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(-) Description

Title :  CRYSTAL STRUCTURE OF RED ABALONE EGG VERL REPEAT 2 WITH LINKER IN COMPLEX WITH SPERM LYSIN AT 1.8 A RESOLUTION
 
Authors :  K. Nishimura, I. Raj, H. Sadat Al-Hosseini, D. De Sanctis, L. Jovine
Date :  21 Dec 16  (Deposition) - 14 Jun 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
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, Sperm 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 Common: HUMAN
    Expression System Taxid: 9606
    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 Plasmid: PHLSEC
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Gene: VERL
    Mutation: YES
    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  (4, 20)

Asymmetric Unit (4, 20)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GOL12Ligand/IonGLYCEROL
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PGE2Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL8Ligand/IonGLYCEROL
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PGE-1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL4Ligand/IonGLYCEROL
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PGE2Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:86 , LYS A:90 , ARG A:113 , ASP H:210 , GOL H:902binding site for residue GOL A 201
02AC2SOFTWAREMET A:128 , ASP B:177 , PHE B:181 , ILE B:193 , ARG B:195 , LYS D:253binding site for residue GOL B 901
03AC3SOFTWAREASN B:254 , NAG B:905binding site for residue GOL B 902
04AC4SOFTWAREGLY B:247 , TYR B:249 , LYS F:235 , LEU F:236binding site for residue CL B 903
05AC5SOFTWAREARG B:265 , ASP B:275 , HOH B:1002 , GLY D:247 , TYR D:249 , HOH D:1009binding site for residue GOL B 904
06AC6SOFTWAREASN C:140 , HOH C:1003binding site for residue GOL C 900
07AC7SOFTWAREPRO B:248 , SER B:250 , VAL B:258 , PRO D:273 , THR D:274 , ASP D:275 , HOH D:1008 , LYS F:235binding site for residue GOL D 901
08AC8SOFTWARETYR D:249 , HOH D:1001 , HOH D:1044 , HOH D:1046binding site for residue GOL D 902
09AC9SOFTWAREGLU B:292 , THR D:174 , LEU D:202 , TRP D:268 , PRO D:272binding site for residue GOL D 903
10AD1SOFTWARETYR E:118 , ASP E:121binding site for residue GOL E 901
11AD2SOFTWARELYS B:235 , LEU B:236 , GLY F:247 , TYR F:249binding site for residue CL F 401
12AD3SOFTWAREARG A:47 , LEU G:85 , ASN G:88binding site for residue PGE G 900
13AD4SOFTWARELYS G:66 , GLU G:137binding site for residue PGE G 901
14AD5SOFTWAREPRO F:248 , SER F:250 , PRO H:273 , THR H:274 , ASP H:275binding site for residue GOL H 901
15AD6SOFTWAREGOL A:201 , HOH F:518 , ASP H:210 , TRP H:246 , TYR H:249 , HOH H:1001 , HOH H:1039binding site for residue GOL H 902
16AD7SOFTWAREASN B:254 , THR B:256 , VAL B:257 , PRO B:283 , GOL B:902binding site for Mono-Saccharide NAG B 905 bound to ASN B 254
17AD8SOFTWAREASN D:254 , VAL D:257 , HOH D:1041 , HIS G:56 , ASP G:121binding site for Mono-Saccharide NAG D 904 bound to ASN D 254
18AD9SOFTWAREASN F:254 , THR F:256 , HOH F:507binding site for Mono-Saccharide NAG F 402 bound to ASN F 254
19AE1SOFTWAREHIS C:56 , ASP C:121 , ASP C:125 , LYS H:253 , ASN H:254 , THR H:256 , HOH H:1011binding site for Mono-Saccharide NAG H 903 bound to ASN H 254

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1B:182 -B:280
2B:211 -B:243
3B:294 -D:201
4D:182 -D:280
5D:211 -D:243
6F:182 -F:280
7F:211 -F:243
8F:294 -H:201
9H:182 -H:280
10H:211 -H:243

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Gly B:247 -Pro B:248
2Gly D:247 -Pro D:248
3Ser D:285 -Pro D:286
4Gly F:247 -Pro F:248
5Gly H:247 -Pro H:248

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5MR3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5MR3)

(-) Exons   (0, 0)

(no "Exon" information available for 5MR3)

(-) 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 ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhh......hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mr3 A  28 FLNKAFEVALKVQIIAGFDRGLVKWLRVHGRTLSTVQKKALYFVNRRYMQTHWANYMLWINKKIDALGRTPVVGDYTRLGAEIGRRIDMAYFYDFLKDKNMIPKYLPYMEEINRMRPADVPVKYM 152
                                    37        47        57        67        77        87        97       107       117       127       137       147     


Chain B from PDB  Type:PROTEIN  Length:117
                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee........eeeeeee.....eeeeee..eeeee....eeeeeeee............ee.eeeeee..eeeeeeeeeeeeee......eeeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 5mr3 B 175 GIDWDVFCSQNENIPAKFISRLVAPVEKMDVDCSNGLVPITHEHGFNMMLIQYTRNKLLDSPGMCVFWGPYSVPKNDTVVLYTVTARLKWSEGPPTDLSIQCYMPKSPDAPKPEACL 295
                                   184       194    || 208       218       228       238       248       258       268       278       288       
                                                  199|                                                                                           
                                                   204                                                                                           


Chain C from PDB  Type:PROTEIN  Length:127
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhh......hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mr3 C  26 PKFLNKAFEVALKVQIIAGFDRGLVKWLRVHGRTLSTVQKKALYFVNRRYMQTHWANYMLWINKKIDALGRTPVVGDYTRLGAEIGRRIDMAYFYDFLKDKNMIPKYLPYMEEINRMRPADVPVKYM 152
                                    35        45        55        65        75        85        95       105       115       125       135       145       


Chain D from PDB  Type:PROTEIN  Length:110
                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee........eeeeeee.......eeeeeeee..eeeee....eeeeeee............eeeeee..eeeeeeeeeeeeeee.....eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 5mr3 D 174 TGIDWDVFCSQNENIPAKFISRLVAPKCLAVEKMDVDCSNGLVPITHEHGFNMMLIQYTRDSPGMCVFWGPYSVPKNDTVVLYTVTARLKWSEGPPTDLSIQCYMPKSPD 287
                                   183       193       203       213       223       233|      247       257       267       277       287
                                                                                     233|                                                 
                                                                                      238                                                 


Chain E from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhh......hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mr3 E  20 SWHYVEPKFLNKAFEVALKVQIIAGFDRGLVKWLRVHGRTLSTVQKKALYFVNRRYMQTHWANYMLWINKKIDALGRTPVVGDYTRLGAEIGRRIDMAYFYDFLKDKNMIPKYLPYMEEINRMRPADVPVKYM 152
                                    29        39        49        59        69        79        89        99       109       119       129       139       149   


Chain F from PDB  Type:PROTEIN  Length:107
                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee........eeeeeee.....eeeeee..eeeee....eeeeeeee............ee.eeeeee..eeeeeeeeeeeeee......eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 5mr3 F 175 GIDWDVFCSQNENIPAKFISRLVAPVEKMDVDCSNGLVPITHEHGFNMMLIQYTRNKLLDSPGMCVFWGPYSVPKNDTVVLYTVTARLKWSEGPPTDLSIQCYMPKC 294
                                   184       194    || 208       218       228       238       248       258       268       278     ||
                                                  199|                                                                             284|
                                                   204                                                                              294


Chain G from PDB  Type:PROTEIN  Length:129
                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhhhhhhhh......hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mr3 G  24 VEPKFLNKAFEVALKVQIIAGFDRGLVKWLRVHGRTLSTVQKKALYFVNRRYMQTHWANYMLWINKKIDALGRTPVVGDYTRLGAEIGRRIDMAYFYDFLKDKNMIPKYLPYMEEINRMRPADVPVKYM 152
                                    33        43        53        63        73        83        93       103       113       123       133       143         


Chain H from PDB  Type:PROTEIN  Length:111
                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee........eeeeeee.......eeeeeeee..eeeee....eeeeeee................eeeeee..eeeeeeeeeeeeeee.....eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 5mr3 H 175 GIDWDVFCSQNENIPAKFISRLVAPKCLAVEKMDVDCSNGLVPITHEHGFNMMLIQYTRNKLLDSPGMCVFWGPYSVPKNDTVVLYTVTARLKWSEGPPTDLSIQCYMPKS 285
                                   184       194       204       214       224       234       244       254       264       274       284
   Legend:   → Mismatch (orange background)
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  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 5MR3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5MR3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5MR3)

(-) Gene Ontology  (3, 3)

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  5mr3
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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 5iib
        Q8WR62_HALRU | Q8WR62: 5ii4 5ii5 5iia 5iib 5iic 5mr2

(-) Related Entries Specified in the PDB File

1lis LYSIN
1lyn LYSIN
2lis LYSIN
2lyn LYSIN
3d4c ZP3
3d4g ZP3
3ef7 ZP3
3nk3 ZP3
3nk4 ZP3
5ii4 VR1+
5ii5 VR1
5ii7 LYSIN_S-SAD
5ii8 LYSIN_HR
5ii9 LYSIN_MONOCLINIC
5iia VR3-LYSIN
5iib VR3-LYSIN
5iic VR3