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(-) Description

Title :  RAGE IS A NUCLEIC ACID RECEPTOR THAT PROMOTES INFLAMMATORY RESPONSES TO DNA.
 
Authors :  T. Jin, J. Jiang, T. Xiao
Date :  19 Jan 14  (Deposition) - 30 Apr 14  (Release) - 30 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B,E,F
Keywords :  Ig Fold, Dna Binding, Transport Protein, Signaling Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. M. Sirois, T. Jin, A. L. Miller, D. Bertheloot, H. Nakamura, G. L. Horvath, A. Mian, J. Jiang, J. Schrum, L. Bossaller, K. Pelka, N. Garbi, Y. Brewah, J. Tian, C. Chang, P. S. Chowdhury, G. P. Sims, R. Kolbeck, A. J. Coyle, A. A. Humbles, T. S. Xiao, E. Latz
Rage Is A Nucleic Acid Receptor That Promotes Inflammatory Responses To Dna.
J. Exp. Med. V. 210 2447 2013
PubMed-ID: 24081950  |  Reference-DOI: 10.1084/JEM.20120201

(-) Compounds

Molecule 1 - ADVANCED GLYCOSYLATION END PRODUCT-SPECIFIC RECEPTOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 23-237
    Gene: AGER, RAGE
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RAGE, RECEPTOR FOR ADVANCED GLYCOSYLATION END PRODUCTS
 
Molecule 2 - 5'-D(*CP*CP*AP*TP*GP*AP*CP*TP*GP*TP*AP*GP*GP*AP*AP*AP*CP*TP *CP*TP*AP*GP*A)-3'
    Chains: E
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'-D(*CP*TP*CP*TP*AP*GP*AP*GP*TP*TP*TP*CP*CP*TP*AP*CP*AP*GP *TP*CP*AP*TP*G)-3'
    Chains: F
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4OI8)

(-) Sites  (0, 0)

(no "Site" information available for 4OI8)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:38 -A:99
2A:144 -A:208
3B:38 -B:99
4B:144 -B:208

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Pro A:45 -Pro A:46
2Asn A:105 -Gly A:106
3Tyr A:150 -Pro A:151
4Pro B:45 -Pro B:46
5Arg B:104 -Asn B:105
6Asn B:105 -Gly B:106
7Tyr B:150 -Pro B:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4OI8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OI8)

(-) Exons   (0, 0)

(no "Exon" information available for 4OI8)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eee...........eeeeeeee......eee.....hhhhhh.ee.....eee...hhhh.eeeeeeee.....eeeeeeeeeee...eeeeee....eee....eeeeeeeeeee....eeeeee..ee.......eeeeeeeee......eeeeeeeee...........eeeeee........ee......eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oi8 A  23 AQNITARIGEPLVLKCKGAPKKPPQRLEWKLNTGRTEAWKVLSPQGGGPWDSVARVLPNGSLFLPAVGIQDEGIFRCQAMNRNGKETKSNYRVRVYQIPGKPEIVDSASELTAGVPNKVGTCVSEGSYPAGTLSWHLDGKPLVPNEKGVSVKEQTRRHPETGLFTLQSELMVTPARGGDPRPTFSCSFSPGLPRHRALRTAPIQPRVWEPV 233
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232 


Chain B from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....eee............eeeeeee......eee.....hhhhhh.ee.....eee...hhhh.eeeeeeee.....eeeeeeeeeee......eee....eee.....eeeeeeeeee....eeeeee..ee........eeeeeeee......eeeeeeee............eeeeee........ee......eee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oi8 B  21 VDAQNITARIGEPLVLKCKGAPKKPPQRLEWKLNTGRTEAWKVLSPQGGGPWDSVARVLPNGSLFLPAVGIQDEGIFRCQAMNRNGKETKSNYRVRVYQIPGKPEIVDSASELTAGVPNKVGTCVSEGSYPAGTLSWHLDGKPLVPNEKGVSVKEQTRRHPETGLFTLQSELMVTPARGGDPRPTFSCSFSPGLPRHRALRTAPIQPRVWEPVPL 235
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230     


Chain E from PDB  Type:DNA  Length:23
                                                       
                 4oi8 E   1 CCATGACTGTAGGAAACTCTAGA  23
                                    10        20   


Chain F from PDB  Type:DNA  Length:23
                                                       
                 4oi8 F   2 CTCTAGAGTTTCCTACAGTCATG  24
                                    11        21
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4OI8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OI8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OI8)

(-) Gene Ontology  (73, 73)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Arg B:104 - Asn B:105   [ RasMol ]  
    Asn A:105 - Gly A:106   [ RasMol ]  
    Asn B:105 - Gly B:106   [ RasMol ]  
    Pro A:45 - Pro A:46   [ RasMol ]  
    Pro B:45 - Pro B:46   [ RasMol ]  
    Tyr A:150 - Pro A:151   [ RasMol ]  
    Tyr B:150 - Pro B:151   [ RasMol ]  
 

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  4oi8
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  RAGE_HUMAN | Q15109
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RAGE_HUMAN | Q15109: 1pwi 2bjp 2e5e 2ens 2l7u 2le9 2lmb 2m1k 2mjw 2mov 3cjj 3o3u 4lp4 4lp5 4of5 4ofv 4oi7 4p2y 4xyn 4ybh 5d7f

(-) Related Entries Specified in the PDB File

4oi7