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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN RAGE ECTODOMAIN (VC1C2 FRAGMENT) IN COMPLEX WITH HUMAN S100A6
 
Authors :  L. Yatime, G. R. Andersen
Date :  18 Feb 15  (Deposition) - 02 Mar 16  (Release) - 14 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Signaling Complex, Pattern Recognition Receptor, Dimerization, Ef- Hand Calcium Binding Protein, Immunoglobulin Domain, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Yatime, C. Betzer, R. K. Jensen, S. Mortensen, P. H. Jensen, G. R. Andersen
The Structure Of The Rage:S100A6 Complex Reveals A Unique Mode Of Homodimerization For S100 Proteins.
Structure V. 24 2043 2016
PubMed-ID: 27818100  |  Reference-DOI: 10.1016/J.STR.2016.09.011

(-) Compounds

Molecule 1 - ADVANCED GLYCOSYLATION END PRODUCT-SPECIFIC RECEPTOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PETM11
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: V, C1 AND C2 DOMAINS (VC1C2 MODULE), FULL-LENGTH ECTODOMAIN, UNP RESIDUES 23-323
    Gene: AGER, RAGE
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RECEPTOR FOR ADVANCED GLYCOSYLATION END PRODUCTS
 
Molecule 2 - PROTEIN S100-A6
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PETM11
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: S100A6, CACY
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CALCYCLIN,GROWTH FACTOR-INDUCIBLE PROTEIN 2A9,MLN 4, PROLACTIN RECEPTOR-ASSOCIATED PROTEIN,PRA,S100 CALCIUM-BINDING PROTEIN A6

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 17)

Asymmetric Unit (4, 17)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2CA2Ligand/IonCALCIUM ION
3CL5Ligand/IonCHLORIDE ION
4ZN7Ligand/IonZINC ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
3CL-1Ligand/IonCHLORIDE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:160 , ASP A:201 , CL A:406 , CL A:407binding site for residue ZN A 401
02AC2SOFTWAREASP A:128 , HIS A:180 , GLU A:182binding site for residue ZN A 402
03AC3SOFTWAREGLU A:32 , HIS A:217 , HOH A:507 , HOH A:550binding site for residue ZN A 403
04AC4SOFTWAREHIS A:270 , CL A:408 , HOH A:544binding site for residue ZN A 404
05AC5SOFTWAREGLU A:132 , ARG A:228 , ZN A:412 , PHE B:16 , HIS B:17 , HIS B:27binding site for residue CL A 405
06AC6SOFTWAREASP A:160 , ASP A:201 , ZN A:401 , CL A:407binding site for residue CL A 406
07AC7SOFTWAREASP A:160 , ASP A:201 , ZN A:401 , CL A:406 , HOH A:640 , HOH B:206binding site for residue CL A 407
08AC8SOFTWAREHIS A:270 , ZN A:404binding site for residue CL A 408
09AC9SOFTWARELYS A:169binding site for residue ACT A 409
10AD1SOFTWAREARG A:77 , LEU A:79 , VAL A:302 , THR A:304binding site for residue ACT A 410
11AD2SOFTWARETHR A:55 , ARG A:57 , TRP A:72 , ASP A:93binding site for residue ACT A 411
12AD3SOFTWAREGLU A:132 , CL A:405 , HIS B:17 , HIS B:27binding site for residue ZN A 412
13AD4SOFTWARECYS B:3 , ARG B:55 , ASP B:59 , HOH B:201 , HOH B:205binding site for residue ZN B 101
14AD5SOFTWAREGLU B:41 , CL B:103binding site for residue ZN B 102
15AD6SOFTWAREGLU B:41 , ZN B:102binding site for residue CL B 103
16AD7SOFTWARESER B:20 , GLU B:23 , ASP B:25 , THR B:28 , GLU B:33 , HOH B:207binding site for residue CA B 104
17AD8SOFTWAREASP B:61 , ASN B:63 , ASP B:65 , GLU B:67 , GLU B:72 , HOH B:224binding site for residue CA B 105

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:38 -A:99
2A:144 -A:208
3A:259 -A:301

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Pro A:45 -Pro A:46
2Asn A:105 -Gly A:106
3Tyr A:150 -Pro A:151
4Leu A:214 -Pro A:215
5Glu A:243 -Pro A:244

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YBH)

(-) 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:302
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....eee...........eeeeeeee......eee............ee.....eee...hhhh.eeeeeeee.....eeeeeeeeeee......eee....eee....eeeeeeeeeee....eeeeee..eee.......eeeeeeee......eeeeeeeee...........eeeeee........ee......eee........eeeee....ee....eeeeeee.......eeeeee..ee.......eeeee..hhhhheeeeeeeee..eeeee...eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ybh A  21 AMAQNITARIGEPLVLKCKGAPKKPPQRLEWKLNTGRTEAWKVLSPQGGGPWDSVARVLPNGSLFLPAVGIQDEGIFRCQAMNRNGKETKSNYRVRVYQIPGKPEIVDSASELTAGVPNKVGTCVSEGSYPAGTLSWHLDGKPLVPNEKGVSVKEQTRRHPETGLFTLQSELMVTPARGGDPRPTFSCSFSPGLPRHRALRTAPIQPRVWEPVPLEEVQLVVEPEGGAVAPGGTVTLTCEVPAQPSPQIHWMKDGVPLPLPPSPVLILPEIGPQDQGTYSCVATHSSHGPQESRAVSISIIE 322
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320  


Chain B from PDB  Type:PROTEIN  Length:89
                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 4ybh B   2 ACPLDQAIGLLVAIFHKYSGREGDKHTLSKKELKELIQKELTIGSKLQDAEIARLMEDLDRNKDQEVNFQEYVTFLGALALIYNEALKG  90
                                    11        21        31        41        51        61        71        81
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 4YBH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (89, 96)

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  Cis Peptide Bonds
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  4ybh
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  RAGE_HUMAN | Q15109
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  S10A6_HUMAN | P06703
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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 4oi8 4p2y 4xyn 5d7f
        S10A6_HUMAN | P06703: 1k8u 1k96 1k9k 1k9p 2m1k

(-) Related Entries Specified in the PDB File

4p2y 4P2Y REPRESENTS THE STRUCTURE OF THE COMPLEX BETWEEN HUMAN RAGE ECTODOMAIN AND MOUSE S100A6