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

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Advanced glycosylation end product-specific receptor

Homo sapiens

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 23–323	Fragment：V, C1 and C2 domains (VC1C2 module), full-length ectodomain, UNP residues 23-323	Protein S100-A6 × 2 （P14069） ZN ZINC ION × 12 CL CHLORIDE ION × 8 ACT ACETATE ION × 8 CA CALCIUM ION × 4 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.2 M Zn acetate, 0.1 M Na cacodylate pH 6.5, 9% isopropanol	Resolution 2.35 Å R-free 0.235

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 9S2X	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2E5E Solution Structure of Variable-type Domain of Human Receptor for Advanced Glycation Endproducts Deposited 2006-12-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–121（99 aa） Fragment：VARIABLE-TYPE DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；298 K；Pressure 1 NMR sample composition 0.2mM Variable-type Domain of Receptor for Advanced Glycation Endproducts U-15N, 13C; 20mM phosphate buffer NA, 100mM NA2SO4; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.2mM Variable-type Domain of Receptor for Advanced Glycation Endproducts; 20mM phosphate buffer NA, 100mM NA2SO4; 100% D2O \| 100% D2O	Resolution not provided
2ENS Solution structure of the third ig-like domain from human Advanced glycosylation end product-specific receptor Deposited 2007-03-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 235–323（89 aa） Fragment：Ig-like domain, UNP residues 235-323	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1.17mM 13C,15N-laveled protein; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2L7U Structure of CEL-PEP-RAGE V domain complex Deposited 2010-12-23	Different construct 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 23–125（103 aa） Fragment：Ig-like V-type domain residues 23-125	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 130；Pressure ambient NMR sample composition 0.1 mM [U-100% 13C; U-100% 15N] V domain, 0.3 mM CEL-PEP, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.32 mM [U-100% 13C; U-100% 15N] V domain, 1 mM CEL-PEP, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2LE9 RAGEC2-S100A13 tetrameric complex Deposited 2011-06-14	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 235–327（93 aa） Fragment：UNP RESIDUES 235-327 Chain D 235–327（93 aa） Fragment：UNP RESIDUES 235-327	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient NMR sample composition 1.1 mM [U-100% 13C; U-100% 15N] entity_1-1, 1.1 mM entity_2-2, 25 mM sodium phosphate-3, 100 mM sodium chloride-4, 1 mM DTT-5, 0.02 mM sodium azide-6, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1.2 mM entity_1-7, 1.2 mM [U-100% 13C; U-100% 15N] entity_2-8, 25 mM sodium phosphate-9, 100 mM sodium chloride-10, 1 mM DTT-11, 0.02 mM sodium azide-12, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2LMB Solution Structure of C-terminal RAGE (ctRAGE) Deposited 2011-11-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 363–404（42 aa） Fragment：residues 363-404	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 130；Pressure ambient NMR sample composition 300 uM [U-99% 13C; U-99% 15N] ctRAGE, 10 % [U-100% 2H] D2O, 10 mM potassium phosphate, 100 mM sodium chloride, 0.02 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2M1K Interaction of Human S100A6 (C3S) with V domain of Receptor for Advanced Glycation End products (RAGE) Deposited 2012-11-29	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 23–121（99 aa） Fragment：UNP residues 23-121 Chain C 23–121（99 aa） Fragment：UNP residues 23-121	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 1.0 mM [U-100% 13C; U-100% 15N] S100A6 C3S, 20 mM TRIS, 10 mM Calcium chloride, 0.01 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2MJW Structural Insights into Calcium Bound S100P - V Domain of the receptor for advanced glycation end products (RAGE) Complex Deposited 2014-01-19	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 23–121（99 aa） Fragment：UNP RESIDUES 23-121 Chain C 23–121（99 aa） Fragment：UNP RESIDUES 23-121	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 0.6 mM [U-100% 13C; U-100% 15N] entity_1-1, 0.6 mM [U-100% 13C; U-100% 15N] entity_2-2, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2MOV Receptor for Advanced Glycation End Products (RAGE) Specifically Recognizes Methylglyoxal Derived AGEs. Deposited 2014-05-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–125（103 aa） Fragment：UNP residues 23-125	Not recorded	IOR N~5~-[(5R)-5-methyl-4-oxo-4,5-dihydro-1H-imidazol-2-yl]-L-ornithine × 1	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Pressure ambient NMR sample composition 0.1 mM [U-13C; U-15N] Methylglyoxal-derived hydroimidazolones isoform 1, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3CJJ Crystal structure of human rage ligand-binding domain Deposited 2008-03-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–240（218 aa） Fragment：V and C1 domain, ligand-binding domain	Not recorded	ACT ACETATE ION × 1 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1M Na cacodylate, 0.2M Zn acetate, 11% PEG 8000, pH 6.5, vapor diffusion, hanging drop, temperature 298K	Resolution 1.85 Å R-free 0.240
3O3U Crystal Structure of Human Receptor for Advanced Glycation Endproducts (RAGE) Deposited 2010-07-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain N 23–231（209 aa） Fragment：MBP: UNP residues 28-384, RAGE: UNP residues 23-231	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；200 mM Li sulfate, 100 mM Tris-HCl, pH 7.5 and 10% (w/v) polyethylene glycol 4,000 , VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.50 Å R-free 0.184
4LP4 Crystal structure of the human RAGE VC1 fragment in space group P62 Deposited 2013-07-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–231（209 aa） Fragment：V and C1 domains (VC1 fragment), ectodomain fragment (UNP residues 23-231)	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；2.5 M sodium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.40 Å R-free 0.217
4LP4 Crystal structure of the human RAGE VC1 fragment in space group P62 Deposited 2013-07-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 23–231（209 aa） Fragment：V and C1 domains (VC1 fragment), ectodomain fragment (UNP residues 23-231)	Not recorded	NA SODIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；2.5 M sodium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.40 Å R-free 0.217
4LP5 Crystal structure of the full-length human RAGE extracellular domain (VC1C2 fragment) Deposited 2013-07-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 23–323（301 aa） Fragment：V, C1 and C2 domains (VC1C2 fragment), full-length ectodomain (UNP residues 23-323)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.1 M Tris, 10% Ethanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.80 Å R-free 0.286
4LP5 Crystal structure of the full-length human RAGE extracellular domain (VC1C2 fragment) Deposited 2013-07-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–323（301 aa） Fragment：V, C1 and C2 domains (VC1C2 fragment), full-length ectodomain (UNP residues 23-323)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.1 M Tris, 10% Ethanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.80 Å R-free 0.286
4OF5 Refinement of RAGE-DNA complex in 3S59 without DNA Deposited 2014-01-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–237（215 aa） Fragment：VC1 fragment	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；298 K；10% PEG6000, 0.1 M Tris_HCl pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.235
4OF5 Refinement of RAGE-DNA complex in 3S59 without DNA Deposited 2014-01-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 23–237（215 aa） Fragment：VC1 fragment	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；298 K；10% PEG6000, 0.1 M Tris_HCl pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.235
4OFV Refinement of RAGE-DNA complex in 3S58 without DNA Deposited 2014-01-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–235（213 aa） Fragment：VC1 fragment	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.4；298 K；12% PEG6000, 0.1 M Tris-HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.10 Å R-free 0.240
4OFV Refinement of RAGE-DNA complex in 3S58 without DNA Deposited 2014-01-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 23–235（213 aa） Fragment：VC1 fragment	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.4；298 K；12% PEG6000, 0.1 M Tris-HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.10 Å R-free 0.240
4OI7 RAGE recognizes nucleic acids and promotes inflammatory responses to DNA Deposited 2014-01-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 23–237（215 aa） Fragment：UNP residues 23-237 Chain B 23–237（215 aa） Fragment：UNP residues 23-237	Not recorded	EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；298 K；12% PEG6000, 0.1 M Tris-HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.10 Å R-free 0.237
4OI8 RAGE is a nucleic acid receptor that promotes inflammatory responses to DNA. Deposited 2014-01-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 23–237（215 aa） Fragment：UNP residues 23-237 Chain B 23–237（215 aa） Fragment：UNP residues 23-237	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；298 K；0.1 M HEPES, pH 7.4, 5% PEG6000, 5% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.10 Å R-free 0.267
4P2Y Crystal structure of the human RAGE ectodomain (fragment VC1C2) in complex with mouse S100A6 Deposited 2014-03-05	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 23–323（301 aa） Fragment：V, C1 and C2 domains (VC1C2 module), full-length ectodomain, UNP residues 23-323	Not recorded	ZN ZINC ION × 6 CL CHLORIDE ION × 6 ACT ACETATE ION × 7 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.2 M Zn acetate, 0.1 M Na cacodylate pH 6.5, 10% isopropanol	Resolution 2.30 Å R-free 0.207
4P2Y Crystal structure of the human RAGE ectodomain (fragment VC1C2) in complex with mouse S100A6 Deposited 2014-03-05	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 23–323（301 aa） Fragment：V, C1 and C2 domains (VC1C2 module), full-length ectodomain, UNP residues 23-323	Not recorded	ZN ZINC ION × 24 CL CHLORIDE ION × 24 ACT ACETATE ION × 28 CA CALCIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.2 M Zn acetate, 0.1 M Na cacodylate pH 6.5, 10% isopropanol	Resolution 2.30 Å R-free 0.207
4P2Y Crystal structure of the human RAGE ectodomain (fragment VC1C2) in complex with mouse S100A6 Deposited 2014-03-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 23–323（301 aa） Fragment：V, C1 and C2 domains (VC1C2 module), full-length ectodomain, UNP residues 23-323	Not recorded	ZN ZINC ION × 12 CL CHLORIDE ION × 12 ACT ACETATE ION × 14 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.2 M Zn acetate, 0.1 M Na cacodylate pH 6.5, 10% isopropanol	Resolution 2.30 Å R-free 0.207
4YBH Crystal structure of the human RAGE ectodomain (VC1C2 fragment) in complex with human S100A6 Deposited 2015-02-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 23–323（301 aa） Fragment：V, C1 and C2 domains (VC1C2 module), full-length ectodomain, UNP residues 23-323	Not recorded	ZN ZINC ION × 14 CL CHLORIDE ION × 10 ACT ACETATE ION × 6 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.2 M Zn acetate, 0.1 M Na cacodylate pH 6.5, 10% isopropanol	Resolution 2.40 Å R-free 0.233
5D7F X-ray structure of Ca(2+)-S100B with human RAGE-derived W72 peptide Deposited 2015-08-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain P 65–79（15 aa）	Not recorded	CA CALCIUM ION × 4 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；100mM Na cacodylate pH 6.8, 22% w/v PEG 3350, 5mM CaCl2	Resolution 1.30 Å R-free 0.183
6VXG Structure of the C-terminal Domain of RAGE and Its Inhibitor Deposited 2020-02-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 363–404（42 aa） Fragment：C-terminal residues 363-404	Not recorded	RQV N-(4-{7-cyano-4-[(morpholin-4-yl)methyl]quinolin-2-yl}phenyl)acetamide × 1	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 10；Pressure 1 NMR sample composition 300 uM [U-100% 13C; U-100% 15N] C-terminal RAGE, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
6XQ1 Receptor for Advanced Glycation End Products VC1 domain in complex with 3-(3-((4-(4-carboxyphenoxy)benzyl)oxy)phenyl)-1H-indole-2-carboxylic acid Deposited 2020-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 23–231（209 aa） Fragment：VC1 domain, resdues 23-231 Chain B 23–231（209 aa） Fragment：VC1 domain, resdues 23-231	Not recorded	ACT ACETATE ION × 14 CL CHLORIDE ION × 4 V74 3-[3-({[3-(4-carboxyphenoxy)phenyl]methoxy}methyl)phenyl]-1H-indole-2-carboxylic acid × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；2.5 M NaOAc (pH 7.5)	Resolution 1.51 Å R-free 0.197
6XQ3 Receptor for Advanced Glycation End Products VC1 domain in complex with 3-(3-(((3-(4-Carboxyphenoxy)benzyl)oxy)methyl)phenyl)-1H-indole-2-carboxylic acid Deposited 2020-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 23–231（209 aa） Fragment：VC1 domain, resdues 23-231 Chain B 23–231（209 aa） Fragment：VC1 domain, resdues 23-231	Not recorded	ACT ACETATE ION × 8 CL CHLORIDE ION × 4 V6Y 3-(3-{[3-(4-carboxyphenoxy)phenyl]methoxy}phenyl)-1H-indole-2-carboxylic acid × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；2.5 M NaOAc (pH 7.5)	Resolution 1.71 Å R-free 0.220
6XQ5 Receptor for Advanced Glycation End Products VC1 domain in complex with Fragment 1 Deposited 2020-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 23–231（209 aa） Fragment：VC1 domain, resdues 23-231 Chain B 23–231（209 aa） Fragment：VC1 domain, resdues 23-231	Not recorded	ACT ACETATE ION × 14 CL CHLORIDE ION × 4 V6M 7-methyl-3-phenyl-1H-indole-2-carboxylic acid × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；2.5 M NaOAc (pH 7.5)	Resolution 1.80 Å R-free 0.196
6XQ6 Receptor for Advanced Glycation End Products VC1 domain in complex with Fragment 11 Deposited 2020-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 23–231（209 aa） Fragment：VC1 domain, resdues 23-231 Chain B 23–231（209 aa） Fragment：VC1 domain, resdues 23-231	Not recorded	ACT ACETATE ION × 14 CL CHLORIDE ION × 4 V6P 3-phenoxyphenol × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；2.5 M NaOAc (pH 7.5)	Resolution 1.90 Å R-free 0.221
6XQ7 Receptor for Advanced Glycation End Products VC1 domain in complex with Fragment 5 Deposited 2020-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 23–231（209 aa） Fragment：VC1 domain, resdues 23-231 Chain B 23–231（209 aa） Fragment：VC1 domain, resdues 23-231	Not recorded	ACT ACETATE ION × 18 V6V 5-bromo-3-methyl-1H-indole-2-carboxylic acid × 14 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；2.5 M NaOAc (pH 7.5)	Resolution 1.80 Å R-free 0.222
6XQ8 Receptor for Advanced Glycation End Products VC1 domain in complex with Fragments 1 & 11 Deposited 2020-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 23–231（209 aa） Fragment：VC1 domain, resdues 23-231 Chain B 23–231（209 aa） Fragment：VC1 domain, resdues 23-231	Not recorded	ACT ACETATE ION × 12 V6M 7-methyl-3-phenyl-1H-indole-2-carboxylic acid × 4 V6P 3-phenoxyphenol × 6 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；2.5 M NaOAc (pH 7.5)	Resolution 1.82 Å R-free 0.218
6XQ9 Receptor for Advanced Glycation End Products VC1 domain in complex with Fragments 1 & 13 Deposited 2020-07-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–231（209 aa） Fragment：VC1 domain, resdues 23-231	Not recorded	ACT ACETATE ION × 2 V6S 4-(3-hydroxyphenoxy)benzoic acid × 2 V6M 7-methyl-3-phenyl-1H-indole-2-carboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；2.5 M NaOAc (pH 7.5)	Resolution 2.30 Å R-free 0.239
6XQ9 Receptor for Advanced Glycation End Products VC1 domain in complex with Fragments 1 & 13 Deposited 2020-07-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 23–231（209 aa） Fragment：VC1 domain, resdues 23-231	Not recorded	ACT ACETATE ION × 2 V6S 4-(3-hydroxyphenoxy)benzoic acid × 2 V6M 7-methyl-3-phenyl-1H-indole-2-carboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；2.5 M NaOAc (pH 7.5)	Resolution 2.30 Å R-free 0.239
7LML Receptor for Advanced Glycation End Products VC1 domain in complex with 3-(3-(((3-(4-Carboxyphenoxy)benzyl)oxy)methyl)phenyl)-1H-indole-2-carboxylic acid Deposited 2021-02-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–231（209 aa） Fragment：VC1 domain, resdues 23-231 Chain B 23–231（209 aa） Fragment：VC1 domain, resdues 23-231	Not recorded	ACT ACETATE ION × 6 CL CHLORIDE ION × 2 Y6S 6-iodanyl-1~{H}-indole-2-carboxylic acid × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；2.5 M NaOAc (pH 7.5)	Resolution 2.15 Å R-free 0.235
7LMW Receptor for Advanced Glycation End Products VC1 domain in complex with 3-(3-((4-(4-carboxyphenoxy)benzyl)oxy)phenyl)-1H-indole-2-carboxylic acid Deposited 2021-02-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–231（209 aa） Fragment：VC1 domain, resdues 23-231 Chain B 23–231（209 aa） Fragment：VC1 domain, resdues 23-231	Not recorded	Y6P 7-methyl-3-(1~{H}-pyrazol-4-yl)-1~{H}-indole-2-carboxylic acid × 6 ACT ACETATE ION × 5 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；2.5 M NaOAc (pH 7.5)	Resolution 2.50 Å R-free 0.256
8I9M The RAGE and HMGB1 complex Deposited 2023-02-07	Different construct 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 B 23–233（211 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.19 Å
9D36 Structure of the C-terminal Domain of RAGE and Its Inhibitor Deposited 2024-08-09	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 362–404（43 aa）	Not recorded	A1A2E 4-[(morpholin-4-yl)methyl]-2-{4-[(2R)-5-oxopyrrolidin-2-yl]phenyl}quinoline-7-carbonitrile × 1	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 60；Pressure 1 NMR sample composition 40 uM [U-13C; U-15N] ctRAGE, 100 uM RAGE406R, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 40 uM [U-13C; U-15N] ctRAGE, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

31 other PDB entries and 38 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RAGE_HUMAN
Isoform	Q15109-10
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–304； UniProt 23–323

Protein S100-A6

Mus musculus

UniProt P14069

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 1–89	Mutation：Y84C	Advanced glycosylation end product-specific receptor × 2 （Q15109） ZN ZINC ION × 12 CL CHLORIDE ION × 8 ACT ACETATE ION × 8 CA CALCIUM ION × 4 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.2 M Zn acetate, 0.1 M Na cacodylate pH 6.5, 9% isopropanol	Resolution 2.35 Å R-free 0.235

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9S2X	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4P2Y Crystal structure of the human RAGE ectodomain (fragment VC1C2) in complex with mouse S100A6 Deposited 2014-03-05	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–89（89 aa）	Not recorded	ZN ZINC ION × 6 CL CHLORIDE ION × 6 ACT ACETATE ION × 7 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.2 M Zn acetate, 0.1 M Na cacodylate pH 6.5, 10% isopropanol	Resolution 2.30 Å R-free 0.207
4P2Y Crystal structure of the human RAGE ectodomain (fragment VC1C2) in complex with mouse S100A6 Deposited 2014-03-05	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 1–89（89 aa）	Not recorded	ZN ZINC ION × 24 CL CHLORIDE ION × 24 ACT ACETATE ION × 28 CA CALCIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.2 M Zn acetate, 0.1 M Na cacodylate pH 6.5, 10% isopropanol	Resolution 2.30 Å R-free 0.207
4P2Y Crystal structure of the human RAGE ectodomain (fragment VC1C2) in complex with mouse S100A6 Deposited 2014-03-05	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–89（89 aa）	Not recorded	ZN ZINC ION × 12 CL CHLORIDE ION × 12 ACT ACETATE ION × 14 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.2 M Zn acetate, 0.1 M Na cacodylate pH 6.5, 10% isopropanol	Resolution 2.30 Å R-free 0.207

1 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	S10A6_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–91； UniProt 1–89

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9s2x
Deposition date deposition_date	2025-07-23
最后修订 last_revision	2026-05-13
Structure title title	Crystal structure of the human RAGE ectodomain in complex with murine S100A6 mutant Y84C
Keywords keywords	signaling complex, S100 alarmin, RAGE receptor, homodimerization, disulfide crosslinking, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	35.33 Å
Radius of gyration Rg (electron density) rg_electron	36.26 Å
Forward intensity I(0) i0	31045100.00
Molecular weight molecular_weight	43205.0 kDa
Excluded volume excluded_volume	53852 Å³
Envelope volume envelope_volume	76778 Å³
Hydration-shell volume shell_volume	21233 Å³
Envelope diameter envelope_diameter	125.7 Å
Shell Rg shell_rg	34.88 Å
Envelope Rg envelope_rg	36.18 Å
Shape Rg shape_rg	36.29 Å
Total Rg total_rg	36.05 Å
Total atoms total_atoms	3006
Residues n_residues	390
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	129.0 Å
Rg (real space) rg_real	36.00 Å
Rg uncertainty (real space) rg_real_error	1.35 Å
I(0) (real space) i0_real	3.1050e+07
I(0) uncertainty (real space) i0_real_error	5.5930e+05
Rg (reciprocal space) rg_reciprocal	35.59 Å
I(0) (reciprocal space) i0_reciprocal	31030000.0000
Solution quality estimate total_estimate	0.6618
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.9 Å
Skewness Skewness skewness	0.621
Kurtosis Kurtosis kurtosis	-0.395
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1417000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria 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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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Advanced glycosylation end product-specific receptor
Molecular weight formula_weight	32680.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3222

GAMAQNITARIGEPLVLKCKGAPKKPPQRLEWKLNTGRTEAWKVLSPQGGGPWDSVARVLPNGSLFLPAVGIQDEGIFRCQAMNRNGKETKSNYRVRVYQIPGKPEIVDSASELTAGVPNKVGTCVSEGSYPAGTLSWHLDGKPLVPNEKGVSVKEQTRRHPETGLFTLQSELMVTPARGGDPRPTFSCSFSPGLPRHRALRTAPIQPRVWEPVPLEEVQLVVEPEGGAVAPGGTVTLTCEVPAQPSPQIHWMKDGVPLPLPPSPVLILPEIGPQDQGTYSCVATHSSHGPQESRAVSISIIEP

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Protein S100-A6
Molecular weight formula_weight	10132.7 kDa
Mutation mutation	Y84C
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GAMACPLDQAIGLLVAIFHKYSGKEGDKHTLSKKELKELIQKELTIGSKLQDAEIARLMDDLDRNKDQEVNFQEYVAFLGALALICNEALK

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	205

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8. Citations (1)

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Unit-cell length a length_a	75.650 Å
Unit-cell length b length_b	113.010 Å
Unit-cell length c length_c	139.510 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	43.907 Å
R factor r_factor	0.2059
R_work r_work	0.2043
R_free 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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Advanced glycosylation end product-specific receptor

State in the Current Structure

Other States of the Same Protein in the Database

Protein S100-A6

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)