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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN RAGE VC1 FRAGMENT IN SPACE GROUP P62
 
Authors :  L. Yatime, G. R. Andersen
Date :  15 Jul 13  (Deposition) - 16 Oct 13  (Release) - 18 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Immunoglobulin Fold, Pattern Recognition Receptor, Signaling Receptor, Membrane, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Yatime, G. R. Andersen
Structural Insights Into The Oligomerization Mode Of The Human Receptor For Advanced Glycation End-Products.
Febs J. V. 280 6556 2013
PubMed-ID: 24119142  |  Reference-DOI: 10.1111/FEBS.12556

(-) Compounds

Molecule 1 - ADVANCED GLYCOSYLATION END PRODUCT-SPECIFIC RECEPTOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETM11
    Expression System Strain: SHUFFLE T7 EXPRESS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: V AND C1 DOMAINS (VC1 FRAGMENT), ECTODOMAIN FRAGMENT (UNP RESIDUES 23-231)
    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  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1NA4Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:21 , ILE A:96 , HOH A:401BINDING SITE FOR RESIDUE NA A 301
2AC2SOFTWAREGLU A:59 , ARG B:179 , HOH B:489BINDING SITE FOR RESIDUE NA B 301
3AC3SOFTWAREARG A:179 , GLU B:59BINDING SITE FOR RESIDUE NA B 302
4AC4SOFTWAREALA B:21 , ILE B:96BINDING SITE FOR RESIDUE NA B 303

(-) 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  (4, 4)

Asymmetric Unit
No.Residues
1Pro A:45 -Pro A:46
2Tyr A:150 -Pro A:151
3Pro B:45 -Pro B:46
4Tyr B:150 -Pro B:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LP4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LP4)

(-) Exons   (0, 0)

(no "Exon" information available for 4LP4)

(-) 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:212
                                                                                                                                                                                                                                                    
               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......eee....eee....eeeeeeeeeee....eeeeee..eee......eeeeeeeee......eeeeeeeee...........eeeeee........ee......eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lp4 A  20 GAMAQNITARIGEPLVLKCKGAPKKPPQRLEWKLNTGRTEAWKVLSPQGGGPWDSVARVLPNGSLFLPAVGIQDEGIFRCQAMNRNGKETKSNYRVRVYQIPGKPEIVDSASELTAGVPNKVGTCVSEGSYPAGTLSWHLDGKPLVPNEKGVSVKEQTRRHPETGLFTLQSELMVTPARGGDPRPTFSCSFSPGLPRHRALRTAPIQPRVWE 231
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229  


Chain B from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               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......eee....eee....eeeeeeeeeee....eeeeee..eee......eeeeeeeee......eeeeeeeee...........eeeeee........ee......eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lp4 B  20 GAMAQNITARIGEPLVLKCKGAPKKPPQRLEWKLNTGRTEAWKVLSPQGGGPWDSVARVLPNGSLFLPAVGIQDEGIFRCQAMNRNGKETKSNYRVRVYQIPGKPEIVDSASELTAGVPNKVGTCVSEGSYPAGTLSWHLDGKPLVPNEKGVSVKEQTRRHPETGLFTLQSELMVTPARGGDPRPTFSCSFSPGLPRHRALRTAPIQPRVWE 231
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229
   Legend:   → Mismatch (orange background)
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  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 4LP4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LP4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LP4)

(-) Gene Ontology  (73, 73)

Asymmetric Unit(hide GO term definitions)

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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 4lp5 4of5 4ofv 4oi7 4oi8 4p2y 4xyn 4ybh 5d7f

(-) Related Entries Specified in the PDB File

4lp5