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(-) Description

Title :  CRYSTAL STRUCTURE OF RED ABALONE EGG VERL REPEAT 3 IN COMPLEX WITH SPERM LYSIN AT 1.64 A RESOLUTION (CRYSTAL FORM II)
 
Authors :  I. Raj, H. Sadat Al-Hosseini, K. Nishimura, D. De Sanctis, L. Jovine
Date :  01 Mar 16  (Deposition) - 14 Jun 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.64
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cell Adhesion, Fertilization, Egg-Sperm Interaction, Gamete Recognition, Sperm Receptor, Egg Coat, Vitelline Envelope, Zp Domain, Zp-N Domain, Sperm Acrosome, Egg Coat Penetration (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Raj, H. Sadat Al Hosseini, E. Dioguardi, K. Nishimura, L. Han, A. Villa, D. De Sanctis, L. Jovine
Structural Basis Of Egg Coat-Sperm Recognition At Fertilization.
Cell V. 169 1315 2017
PubMed-ID: 28622512  |  Reference-DOI: 10.1016/J.CELL.2017.05.033
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EGG-LYSIN
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK-293S
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Expression System Vector: PHLSEC
    Expression System Vector Type: PLASMID
    Organism Common: CALIFORNIA RED ABALONE
    Organism Scientific: HALIOTIS RUFESCENS
    Organism Taxid: 6454
    Synonym: SPERM-LYSIN
 
Molecule 2 - VITELLINE ENVELOPE SPERM LYSIN RECEPTOR
    Chains: B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK-293S
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Expression System Vector: PHLSEC
    Expression System Vector Type: PLASMID
    Gene: VERL
    Organism Common: CALIFORNIA RED ABALONE
    Organism Scientific: HALIOTIS RUFESCENS
    Organism Taxid: 6454

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SUC1Ligand/IonSUCROSE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:66 , HOH A:1001binding site for residue EPE A 900
2AC2SOFTWARELYS A:89 , LYS A:131 , HOH A:1022 , ASN B:376 , GLY B:377 , LEU B:378 , VAL B:379 , SER B:402 , PRO B:403 , GLY B:404 , MET B:405 , HOH B:616 , HOH B:622 , HOH B:638binding site for residue SUC B 501
3AC3SOFTWAREASN B:373 , TRP B:409 , HOH B:636 , HOH B:643binding site for Mono-Saccharide NAG B 502 bound to ASN B 373
4AC4SOFTWARETHR A:104 , HOH A:1005 , LYS B:416 , ASN B:417 , TYR B:444 , HOH B:644binding site for Mono-Saccharide NAG B 503 bound to ASN B 417

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1B:345 -B:443
2B:374 -B:406

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly B:410 -Pro B:411

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5IIB)

(-) 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:124
                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhh......hhhhhhhhh.hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iib A  28 FLNKAFEVALKVQIIAGFDRGLVKWLRVHGRTLSTVQKKALYFVNRRYMQTHWANYMLWINKKIDALGRTPVVGDYTRLGAEIGRRIDMAYFYDFLKDKNMIPKYLPYMEEINRMRPADVPVKY 151
                                    37        47        57        67        77        87        97       107       117       127       137       147    


Chain B from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee........eeeeeee.....eeeeeeee..eeeee.....eeeeee..hhhhh.........eeeee......eeeeeeeeeeee.....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 5iib B 338 AADWDVYCSQDESIPAKFISRLVTSQALEKTEINCSNGLVPITQEFGINMMLIQYTRNELLDSPGMCVFWGPYSVPKNDTVVLYTVTARLKWSEGPPTNLSIQCYMPK 447
                                   347       357    || 369       379       389       399       409       419       429       439        
                                                  362|                                                                                  
                                                   365
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  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 5IIB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly B:410 - Pro B:411   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        ELYS_HALRU | P04552: 1lis 1lyn 2lis 2lyn 5ii7 5ii8 5ii9 5iia 5mr3
        Q8WR62_HALRU | Q8WR62: 5ii4 5ii5 5iia 5iic 5mr2 5mr3

(-) Related Entries Specified in the PDB File

1lis
1lyn
2lis
2lyn
3d4c
3d4g
3ef7
3nk3
3nk4 RELATED ID: D_1000218044 RELATED DB: PDB RELATED ENTRY UNDER SUBMISSION RELATED ID: D_1000218048 RELATED DB: PDB RELATED ENTRY UNDER SUBMISSION RELATED ID: D_1000218050 RELATED DB: PDB RELATED ENTRY UNDER SUBMISSION RELATED ID: D_1000218079 RELATED DB: PDB RELATED ENTRY UNDER SUBMISSION RELATED ID: D_1000218080 RELATED DB: PDB RELATED ENTRY UNDER SUBMISSION RELATED ID: D_1000218081 RELATED DB: PDB RELATED ENTRY UNDER SUBMISSION RELATED ID: D_1000218190 RELATED DB: PDB RELATED ENTRY UNDER SUBMISSION