formula: 8LJ
Molecular weightTheoretical: 113.115 Da
Chemical component information

ChemComp-8LJ:
(2S)-2,3-dihydro-1H-pyrrole-2-carboxylic acid

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Macromolecule #5: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 5 / Number of copies: 3 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #6: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 6 / Number of copies: 2 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 144216
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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