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(-) Description

Title :  REFINEMENT OF RAGE-DNA COMPLEX IN 3S59 WITHOUT DNA
 
Authors :  L. Yatime, G. R. Andersen
Date :  14 Jan 14  (Deposition) - 23 Apr 14  (Release) - 18 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Membrane, Signaling Proteinig Domain, Receptor, S100 Proteins Ab Oligomer Age Dna, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Yatime, G. R. Andersen
The Specificity Of Dna Recognition By The Rage Receptor.
J. Exp. Med. V. 211 749 2014
PubMed-ID: 24778420  |  Reference-DOI: 10.1084/JEM.20132526

(-) Compounds

Molecule 1 - ADVANCED GLYCOSYLATION END PRODUCT-SPECIFIC RECEPTOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: VC1 FRAGMENT
    Gene: AGER, RAGE
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RECEPTOR FOR ADVANCED GLYCOSYLATION END PRODUCTS

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4OF5)

(-) Sites  (0, 0)

(no "Site" information available for 4OF5)

(-) SS Bonds  (4, 4)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric 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
5Asn B:105 -Gly B:106
6Tyr B:150 -Pro B:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4OF5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OF5)

(-) Exons   (0, 0)

(no "Exon" information available for 4OF5)

(-) Sequences/Alignments

Asymmetric 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...........eeeeeee.......eee............ee.....eee...hhhhheeeeeeeee...eeeeeeeeeeee......eee....eee....eeeeeeeeeee....eeeeee..ee........eeeeeeee......eeeeeeeee...........eeeeee........ee......eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4of5 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:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eee...........eeeeeee.......eee............ee.....eee...hhhhheeeeeeeee...eeeeeeeeeeee......eee....eee....eeeeeeeeeee....eeeeee..ee........eeeeeeee......eeeeeeeee...........eeeeee........ee......eee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4of5 B  22 DAQNITARIGEPLVLKCKGAPKKPPQRLEWKLNTGRTEAWKVLSPQGGGPWDSVARVLPNGSLFLPAVGIQDEGIFRCQAMNRNGKETKSNYRVRVYQIPGKPEIVDSASELTAGVPNKVGTCVSEGSYPAGTLSWHLDGKPLVPNEKGVSVKEQTRRHPETGLFTLQSELMVTPARGGDPRPTFSCSFSPGLPRHRALRTAPIQPRVWEPVPL 235
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231
   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 4OF5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OF5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OF5)

(-) Gene Ontology  (73, 73)

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  Cis Peptide Bonds
    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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  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 4ofv 4oi7 4oi8 4p2y 4xyn 4ybh 5d7f

(-) Related Entries Specified in the PDB File

3s59 ORIGINAL ENTRY