Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF RED ABALONE EGG VERL REPEAT 3 IN COMPLEX WITH SPERM LYSIN AT 1.7 A RESOLUTION (CRYSTAL FORM I)
 
Authors :  H. Sadat Al-Hosseini, I. Raj, 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 :  1.70
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
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, C, E, G
    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, D, F, H
    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
    Fragment: UNP RESIDUES 340-453
    Gene: VERL
    Organism Common: CALIFORNIA RED ABALONE
    Organism Scientific: HALIOTIS RUFESCENS
    Organism Taxid: 6454

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): ABCD    
Biological Unit 2 (1x):     EFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN B:373 , LEU B:378 , HOH B:5009 , HOH B:5025 , TRP D:409 , NAG D:501 , HOH D:5021binding site for Mono-Saccharide NAG B 501 bound to ASN B 373
2AC2SOFTWAREASN B:417 , VAL B:420binding site for Mono-Saccharide NAG B 502 bound to ASN B 417
3AC3SOFTWARETRP B:409 , NAG B:501 , ASN D:373 , HOH D:5012 , HOH D:5023binding site for Mono-Saccharide NAG D 501 bound to ASN D 373
4AC4SOFTWAREASN D:417 , THR D:419binding site for Mono-Saccharide NAG D 502 bound to ASN D 417
5AC5SOFTWAREASN F:373 , LEU F:378 , HOH F:5007 , HOH F:5027 , TRP H:409 , NAG H:501 , HOH H:5021binding site for Mono-Saccharide NAG F 501 bound to ASN F 373
6AC6SOFTWARELYS A:124 , ASP A:125 , ASN A:127 , ASN F:417 , HOH F:5020binding site for Mono-Saccharide NAG F 502 bound to ASN F 417
7AC7SOFTWARETRP F:409 , NAG F:501 , HOH F:5023 , ASN H:373 , LEU H:378 , HOH H:5015 , HOH H:5030binding site for Mono-Saccharide NAG H 501 bound to ASN H 373
8AC8SOFTWAREASN H:417 , THR H:419 , TYR H:444binding site for Mono-Saccharide NAG H 502 bound to ASN H 417

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1B:345 -B:443
2B:374 -B:406
3D:345 -D:443
4D:374 -D:406
5F:345 -F:443
6F:374 -F:406
7H:345 -H:443
8H:374 -H:406

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly B:410 -Pro B:411
2Gly D:410 -Pro D:411
3Gly F:410 -Pro F:411
4Gly H:410 -Pro H:411

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5IIA)

(-) 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:125
                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhhhhhh......hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iia A  28 FLNKAFEVALKVQIIAGFDRGLVKWLRVHGRTLSTVQKKALYFVNRRYMQTHWANYMLWINKKIDALGRTPVVGDYTRLGAEIGRRIDMAYFYDFLKDKNMIPKYLPYMEEINRMRPADVPVKYM 152
                                    37        47        57        67        77        87        97       107       117       127       137       147     


Chain B from PDB  Type:PROTEIN  Length:107
                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee........eeeeeee...eeeeeeee..eeeee....eeeeeeee............ee.eeeeee..eeeeeeeeeeeeeee.....eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 5iia B 338 AADWDVYCSQDESIPAKFISRLVTALEKTEINCSNGLVPITQEFGINMMLIQYTRNELLDSPGMCVFWGPYSVPKNDTVVLYTVTARLKWSEGPPTNLSIQCYMPKS 448
                                   347       357   ||  371       381       391       401       411       421       431       441       
                                                 361|                                                                                  
                                                  366                                                                                  


Chain C from PDB  Type:PROTEIN  Length:125
                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhhhhhh......hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iia C  28 FLNKAFEVALKVQIIAGFDRGLVKWLRVHGRTLSTVQKKALYFVNRRYMQTHWANYMLWINKKIDALGRTPVVGDYTRLGAEIGRRIDMAYFYDFLKDKNMIPKYLPYMEEINRMRPADVPVKYM 152
                                    37        47        57        67        77        87        97       107       117       127       137       147     


Chain D from PDB  Type:PROTEIN  Length:107
                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee........eeeeeee..eeeeeeee..eeeee....eeeeeeee............ee.eeeeee..eeeeeeeeeeeeeee.....eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 5iia D 337 AAADWDVYCSQDESIPAKFISRLQALEKTEINCSNGLVPITQEFGINMMLIQYTRNELLDSPGMCVFWGPYSVPKNDTVVLYTVTARLKWSEGPPTNLSIQCYMPKS 448
                                   346       356  ||   371       381       391       401       411       421       431       441       
                                                359|                                                                                   
                                                 365                                                                                   


Chain E from PDB  Type:PROTEIN  Length:125
                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhhhhhh......hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iia E  28 FLNKAFEVALKVQIIAGFDRGLVKWLRVHGRTLSTVQKKALYFVNRRYMQTHWANYMLWINKKIDALGRTPVVGDYTRLGAEIGRRIDMAYFYDFLKDKNMIPKYLPYMEEINRMRPADVPVKYM 152
                                    37        47        57        67        77        87        97       107       117       127       137       147     


Chain F from PDB  Type:PROTEIN  Length:105
                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee........eeeeeee..eeeeeeee..eeeee....eeeeeeee............ee.eeeeee..eeeeeeeeeeeeeee.....eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 5iia F 339 ADWDVYCSQDESIPAKFISRLVALEKTEINCSNGLVPITQEFGINMMLIQYTRNELLDSPGMCVFWGPYSVPKNDTVVLYTVTARLKWSEGPPTNLSIQCYMPKS 448
                                   348       358 ||    373       383       393       403       413       423       433       443     
                                               360|                                                                                  
                                                366                                                                                  


Chain G from PDB  Type:PROTEIN  Length:126
                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhhhhhh......hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5iia G  27 KFLNKAFEVALKVQIIAGFDRGLVKWLRVHGRTLSTVQKKALYFVNRRYMQTHWANYMLWINKKIDALGRTPVVGDYTRLGAEIGRRIDMAYFYDFLKDKNMIPKYLPYMEEINRMRPADVPVKYM 152
                                    36        46        56        66        76        86        96       106       116       126       136       146      


Chain H from PDB  Type:PROTEIN  Length:102
                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee........eeeeeee.eeeeeeee..eeeee....eeeeeeee............ee.eeeeee..eeeeeeeeeeeeeee.....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 5iia H 340 DWDVYCSQDESIPAKFISRLALEKTEINCSNGLVPITQEFGINMMLIQYTRNELLDSPGMCVFWGPYSVPKNDTVVLYTVTARLKWSEGPPTNLSIQCYMPK 447
                                   349       359|      375       385       395       405       415       425       435       445  
                                             359|                                                                                 
                                              366
   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 5IIA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly B:410 - Pro B:411   [ RasMol ]  
    Gly D:410 - Pro D:411   [ RasMol ]  
    Gly F:410 - Pro F:411   [ RasMol ]  
    Gly H:410 - Pro H:411   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5iia
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  ELYS_HALRU | P04552
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  Q8WR62_HALRU | Q8WR62
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  ELYS_HALRU | P04552
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q8WR62_HALRU | Q8WR62
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1lis
1lyn
2lis
2lyn
3d4c
3d4g
3ef7
3nk3
3nk4 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_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_1000218323 RELATED DB: PDB RELATED ENTRY UNDER SUBMISSION