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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN MDGA1 AND HUMAN NEUROLIGIN-2 COMPLEX
 
Authors :  H. M. Kim, J. A. Kim, D. Kim
Date :  05 Apr 17  (Deposition) - 12 Jul 17  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.14
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Immunogloubulin-Like Domain, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Kim, D. Kim, S. Y. Won, K. A. Han, D. Park, E. Cho, N. Yun, H. J. An, J. W. Um, E. Kim, J. O. Lee, J. Ko, H. M. Kim
Structural Insights Into Modulation Of Neurexin-Neuroligin Trans-Synaptic Adhesion By Mdga1/Neuroligin-2 Complex
Neuron V. 94 1121 2017
PubMed-ID: 28641111  |  Reference-DOI: 10.1016/J.NEURON.2017.05.034

(-) Compounds

Molecule 1 - NEUROLIGIN-2
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Plasmid: PACGP67A
    Expression System Strain: HI5
    Expression System Taxid: 7108
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 42-610
    Gene: NLGN2, KIAA1366
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - MAM DOMAIN-CONTAINING GLYCOSYLPHOSPHATIDYLINOSITOL ANCHOR PROTEIN 1
    Chains: B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Plasmid: PACGP67A
    Expression System Strain: HI5
    Expression System Taxid: 7108
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 19-330
    Gene: MDGA1, MAMDC3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GPI AND MAM PROTEIN,GPIM,GLYCOSYLPHOSPHATIDYLINOSITOL-MAM, MAM DOMAIN-CONTAINING PROTEIN 3

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 10)
No.NameCountTypeFull Name
1NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:522 , PHE A:523 , SER A:524binding site for Mono-Saccharide NAG A 701 bound to ASN A 522
2AC2SOFTWAREASN B:235binding site for Mono-Saccharide NAG B 403 bound to ASN B 235
3AC3SOFTWAREASN B:257binding site for Mono-Saccharide NAG B 404 bound to ASN B 257
4AC4SOFTWAREGLY B:278 , TYR B:305 , ASN B:307 , LYS B:319binding site for Poly-Saccharide residues NAG B 401 through NAG B 402 bound to ASN B 307

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:106 -A:141
2A:317 -A:328
3A:487 -A:521
4B:60 -B:108
5B:157 -B:214
6B:262 -B:308

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5XEQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5XEQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5XEQ)

(-) Exons   (0, 0)

(no "Exon" information available for 5XEQ)

(-) 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:525
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....eee.eeee.......eeeeeeeee......................eee.....................hhhhhhhhhhhhhhhh.......eeeeee...eeeeeee........hhhhh.hhhhhhhhh.eeeee...hhhhhhh.........hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhhhh........eeeee............hhhhhhhhhhhhh.....hhhhhhhhhh..hhhhhhh.......................hhhhhhhh......eeeeeee...hhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee...................hhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh........................eeee....eee...hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5xeq A  42 PVVNTAYGRVRGVRRELNNEILGPVVQFLGVPYATPPLGARRFQPPEAPASWPGVRQATTLPPACPQNLHGALPAIMLPVWFTDNLEAAATYVQNQSEDCLYLNLYVPGKKPVMLFLHGGSYMEGTGNMFDGSVLAAYGNVIVATLNYRLGVLGFLSTGDQAAKGNYGLLDQIQALRWLSENIAHFGGDPERITIFGSGAGASCVNLLILSHHSEGLFQKAIAQSGTAISSWSVNYQPLKYTRLLAAKVGCDREDSAEAVECLRRKPSRELVDQDVQPARYHIAFGPVVDGDVVPDDPEILMQQGEFLNYDMLIGVNQGEGLKFVEVSASAFDFTVSNFVDNLYGYPEGKDVLRETIKFMYTDWADRDNGEMRRKTLLALFTDHQWVAPAVATAKLHADYQSPVYFYTFYHHCQAEGRPEWADAAHGDELPYVFGVPMVGATDLFPCNFSKNDVMLSAVVMTYWTNFAKTGDPNQPVPNRFEEVVWSKFNSKEKQYLHIGLKPRVRDNYRANKVAFWLELVPHLH 609
                                    51        61        71        81        91       101       111       121       131       141       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386     ||404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       564       574       584       594       604     
                                                                                                                                     149|                                                                                                                                                                                                                      392|                                                                                                                                                    552|                                              
                                                                                                                                      175                                                                                                                                                                                                                       401                                                                                                                                                     563                                              


Chain B from PDB  Type:PROTEIN  Length:292
                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...........eeeee....eeeeeeee.....eeeeee............eeee...hhhhh.eeeeeee......eeeeeeeeee.....eeeee............eeeeee.......eeeeee............eeee........eeeeee.........eeeeeee.........eeeeee........eeee....eeee.....eeeeeeeee.....eee.................eeee...hhhhheeeeeeee......eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5xeq B  26 QAQIVHAGQACVVKEDERVYTIREGDTLMLQCLVTGHPRPQVRWTKTAGSAETSVFNETLRIERIARTQGGRYYCKAENGVGVPAIKSIRVDVQYLDEPMLTVHQTVRGNFYQEKTVFLRCTVNSNPPARFIWKRGSDTLSHSQDNGVDIYEPLYTQGETKVLKLKNLRPQDYASYTCQVSVRNVCGIPDKAITFRLTNTTAPPALKLSVNETLVVNPGENVTVQCLLTGGDPLPQLQWSHGPGPLPLGALAQGGTLSIPSVQARDSGYYNCTATNNVGNPAKKTVNLLVRS 328
                                    35     || 48        58        68        78||      93       103       113       123       133     ||146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326  
                                          41|                                79|                                                   139|                                                                                                                                                                                         
                                           45                                 85                                                    143
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5XEQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5XEQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5XEQ)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5XEQ)

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 Related Entries

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        MDGA1_HUMAN | Q8NFP4: 5v5v 5v5w

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