4OI7: PDB entry 4OI7

RAGE recognizes nucleic acids and promotes inflammatory responses to DNA. Determined by X-ray diffraction at 3.1 Å resolution. Released 30 Apr 2014.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,228
Mol. weight: 62.14 kDa
Released: 30 Apr 2014

Explore 4OI7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4OI7 contains 11 α-helices and 42 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: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	24-29	6	1
β-strand	34-36	3	2
α-helix	37-38	2
β-strand	48-55	8	1
β-strand	62-64	3	1
α-helix	71-74	4
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	120-121	2
β-strand	122-127	6	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	162-163	2	6
β-strand	171-179	9	4
β-strand	186-194	9	4
α-helix	196-197	2
β-strand	206-211	6	6
β-strand	220-221	2	6
β-strand	225	1	6
β-strand	228-230	3	5

Chain B: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	23	1
β-strand	24-29	6	7
β-strand	34-36	3	8
β-strand	49-55	7	7
β-strand	62-64	3	7
α-helix	71-74	4
β-strand	77-78	2	8
β-strand	84-86	3	8
α-helix	91-93	3
β-strand	95-102	8	7
β-strand	108-118	11	7
β-strand	119	1	9
α-helix	121-124	4
β-strand	125-127	3	10
β-strand	132-134	3	11
β-strand	140-149	10	10
β-strand	150	1	9
β-strand	154-159	6	12
β-strand	162-163	2	12
β-strand	172-179	8	10
β-strand	186-193	8	10
α-helix	196-197	2
β-strand	206-211	6	12
β-strand	220-221	2	12
β-strand	225	1	12
β-strand	228-230	3	11
α-helix	231-234	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Advanced glycosylation end product-specific receptor	A, B	protein	223	Homo sapiens	Q15109 (AlphaFold model)
5'-d(cptpgpcpapapcpgpaptpgpcptpapcpgpapapcpgptpg)-3'	E	DNA	22
5'-d(cpapcpgptptpcpgptpapgpcpaptpcpgptptpgpcpapg)-3'	F	DNA	22

Sequence of entity 1 (A, B), FASTA

>4OI7_1 Advanced glycosylation end product-specific receptor (chains A, B)
GSVDAQNITARIGEPLVLKCKGAPKKPPQRLEWKLNTGRTEAWKVLSPQGGGPWDSVARV
LPNGSLFLPAVGIQDEGIFRCQAMNRNGKETKSNYRVRVYQIPGKPEIVDSASELTAGVP
NKVGTCVSEGSYPAGTLSWHLDGKPLVPNEKGVSVKEQTRRHPETGLFTLQSELMVTPAR
GGDPRPTFSCSFSPGLPRHRALRTAPIQPRVWEPVPLEEAAAS

Sequence of entity 2 (E), FASTA

>4OI7_2 5'-D(*CP*TP*GP*CP*AP*AP*CP*GP*AP*TP*GP*CP*TP*AP*CP*GP*AP*AP*CP*GP*TP*G)-3' (chains E)
CTGCAACGATGCTACGAACGTG

Sequence of entity 3 (F), FASTA

>4OI7_3 5'-D(*CP*AP*CP*GP*TP*TP*CP*GP*TP*AP*GP*CP*AP*TP*CP*GP*TP*TP*GP*CP*AP*G)-3' (chains F)
CACGTTCGTAGCATCGTTGCAG

Primary citation

RAGE is a nucleic acid receptor that promotes inflammatory responses to DNA. Sirois, C.M., Jin, T., Miller, A.L. et al. J Exp Med (2013) 210:2447-2463. DOI 10.1084/jem.20120201 · 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…
4P2Y 2.3 Å, Crystal structure of the human RAGE ectodomain (fragment VC1C2) in complex with mouse…
6XQ9 2.3 Å, Receptor for Advanced Glycation End Products VC1 domain in complex with Fragments 1 & 13

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