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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN IZUMO1-JUNO COMPLEX (CRYSTAL FORM 3)
 
Authors :  U. Ohto, H. Ishida, T. Shimizu
Date :  26 Apr 16  (Deposition) - 22 Jun 16  (Release) - 29 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.86
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Fertilization, Izumo1, Juno, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  U. Ohto, H. Ishida, E. Krayukhina, S. Uchiyama, N. Inoue, T. Shimizu
Structure Of Izumo1-Juno Reveals Sperm-Oocyte Recognition During Mammalian Fertilization
Nature V. 534 566 2016
PubMed-ID: 27309808  |  Reference-DOI: 10.1038/NATURE18596

(-) Compounds

Molecule 1 - IZUMO SPERM-EGG FUSION PROTEIN 1
    ChainsA, C
    EngineeredYES
    Expression SystemDROSOPHILA
    Expression System Taxid7215
    FragmentUNP RESIDUES 20-255
    GeneIZUMO1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymOOCYTE BINDING/FUSION FACTOR,OBF,SPERM-SPECIFIC PROTEIN IZUMO
 
Molecule 2 - SPERM-EGG FUSION PROTEIN JUNO
    ChainsB, D
    EngineeredYES
    Expression SystemDROSOPHILA
    Expression System Taxid7215
    FragmentUNP RESIDUES 20-228
    GeneIZUMO1R, FOLR4, JUNO
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymFOLATE RECEPTOR 4,FOLATE RECEPTOR DELTA,FR-DELTA,IZUMO1 RECEPTOR PROTEIN JUNO

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SO41Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:194 , ASP A:195 , LYS A:212binding site for residue SO4 A 302
2AC2SOFTWARETRP B:50 , SER B:100 , ASN B:102 , ASN B:217 , ASN B:219binding site for residue CL B 302
3AC3SOFTWARECYS A:25 , PRO A:27 , GLU A:80 , LEU A:83 , LYS A:154 , SER D:203 , ARG D:205binding site for residue SO4 D 302
4AC4SOFTWARETRP D:50 , SER D:100 , ASN D:102 , ASN D:217 , ASN D:219binding site for residue CL D 303
5AC5SOFTWARETRP A:202 , ASN A:204binding site for Mono-Saccharide NAG A 301 bound to ASN A 204
6AC6SOFTWARELYS B:31 , PRO B:70 , ASN B:73binding site for Mono-Saccharide NAG B 301 bound to ASN B 73
7AC7SOFTWAREASN C:204 , THR C:206binding site for Mono-Saccharide NAG C 300 bound to ASN C 204
8AC8SOFTWARELYS D:31 , PRO D:70 , ASN D:73binding site for Mono-Saccharide NAG D 301 bound to ASN D 73

(-) SS Bonds  (26, 26)

Asymmetric Unit
No.Residues
1A:22 -A:149
2A:25 -A:152
3A:135 -A:159
4A:139 -A:165
5A:182 -A:233
6B:27 -B:55
7B:47 -B:95
8B:56 -B:99
9B:79 -B:172
10B:86 -B:143
11B:132 -B:206
12B:136 -B:186
13B:149 -B:166
14C:22 -C:149
15C:25 -C:152
16C:135 -C:159
17C:139 -C:165
18C:182 -C:233
19D:27 -D:55
20D:47 -D:95
21D:56 -D:99
22D:79 -D:172
23D:86 -D:143
24D:132 -D:206
25D:136 -D:186
26D:149 -D:166

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5JKE)

(-) 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:232
                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eehhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeeee.....eeeeeeeee....eeeeeee....eeee..hhhhh....eeeeeeeee.....eeeeeee...eeee...hhhhheeeeeeeee......eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jke A  18 RSPWCVICDPSVVLALKSLEKDYLPGHLDAKHHKAMMERVENAVKDFQELAYMGVVDEATLQKGSWSLLKDLKRITDSDVKGDLFVKELFWMLHLQKETFATYVARFQKEAYCPNKCGVMLQTLIWCKNCKKEVHACRKSYDCGERNVEVPQMEDMILDCELNWHQASEGLTDYSFYRVWGNNTETLVSKGKEATLTKPMVGPEDAGSYRCELGSVNSSPATIINFHVTVLP 254
                                    27        37        47        57        67|       82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252  
                                                                            67|                                                                                                                                                                                     
                                                                             73                                                                                                                                                                                     

Chain B from PDB  Type:PROTEIN  Length:203
                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh...................hhhhhhhh.....hhhhhhhhh..........hhhhh..hhhhhhhhhhhhhhhhhh..hhh.ee....ee..eeehhhhhhhhhhhhh..ee........................eehhhhh.hhhhhhhhh....eee...............hhhhh..hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jke B  18 PWGDELLNICMNAKHHKRVPSPEDKLYEECIPWKDNACCTLTTSWEAHLDVSPLYNFSLFHCGLLMPGCRKHFIQAICFYECSPNLGPWIQPVGERVVNVPLCQEDCEEWWEDCRMSYTCKSNWRGGWDWSQGKNRCPKGAQCLPFSHYFPTPADLCEKTWSNSFKASPERRNSGRCLQKWFEPAQGNPNVAVARLFASEFLE 232
                                    27        37        47        57        67        77        87        97       107  ||   129       139       149       159       169       179       189       199       209       219       229   
                                                                                                                      110|                                                                                                             
                                                                                                                       123                                                                                                             

Chain C from PDB  Type:PROTEIN  Length:232
                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eehhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeee.....eeeeeee......eeeeeee....eeee..hhhhh....eeeeeeeee.....eeeeeee...eeee...hhhhheeeeeeeee......eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jke C  18 RSPWCVICDPSVVLALKSLEKDYLPGHLDAKHHKAMMERVENAVKDFQELAYMGVVDEATLQKGSWSLLKDLKRITDSDVKGDLFVKELFWMLHLQKETFATYVARFQKEAYCPNKCGVMLQTLIWCKNCKKEVHACRKSYDCGERNVEVPQMEDMILDCELNWHQASEGLTDYSFYRVWGNNTETLVSKGKEATLTKPMVGPEDAGSYRCELGSVNSSPATIINFHVTVLP 254
                                    27        37        47        57        67|       82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252  
                                                                            67|                                                                                                                                                                                     
                                                                             73                                                                                                                                                                                     

Chain D from PDB  Type:PROTEIN  Length:203
                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh...................hhhhhhhh.....hhhhhhhhh..........hhhhh..hhhhhhhhhhhhhhhhhh..hhh.ee....ee..eeehhhhhhhhhhhhh..ee........................eehhhhh.hhhhhhhhh....eee...............hhhhh..hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jke D  18 PWGDELLNICMNAKHHKRVPSPEDKLYEECIPWKDNACCTLTTSWEAHLDVSPLYNFSLFHCGLLMPGCRKHFIQAICFYECSPNLGPWIQPVGERVVNVPLCQEDCEEWWEDCRMSYTCKSNWRGGWDWSQGKNRCPKGAQCLPFSHYFPTPADLCEKTWSNSFKASPERRNSGRCLQKWFEPAQGNPNVAVARLFASEFLE 232
                                    27        37        47        57        67        77        87        97       107  ||   129       139       149       159       169       179       189       199       209       219       229   
                                                                                                                      110|                                                                                                             
                                                                                                                       123                                                                                                             

   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 5JKE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 21)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        IZUM1_HUMAN | Q8IYV95f4e 5f4t 5f4v 5jk9 5jkc 5jkd
        JUNO_HUMAN | A6ND015f4e 5f4q 5jka 5jkb 5jkc 5jkd

(-) Related Entries Specified in the PDB File

5jk9 5jka 5jkb 5jkc 5jkd