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9s2x

Crystal structure of the human RAGE ectodomain in complex with murine S100A6 mutant Y84C

Method: X-RAY DIFFRACTION D_max: 129.0 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s2x
deposition_date	2025-07-23
last_revision	2026-05-13
title	Crystal structure of the human RAGE ectodomain in complex with murine S100A6 mutant Y84C
keywords	signaling complex, S100 alarmin, RAGE receptor, homodimerization, disulfide crosslinking, SIGNALING PROTEIN; SIGNALING PROTEIN
method	X-RAY DIFFRACTION

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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	35.33 Å
rg_electron	36.26 Å
i0	31045100.00
molecular_weight	43205.0 kDa
excluded_volume	53852 Å³
envelope_volume	76778 Å³
shell_volume	21233 Å³
envelope_diameter	125.7 Å
shell_rg	34.88 Å
envelope_rg	36.18 Å
shape_rg	36.29 Å
total_rg	36.05 Å
total_atoms	3006
n_residues	390
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	129.0 Å
rg_real	36.00 Å
rg_real_error	1.35 Å
i0_real	3.1050e+07
i0_real_error	5.5930e+05
rg_reciprocal	35.59 Å
i0_reciprocal	31030000.0000
total_estimate	0.6618
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	22.9 Å
skewness	0.621
kurtosis	-0.395
angular_range	— – 0.2250 Å⁻¹
current_alpha	0.0000
highest_alpha	1417000.0000
n_real_points	46
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.460; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.218; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Advanced glycosylation end product-specific receptor
formula_weight	32680.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3222

GAMAQNITARIGEPLVLKCKGAPKKPPQRLEWKLNTGRTEAWKVLSPQGGGPWDSVARVLPNGSLFLPAVGIQDEGIFRCQAMNRNGKETKSNYRVRVYQIPGKPEIVDSASELTAGVPNKVGTCVSEGSYPAGTLSWHLDGKPLVPNEKGVSVKEQTRRHPETGLFTLQSELMVTPARGGDPRPTFSCSFSPGLPRHRALRTAPIQPRVWEPVPLEEVQLVVEPEGGAVAPGGTVTLTCEVPAQPSPQIHWMKDGVPLPLPPSPVLILPEIGPQDQGTYSCVATHSSHGPQESRAVSISIIEP

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	Protein S100-A6
formula_weight	10132.7 kDa
mutation	Y84C
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

GAMACPLDQAIGLLVAIFHKYSGKEGDKHTLSKKELKELIQKELTIGSKLQDAEIARLMDDLDRNKDQEVNFQEYVAFLGALALICNEALK

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Escherichia coli BL21(DE3)

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	6

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	4

Entity 5 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	4

Entity 6 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	205

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6. Citations (1)

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length_a	75.650 Å
length_b	113.010 Å
length_c	139.510 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	I 2 2 2
int_tables_number	23
crystal_system	—

resolution	2.350 Å
resolution_low	43.907 Å
r_factor	0.2059
r_work	0.2043
r_free	0.2352

fit	/app/data/saxs_computation/s2/9s2x/9s2x.fit
pddf	/app/data/pr_computation/s2/9s2x/9s2x.pr.out
profile	/app/data/saxs_computation/s2/9s2x/9s2x.dat

Crystal structure of the human RAGE ectodomain in complex with murine S100A6 mutant Y84C

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)