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9j8d

Human Glycine Transporter 1 in the Iclepertin-Bound State with an Inward-Facing Conformation

Method: ELECTRON MICROSCOPY Dmax: 86.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Isoform GlyT-1B of Sodium- and chloride-dependent glycine transporter 1

Homo sapiens

UniProt P48067

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–652 Not recorded A1EBX Iclepertin × 1 CL CHLORIDE ION × 1 CLR CHOLESTEROL × 3 NA SODIUM ION × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9J8D Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6ZBV Inward-open structure of human glycine transporter 1 in complex with a benzoylisoindoline inhibitor and sybody Sb_GlyT1#7 Deposited 2020-06-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 91–239（149 aa）
Chain A 257–684（428 aa）
Not recorded QET [5-fluoranyl-6-(oxan-4-yloxy)-1,3-dihydroisoindol-2-yl]-[5-methylsulfonyl-2-[2,2,3,3,3-pentakis(fluoranyl)propoxy]phenyl]methanone × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7；292.75 K；0.1M ADA pH 7, 13-25% PEG600, 4-14% v/v-1,3-Butanediol
Resolution 3.40 Å R-free 0.259
6ZPL Inward-open structure of human glycine transporter 1 in complex with a benzoylisoindoline inhibitor, sybody Sb_GlyT1#7 and bound Na and Cl ions. Deposited 2020-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 92–684（593 aa）
Chain B 92–684（593 aa）
Mutation：;L153A, S297A, I368A, C633A. N-terminal deletion of residues 1-91 and residues 9-281 of Lichenase (PDB ID 2CIT) have been fused at the N-terminal. C- terminal deletion of residues 685-706 as well as a deletion in the extracellular loop 2 (EL2) between residues 240-256. ; Mutation：;L153A, S297A, I368A, C633A. N-terminal deletion of residues 1-91 and residues 9-281 of Lichenase (PDB ID 2CIT) have been fused at the N-terminal. C- terminal deletion of residues 685-706 as well as a deletion in the extracellular loop 2 (EL2) between residues 240-256. ; QET [5-fluoranyl-6-(oxan-4-yloxy)-1,3-dihydroisoindol-2-yl]-[5-methylsulfonyl-2-[2,2,3,3,3-pentakis(fluoranyl)propoxy]phenyl]methanone × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7；292.75 K；Crystals appeared in 3-10 days in 0.1 M ADA pH 7, 13-25% PEG600, 4-14% v/v, 1,3-Butanediol with the longest dimension of 2-5 um.
Resolution 3.94 Å R-free 0.291
8WFI human glycine transporter 1 in complex with glycine in occluded conformation Deposited 2023-09-19 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 46–614（569 aa）
Not recorded GLY GLYCINE × 1 CL CHLORIDE ION × 1 NA SODIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.58 Å
8WFJ human glycine transporter 1 in complex with ALX-5407 in inward facing conformation Deposited 2023-09-19 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–652（652 aa）
Not recorded W5F ALX5407 × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.35 Å
8WFK human glycine transporter 1 in complex with SSR504734 in outward facing conformation Deposited 2023-09-19 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–652（652 aa）
Not recorded W5O SSR504734 × 1 CL CHLORIDE ION × 1 NA SODIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
8WFL human glycine transporter 1 in complex with PF-03463275 in outward facing conformation Deposited 2023-09-19 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–652（652 aa）
Not recorded W5X PF-3463275 × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
9J8B Human Glycine Transporter 1 in the Apo State with an Inward-Facing Conformation Deposited 2024-08-21 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–652（652 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
9J8C Human Glycine Transporter 1 in the Sarcosine-Bound State with an Occluded Conformation Deposited 2024-08-21 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–652（652 aa）
Not recorded SAR SARCOSINE × 1 CLR CHOLESTEROL × 3 CL CHLORIDE ION × 1 NA SODIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SC6A9_HUMAN
Isoform P48067-3
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–652； UniProt 1–652

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9j8d

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9j8d
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9j8d
Deposition date deposition_date2024-08-21
Structure title titleHuman Glycine Transporter 1 in the Iclepertin-Bound State with an Inward-Facing Conformation
Keywords keywordshuman glycine transporter 1, GlyT1, iclepertin, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier25.43 Å
Radius of gyration Rg (electron density) rg_electron24.47 Å
Forward intensity I(0) i0102661000.00
Molecular weight molecular_weight57170.0 kDa
Excluded volume excluded_volume57453 ų
Envelope volume envelope_volume94858 ų
Hydration-shell volume shell_volume31664 ų
Envelope diameter envelope_diameter89.6 Å
Shell Rg shell_rg32.49 Å
Envelope Rg envelope_rg24.85 Å
Shape Rg shape_rg24.48 Å
Total Rg total_rg25.16 Å
Total atoms total_atoms4345
Residues n_residues530
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax86.2 Å
Rg (real space) rg_real25.41 Å
Rg uncertainty (real space) rg_real_error0.54 Å
I(0) (real space) i0_real1.0270e+08
I(0) uncertainty (real space) i0_real_error1.6250e+06
Rg (reciprocal space) rg_reciprocal25.42 Å
I(0) (reciprocal space) i0_reciprocal102700000.0000
Solution quality estimate total_estimate0.8708
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.6 Å
Skewness Skewness skewness0.396
Kurtosis Kurtosis kurtosis-0.154
Angular range angular_range— – 0.3100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14140000.0000
Real-space data points n_real_points63
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.776; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.988
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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8. Citations (1)

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9. Files and Curves (10)