4P2Y: Human RAGE ectodomain

Crystal structure of the human RAGE ectodomain (fragment VC1C2) in complex with mouse S100A6. Determined by X-ray diffraction at 2.3 Å resolution. Released 11 Mar 2015.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Homo sapiens, Mus musculus
Chains: 2
Atoms: 3,213
Mol. weight: 43.97 kDa
Ligands: CA, ZN
Released: 11 Mar 2015

Explore 4P2Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4P2Y contains 12 α-helices and 33 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 7 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	24-29	6	1
β-strand	34-36	3	2
β-strand	48-55	8	1
β-strand	62-64	3	1
β-strand	77-78	2	2
β-strand	84-86	3	2
α-helix	91-93	3
β-strand	95-102	8	1
β-strand	108-118	11	1
β-strand	119	1	3
α-helix	120-124	5
β-strand	125-127	3	4
β-strand	132-134	3	5
β-strand	139-149	11	4
β-strand	150	1	3
β-strand	154-159	6	6
β-strand	162-164	3	6
β-strand	171-179	9	4
β-strand	186-194	9	4
α-helix	196-197	2
β-strand	206-211	6	6
α-helix	218-219	2
β-strand	220-221	2	6
α-helix	222-224	3
β-strand	225	1	6
β-strand	228-230	3	5
α-helix	232-234	3
β-strand	239-243	5	7
β-strand	248-249	2	8
β-strand	255-260	6	7
β-strand	268-273	6	9
β-strand	276-277	2	9
β-strand	285-288	4	7
α-helix	293-295	3
β-strand	297-305	9	9
β-strand	308-312	5	9
β-strand	316-318	3	9
β-strand	319-320	2	8

Chain B: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	4-20	17
β-strand	29	1	10
α-helix	31-41	11
α-helix	43-45	3
α-helix	50-60	11
β-strand	68	1	10
α-helix	70-88	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Advanced glycosylation end product-specific receptor	A	protein	304	Homo sapiens	Q15109 (AlphaFold model)
Protein S100-A6	B	protein	91	Mus musculus	P14069 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4P2Y_1 Advanced glycosylation end product-specific receptor (chains A)
GAMAQNITARIGEPLVLKCKGAPKKPPQRLEWKLNTGRTEAWKVLSPQGGGPWDSVARVL
PNGSLFLPAVGIQDEGIFRCQAMNRNGKETKSNYRVRVYQIPGKPEIVDSASELTAGVPN
KVGTCVSEGSYPAGTLSWHLDGKPLVPNEKGVSVKEQTRRHPETGLFTLQSELMVTPARG
GDPRPTFSCSFSPGLPRHRALRTAPIQPRVWEPVPLEEVQLVVEPEGGAVAPGGTVTLTC
EVPAQPSPQIHWMKDGVPLPLPPSPVLILPEIGPQDQGTYSCVATHSSHGPQESRAVSIS
IIEP

Sequence of entity 2 (B), FASTA

>4P2Y_2 Protein S100-A6 (chains B)
GAMACPLDQAIGLLVAIFHKYSGKEGDKHTLSKKELKELIQKELTIGSKLQDAEIARLMD
DLDRNKDQEVNFQEYVAFLGALALIYNEALK

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2
ZN	Zinc ion	Zn	6

Water and common crystallization additives (ACT, CL) are not listed.

Primary citation

The Structure of the RAGE:S100A6 Complex Reveals a Unique Mode of Homodimerization for S100 Proteins. Yatime, L., Betzer, C., Jensen, R.K. et al. Structure (2016). DOI 10.1016/j.str.2016.09.011 · PubMed

Other PDB entries of the same protein (UniProt Q15109 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5D7F 1.3 Å, X-ray structure of Ca(2+)-S100B with human RAGE-derived W72 peptide
3O3U 1.5 Å, Crystal Structure of Human Receptor for Advanced Glycation Endproducts (RAGE)
6XQ1 1.51 Å, Receptor for Advanced Glycation End Products VC1 domain in complex with…
6XQ3 1.71 Å, Receptor for Advanced Glycation End Products VC1 domain in complex with…
6XQ5 1.8 Å, Receptor for Advanced Glycation End Products VC1 domain in complex with Fragment 1
6XQ7 1.8 Å, Receptor for Advanced Glycation End Products VC1 domain in complex with Fragment 5
6XQ8 1.82 Å, Receptor for Advanced Glycation End Products VC1 domain in complex with Fragments 1 & 11
3CJJ 1.85 Å, Crystal structure of human rage ligand-binding domain
6XQ6 1.9 Å, Receptor for Advanced Glycation End Products VC1 domain in complex with Fragment 11
7LML 2.15 Å, Receptor for Advanced Glycation End Products VC1 domain in complex with…
6XQ9 2.3 Å, Receptor for Advanced Glycation End Products VC1 domain in complex with Fragments 1 & 13
9S2X 2.35 Å, Crystal structure of the human RAGE ectodomain in complex with murine S100A6 mutant Y84C

Browse structure collections

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