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9r1h

Inward-occluded structure of human glycine transporter 2 bound to substrate glycine

Method: ELECTRON MICROSCOPY D_max: 83.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r1h
deposition_date	2025-04-26
title	Inward-occluded structure of human glycine transporter 2 bound to substrate glycine
keywords	;Transport protein, SLC6A5, neurotransmitter/sodium symporter, Sodium- and chloride-dependent glycine transporter 2, MEMBRANE PROTEIN ;; MEMBRANE PROTEIN
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	25.00 Å
rg_electron	23.89 Å
i0	49565700.00
molecular_weight	61722.0 kDa
excluded_volume	79985 Å³
envelope_volume	89588 Å³
shell_volume	30626 Å³
envelope_diameter	88.6 Å
shell_rg	31.85 Å
envelope_rg	24.25 Å
shape_rg	23.89 Å
total_rg	24.86 Å
total_atoms	4359
n_residues	547
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	83.8 Å
rg_real	24.99 Å
rg_real_error	0.60 Å
i0_real	4.9570e+07
i0_real_error	7.6900e+05
rg_reciprocal	24.99 Å
i0_reciprocal	49570000.0000
total_estimate	0.8726
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.3 Å
skewness	0.396
kurtosis	-0.171
angular_range	— – 0.3150 Å⁻¹
current_alpha	0.0000
highest_alpha	9280000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.801; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.951

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Sodium- and chloride-dependent glycine transporter 2
formula_weight	68976.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4361

MDENKARGNWSSKLDFILSMVGYAVGLGNVWRFPYLAFQNGGGAFLIPYLMMLALAGLPIFFLEVSLGQFASQGPVSVWKAIPALQGCGIAMLIISVLIAIYYNVIICYTLFYLFASFVSVLPWGSCNNPWNTPECKDKTKLLLDSCVISDHPKIQIKNSTFCMTAYPNVTMVNFTSQANKTFVSGSEEYFKYFVLKISAGIEYPGEIRWPLALCLFLAWVIVYASLAKGIKTSGKVVYFTATFPYVVLVILLIRGVTLPGAGAGIWYFITPKWEKLTDATVWKDAATQIFFSLSAAWGGLITLSSYNKFHNNCYRDTLIVTCTNSATSIFAGFVIFSVIGFMANERKVNIENVADQGPGIAFVVYPEALTRLPLSPFWAIIFFLMLLTLGLDTMFATIETIVTSISDEFPKYLRTHKPVFTLGCCICFFIMGFPMITQGGIYMFQLVDTYAASYALVIIAIFELVGISYVYGLQRFCEDIEMMIGFQPNIFWKVCWAFVTPTILTFILCFSFYQWEPMTYGSYRYPNWSMVLGWLMLACSVIWIPIMFVIKMHLAPGRFIERLKLVCSPQPDWGPFLAQHRGERYKNMIDPLGTSSLGLKLPVKDLELGTQC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	GLYCINE
formula_weight	75.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	2

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6. Citations (2)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.02 Å
resolution_method	—
num_particles	162255

fit	/app/data/saxs_computation/r1/9r1h/9r1h.fit
pddf	/app/data/pr_computation/r1/9r1h/9r1h.pr.out
profile	/app/data/saxs_computation/r1/9r1h/9r1h.dat