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(-) Description

Title :  STRUCTURE OF MOUSE CLUSTERED PCDHGC3 EC1-3
 
Authors :  J. M. Nicoludis, S. -Y. Lau, C. P. I. Scharfe, D. S. Marks, W. A. Weihofen,
Date :  27 Apr 15  (Deposition) - 28 Oct 15  (Release) - 18 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protocadherin, Complex, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Nicoludis, S. Y. Lau, C. P. Scharfe, D. S. Marks, W. A. Weihofen, R. Gaudet
Structure And Sequence Analyses Of Clustered Protocadherins Reveal Antiparallel Interactions That Mediate Homophilic Specificity.
Structure V. 23 2087 2015
PubMed-ID: 26481813  |  Reference-DOI: 10.1016/J.STR.2015.09.005

(-) Compounds

Molecule 1 - PROTEIN PCDHGC3
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSPEEDET
    Expression System Strain: BL21-GOLD
    Expression System Taxid: 511693
    Fragment: UNP RESIDUES 30-344
    Gene: PCDHGC3
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: PROTOCADHERIN GAMMA C3,PROTOCADHERIN GAMMA SUBFAMILY C,3

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 20)

Asymmetric/Biological Unit (5, 20)
No.NameCountTypeFull Name
1CA15Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION
3EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5NA1Ligand/IonSODIUM ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:208 , ASN A:210 , ASP A:240 , ASP A:242 , ASN A:246 , ASP A:296binding site for residue CA A 401
02AC2SOFTWAREGLU A:116 , ASP A:173 , GLU A:175 , ASP A:209 , HOH A:697 , HOH A:716binding site for residue CA A 402
03AC3SOFTWAREGLU A:116 , GLU A:175 , ASP A:206 , ALA A:207 , ASP A:209 , ASP A:242binding site for residue CA A 403
04AC4SOFTWAREGLU A:9 , GLU A:10 , ASP A:63 , GLU A:65 , ASP A:100 , HOH A:669binding site for residue CA A 404
05AC5SOFTWAREGLU A:9 , GLU A:65 , ASP A:97 , ILE A:98 , ASP A:100 , ASP A:133binding site for residue CA A 405
06AC6SOFTWAREASN A:99 , ASN A:101 , ASP A:131 , ASP A:133 , ASN A:137 , ASP A:188binding site for residue CA A 406
07AC7SOFTWAREGLU A:225 , GLU A:283 , GLU B:225 , GLU B:283binding site for residue CA A 407
08AC8SOFTWAREGLU A:225 , ASP A:314 , GLU B:225 , ASP B:314binding site for residue CA A 408
09AC9SOFTWAREASP A:281 , GLU A:283 , ASP B:281 , GLU B:283 , HOH B:636 , HOH B:656binding site for residue CA A 409
10AD1SOFTWAREARG A:13 , ASN B:-6 , TYR B:-4 , NA B:407binding site for residue CL A 410
11AD2SOFTWAREHIS A:256 , HOH A:583 , ASP B:159binding site for residue MPD A 411
12AD3SOFTWAREASN B:99 , ASN B:101 , ASP B:131 , ASP B:133 , ASN B:137 , ASP B:188binding site for residue CA B 401
13AD4SOFTWAREGLU B:9 , GLU B:65 , ASP B:97 , ILE B:98 , ASP B:100 , ASP B:133binding site for residue CA B 402
14AD5SOFTWAREGLU B:9 , GLU B:10 , ASP B:63 , GLU B:65 , ASP B:100 , HOH B:724binding site for residue CA B 403
15AD6SOFTWAREGLU B:116 , GLU B:175 , ASP B:206 , ALA B:207 , ASP B:209 , ASP B:242binding site for residue CA B 404
16AD7SOFTWAREGLU B:116 , ASP B:173 , GLU B:175 , ASP B:209 , HOH B:668 , HOH B:711binding site for residue CA B 405
17AD8SOFTWAREASN B:208 , ASN B:210 , ASP B:240 , ASP B:242 , ASN B:246 , ASP B:296binding site for residue CA B 406
18AD9SOFTWAREGLU A:12 , ARG A:13 , CL A:410 , ASN B:-6 , TYR B:-4 , HOH B:678binding site for residue NA B 407
19AE1SOFTWAREGLN A:140 , GLY A:189 , GLY A:190 , THR A:191 , PRO A:192 , ALA A:193 , ASP B:268 , HOH B:719binding site for residue EPE B 408
20AE2SOFTWAREASP A:159 , HIS B:256 , HIS B:305 , HOH B:574binding site for residue MPD B 409

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:68 -A:74
2B:68 -B:74

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asn A:84 -Pro A:85
2Thr A:191 -Pro A:192
3Asn B:84 -Pro B:85
4Thr B:191 -Pro B:192

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ZI8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ZI8)

(-) Exons   (0, 0)

(no "Exon" information available for 4ZI8)

(-) 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:313
                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......eeeehhhhhh.hhhhhhhhh.eee.......eee.....eeee....hhhhhhh.....eeeeeeee....eeeeeeeeee.............eeeeee.......eee........hhhh.eeeeee.....eeeeeee.....eeeeeee..........eeeeeeeeee......eeeeeeeeeee.......ee...eeeeeee.......eeee..ee...hhhhhh.eeee......hhhhheee.....eeee..........eeeeeeeee........eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zi8 A   2 IIHYEILEERERGFPVGNVVTDLGLDLGSLSARRLRVVSGASRRFFEVNWETGEMFVNDRLDREELCGTLPSCTVTLELVVENPLELFSAEVVVQDINDNNPSFPTGEMKLEISEALAPGTRFPLESAHDPDVGSNSLQTYELSHNEYFALRVQTREDGTKYAELVLERALDWEREPSVQLVLTALDGGTPARSATLPIRITVLDANDNAPAFNQSLYRARVREDAPPGTRVAQVLATDLDEGLNGEIVYSFGSHNRAGVRELFALDLVTGVLTIKGRLDFEDTKLHEIYIQAKDKGANPEGAHCKVLVEVVD 314
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311   


Chain B from PDB  Type:PROTEIN  Length:323
                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee..ee..eeeee.......eeeehhhhhh.hhhhhhhhh.ee........eee.....eeee....hhhhhhh.....eeeeeeee....eeeeeeeeee.............eeeeee.......eee........hhhh.eeeeee.....eeeeeee.....eeeeeee..........eeeeeeeeee......eeeeeeeeeee.......ee...eeeeeee.......eeee..ee...hhhhh.eeeee......hhhhheee.....eeee..........eeeeeeeeee.......eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zi8 B  -8 HENLYFQGSTIIHYEILEERERGFPVGNVVTDLGLDLGSLSARRLRVVSGASRRFFEVNWETGEMFVNDRLDREELCGTLPSCTVTLELVVENPLELFSAEVVVQDINDNNPSFPTGEMKLEISEALAPGTRFPLESAHDPDVGSNSLQTYELSHNEYFALRVQTREDGTKYAELVLERALDWEREPSVQLVLTALDGGTPARSATLPIRITVLDANDNAPAFNQSLYRARVREDAPPGTRVAQVLATDLDEGLNGEIVYSFGSHNRAGVRELFALDLVTGVLTIKGRLDFEDTKLHEIYIQAKDKGANPEGAHCKVLVEVVD 314
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311
   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 4ZI8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ZI8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ZI8)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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4zi9