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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN RAGE ECTODOMAIN (FRAGMENT VC1C2) IN COMPLEX WITH MOUSE S100A6
 
Authors :  L. Yatime, G. R. Andersen
Date :  05 Mar 14  (Deposition) - 11 Mar 15  (Release) - 23 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (4x)
Biol. Unit 3:  A,B  (2x)
Keywords :  Signaling Complex, Pattern Recognition Receptor, Dimerization, Ef- Hand Calcium Binding Protein, 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 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
    Expression System Plasmid: PETM11
    Expression System Strain: SHUFFLE T7 EXPRESS
    Expression System Taxid: 562
    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
    Expression System Plasmid: PETM11
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: S100A6, CACY
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: 5B10, CALCYCLIN, PROLACTIN RECEPTOR-ASSOCIATED PROTEIN, S100 CALCIUM-BINDING PROTEIN A6

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (4x): AB
Biological Unit 3 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 21)

Asymmetric Unit (4, 21)
No.NameCountTypeFull Name
1ACT7Ligand/IonACETATE ION
2CA2Ligand/IonCALCIUM ION
3CL6Ligand/IonCHLORIDE ION
4ZN6Ligand/IonZINC ION
Biological Unit 1 (1, 7)
No.NameCountTypeFull Name
1ACT7Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
3CL-1Ligand/IonCHLORIDE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 28)
No.NameCountTypeFull Name
1ACT28Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
3CL-1Ligand/IonCHLORIDE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 14)
No.NameCountTypeFull Name
1ACT14Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
3CL-1Ligand/IonCHLORIDE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:128 , HIS A:180 , GLU A:182binding site for residue ZN A 1001
02AC2SOFTWAREASP A:160 , ASP A:201 , CL A:1007 , CL A:1008binding site for residue ZN A 1002
03AC3SOFTWAREGLU A:32 , HIS A:217 , HOH A:1144 , HOH A:1147binding site for residue ZN A 1003
04AC4SOFTWAREHIS A:270 , CL A:1009 , HOH A:1105binding site for residue ZN A 1004
05AC5SOFTWAREGLU A:132 , ARG A:228 , HIS B:17 , HIS B:27 , ZN B:101binding site for residue CL A 1006
06AC6SOFTWAREASP A:160 , ASP A:201 , ZN A:1002 , CL A:1008binding site for residue CL A 1007
07AC7SOFTWAREASP A:160 , ASP A:201 , ZN A:1002 , CL A:1007binding site for residue CL A 1008
08AC8SOFTWAREHIS A:270 , ZN A:1004binding site for residue CL A 1009
09AC9SOFTWARETHR A:55 , ARG A:57 , TRP A:72 , ASP A:93binding site for residue ACT A 1010
10AD1SOFTWAREASP A:73 , HOH A:1101 , ASP B:65 , GLN B:66 , GLU B:67binding site for residue ACT A 1011
11AD2SOFTWAREARG A:77 , HOH A:1102 , HOH A:1105binding site for residue ACT A 1012
12AD3SOFTWAREARG A:228 , HOH A:1249 , ASN B:69 , GLN B:71 , HOH B:218binding site for residue ACT A 1013
13AD4SOFTWARETHR A:154 , LEU A:155 , GLU A:175 , HOH A:1251binding site for residue ACT A 1014
14AD5SOFTWAREGLU A:132 , CL A:1006 , HIS B:17 , HIS B:27binding site for residue ZN B 101
15AD6SOFTWAREILE B:44binding site for residue CL B 102
16AD7SOFTWAREASP B:61 , ASN B:63 , ASP B:65 , GLU B:67 , GLU B:72 , HOH B:223binding site for residue CA B 103
17AD8SOFTWARESER B:20 , GLU B:23 , ASP B:25 , THR B:28 , GLU B:33 , HOH B:209binding site for residue CA B 104
18AD9SOFTWARECYS B:3 , ARG B:55 , ASP B:59 , HOH B:208binding site for residue ZN B 105
19AE1SOFTWAREASP B:50binding site for residue ACT B 106

(-) 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
2Tyr A:150 -Pro A:151
3Lys A:169 -Gly A:170
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 4P2Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P2Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4P2Y)

(-) 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:301
                                                                                                                                                                                                                                                                                                                                             
               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......eeeeeeeee......eeeeeeeee...........eeeeee........ee......eee........eeeee....ee.....eeeeee.......eeeeee..ee.......eeee...hhhhheeeeeeeee..eeeee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p2y A  21 AMAQNITARIGEPLVLKCKGAPKKPPQRLEWKLNTGRTEAWKVLSPQGGGPWDSVARVLPNGSLFLPAVGIQDEGIFRCQAMNRNGKETKSNYRVRVYQIPGKPEIVDSASELTAGVPNKVGTCVSEGSYPAGTLSWHLDGKPLVPNEKGVSVKEQTRRHPETGLFTLQSELMVTPARGGDPRPTFSCSFSPGLPRHRALRTAPIQPRVWEPVPLEEVQLVVEPEGGAVAPGGTVTLTCEVPAQPSPQIHWMKDGVPLPLPPSPVLILPEIGPQDQGTYSCVATHSSHGPQESRAVSISII 321
                                    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:88
                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 4p2y B   2 ACPLDQAIGLLVAIFHKYSGKEGDKHTLSKKELKELIQKELTIGSKLQDAEIARLMDDLDRNKDQEVNFQEYVAFLGALALIYNEALK  89
                                    11        21        31        41        51        61        71        81
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  - → 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 4P2Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P2Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P2Y)

(-) Gene Ontology  (87, 93)

Asymmetric Unit(hide GO term definitions)

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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 4xyn 4ybh 5d7f

(-) Related Entries Specified in the PDB File

4lp4 4LP4 IS THE STRUCTURE OF THE APO-VC1 FRAGMENT FROM THE ECTODOMAIN OF THE SAME RECEPTOR
4lp5 4LP5 IS THE STRUCTURE OF THE APO-ECTODOMAIN OF THE SAME RECEPTOR