3NK3 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF FULL-LENGTH SPERM RECEPTOR ZP3 AT 2.6 A RESOLUTION

Authors :   M. Monne', L. Jovine

Date :   18 Jun 10 (Deposition) - 10 Nov 10 (Release) - 24 Nov 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Fertilization, Oocyte, Egg Coat, Zona Pellucida, Vitelline Envelope, Zp Domain, Zp Module, Egg-Sperm Interaction, Species-Specific Gamete Recognition, Speciation, Biodiversity, Infertility, Extracellular Matrix, Immunoglobulin-Like Fold, Glycoprotein, Receptor, Secreted, Transmembrane, Cell Adhesion, O-Linked Carbohydrate, T-Antigen, Core-1, External Hydrophobic Patch, Ehp, Internal Hydrophobic Patch, Ihp, Sperm-Combining Site (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Han, M. Monne, H. Okumura, T. Schwend, A. L. Cherry, D. Flot, T. Matsuda, L. Jovine
Insights Into Egg Coat Assembly And Egg-Sperm Interaction From The X-Ray Structure Of Full-Length Zp3.
Cell(Cambridge, Mass. ) V. 143 404 2010
PubMed-ID: 20970175 | Reference-DOI: 10.1016/J.CELL.2010.09.041
(for further references see the PDB file header)

Molecule 1 - ZONA PELLUCIDA 3
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	CHINESE HAMSTER
	Expression System Cell Line	:	DG44 CELLS
	Expression System Plasmid	:	PDEF38/PNEF38
	Expression System Taxid	:	10029
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 21-347
	Organism Common	:	BANTAM,CHICKENS
	Organism Scientific	:	GALLUS GALLUS
	Organism Taxid	:	9031

Molecule 2 - ZONA PELLUCIDA 3
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	CHINESE HAMSTER
	Expression System Cell Line	:	DG44 CELLS
	Expression System Plasmid	:	PDEF38/PNEF38
	Expression System Taxid	:	10029
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 359-382
	Organism Common	:	BANTAM,CHICKENS
	Organism Scientific	:	GALLUS GALLUS
	Organism Taxid	:	9031

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 3)

No.	Name	Count	Type	Full Name
1	A2G	1	Ligand/Ion	N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2	FLC	1	Ligand/Ion	CITRATE ANION
3	GAL	1	Ligand/Ion	BETA-D-GALACTOSE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:168 , HIS A:219 , VAL A:220 , GAL A:901	BINDING SITE FOR RESIDUE A2G A 900
2	AC2	SOFTWARE	A2G A:900	BINDING SITE FOR RESIDUE GAL A 901
3	AC3	SOFTWARE	HIS A:99 , PHE B:72 , THR B:74 , THR B:143 , ASN B:144 , HIS C:385 , HIS C:386 , HIS C:387	BINDING SITE FOR RESIDUE FLC C 910

Asymmetric/Biological Unit

No.	Residues
1	A:58	-	A:152
2	A:90	-	A:111
3	A:229	-	A:295
4	A:251	-	A:335
5	A:313	-	A:332
6	A:334	-	A:340
7	B:58	-	B:152
8	B:90	-	B:111
9	B:229	-	B:295
10	B:251	-	B:335
11	B:313	-	B:332
12	B:334	-	B:340

Asymmetric/Biological Unit

No.	Residues
1	Ser A:240	-	Pro A:241
2	Thr A:266	-	Pro A:267
3	Ser B:240	-	Pro B:241
4	Thr B:266	-	Pro B:267
5	Gly C:375	-	Pro C:376
6	Gly D:375	-	Pro D:376

(no "SAP(SNP)/Variant" information available for 3NK3)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZP_2	PS51034	ZP domain profile.	ZP3_CHICK	57-320	2	A:57-320 B:57-320
2	ZP_1	PS00682	ZP domain signature.	ZP3_CHICK	210-251	2	A:210-251 B:210-251

(no "Exon" information available for 3NK3)

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:284
 aligned with ZP3_CHICK | P79762 from UniProtKB/Swiss-Prot  Length:437

    Alignment length:323
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340   
            ZP3_CHICK    21 YTPWDISWAARGDPSAWSWGAEAHSRAVAGSHPVAVQCQEAQLVVTVHRDLFGTGRLINAADLTLGPAACKHSSLNAAHNTVTFAAGLHECGSVVQVTPDTLIYRTLINYDPSPASNPVIIRTNPAVIPIECHYPRRENVSSNAIRPTWSPFNSALSAEERLVFSLRLMSDDWSTERPFTGFQLGDILNIQAEVSTENHVPLRLFVDSCVAALSPDGDSSPHYAIIDFNGCLVDGRVDDTSSAFITPRPREDVLRFRIDVFRFAGDNRNLIYITCHLKVTPADQGPDPQNKACSFNKARNTWVPVEGSRDVCNCCETGNCEPP 343
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..------------------------------.eeeeee..eeeeeee...........hhheeee......eeee....eeeeeee.....eeeeee..eeeeeeeeeee.......eee...eeeeeeeeeee..---------..e.............eeeeeeee....eee.eeee...eeeeeeeeee..eeeeeeeeeeeeeee.........eeeeee..eeehhhh......eee......eeeeeeeee.eee....eeeeeeeeeeeeee.........eeeee....eeeee...hhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------ZP_2  PDB: A:57-320 UniProt: 57-320                                                                                                                                                                                                                                     ----------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZP_1  PDB: A:210-251 UniProt: 210-251     -------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nk3 A  51 YT------------------------------PVAVQCQEAQLVVTVHRDLFGTGRLINAADLTLGPAACKHSSLNAAHNTVTFAAGLHECGSVVQVTPDTLIYRTLINYDPSPASNPVIIRTNPAVIPIECHYPRR---------PTWSPFNSALSAEERLVFSLRLMSDDWSTERPFTGFQLGDILNIQAEVSTENHVPLRLFVDSCVAALSPDGDSSPHYAIIDFNGCLVDGRVDDTSSAFITPRPREDVLRFRIDVFRFAGDNRNLIYITCHLKVTPADQGPDPQNKACSFNKARNTWVPVEGSRDVCNCCETGNCEPP 343
                             |       -         -         -  |     60        70        80        90       100       110       120       130       140       150      |  -      |170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340   
                             |                             53                                                                                                     157       167                                                                                                                                                                                
                            52

Chain B from PDB  Type:PROTEIN  Length:270
 aligned with ZP3_CHICK | P79762 from UniProtKB/Swiss-Prot  Length:437

    Alignment length:292
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341  
            ZP3_CHICK    52 HPVAVQCQEAQLVVTVHRDLFGTGRLINAADLTLGPAACKHSSLNAAHNTVTFAAGLHECGSVVQVTPDTLIYRTLINYDPSPASNPVIIRTNPAVIPIECHYPRRENVSSNAIRPTWSPFNSALSAEERLVFSLRLMSDDWSTERPFTGFQLGDILNIQAEVSTENHVPLRLFVDSCVAALSPDGDSSPHYAIIDFNGCLVDGRVDDTSSAFITPRPREDVLRFRIDVFRFAGDNRNLIYITCHLKVTPADQGPDPQNKACSFNKARNTWVPVEGSRDVCNCCETGNCEPP 343
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----Zona_pellucida-3nk3B01 B:57-316                                                                                                                                                                                                                                     --------------------------- Pfam domains (1)
           Pfam domains (2) -----Zona_pellucida-3nk3B02 B:57-316                                                                                                                                                                                                                                     --------------------------- Pfam domains (2)
         Sec.struct. author ..eeeeee..eeeeeee...........hhheeee......eeee....eeeeeee.....eeeeee..eeeeeeeeeee.......eee...eeeeeeeeeee..----------------------...eeeeeeee....eee.eeee...eeeeeeeeee.....eeeeeeeeeeee.........eeeeee..eeehhhh......eee......eeeeeeeee.eee....eeeeeeeeeeeeee.........eeeee....eeeee...hhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----ZP_2  PDB: B:57-320 UniProt: 57-320                                                                                                                                                                                                                                     ----------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------ZP_1  PDB: B:210-251 UniProt: 210-251     -------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nk3 B  52 TPVAVQCQEAQLVVTVHRDLFGTGRLINAADLTLGPAACKHSSLNAAHNTVTFAAGLHECGSVVQVTPDTLIYRTLINYDPSPASNPVIIRTNPAVIPIECHYPRR----------------------ERLVFSLRLMSDDWSTERPFTGFQLGDILNIQAEVSTENHVPLRLFVDSCVAALSPDGDSSPHYAIIDFNGCLVDGRVDDTSSAFITPRPREDVLRFRIDVFRFAGDNRNLIYITCHLKVTPADQGPDPQNKACSFNKARNTWVPVEGSRDVCNCCETGNCEPP 343
                                    61        71        81        91       101       111       121       131       141       151     |   -         -       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341  
                                                                                                                                   157                    180

Chain C from PDB  Type:PROTEIN  Length:21
 aligned with ZP3_CHICK | P79762 from UniProtKB/Swiss-Prot  Length:437

    Alignment length:24
                                   377       387    
            ZP3_CHICK   368 VAADVVIGPVLLSADPGAVGQQEE 391
               SCOP domains ------------------------ SCOP domains
               CATH domains ------------------------ CATH domains
               Pfam domains ------------------------ Pfam domains
         Sec.struct. author eeeeeeeeeeeee...---..... Sec.struct. author
                 SAPs(SNPs) ------------------------ SAPs(SNPs)
                PROSITE (1) ------------------------ PROSITE (1)
                PROSITE (2) ------------------------ PROSITE (2)
                 Transcript ------------------------ Transcript
                 3nk3 C 368 VAADVVIGPVLLSADH---HHHHH 388
                                   377     | 384    
                                         383 384

Chain D from PDB  Type:PROTEIN  Length:14
 aligned with ZP3_CHICK | P79762 from UniProtKB/Swiss-Prot  Length:437

    Alignment length:14
                                   377    
            ZP3_CHICK   368 VAADVVIGPVLLSA 381
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                PROSITE (1) -------------- PROSITE (1)
                PROSITE (2) -------------- PROSITE (2)
                 Transcript -------------- Transcript
                 3nk3 D 368 VAADVVIGPVLLSA 381
                                   377

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 '\|'

(no "SCOP Domain" information available for 3NK3)

(no "CATH Domain" information available for 3NK3)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Zona_pellucida] (3)

Family: Zona_pellucida (3)

Gallus gallus (Chicken) (2)

1a	Zona_pellucida-3nk3B01	B:57-316
1b	Zona_pellucida-3nk3B02	B:57-316

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (ZP3_CHICK | P79762)

molecular function
	GO:0032190	acrosin binding	Interacting selectively and non-covalently with acrosin, a protein that is found in the acrosomes of sperm and possesses protease and carbohydrate binding activities.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
biological process
	GO:0007339	binding of sperm to zona pellucida	The process in which the sperm binds to the zona pellucida glycoprotein layer of the egg. The process begins with the attachment of the sperm plasma membrane to the zona pellucida and includes attachment of the acrosome inner membrane to the zona pellucida after the acrosomal reaction takes place.
	GO:0035803	egg coat formation	Construction of an egg coat, a specialized extracellular matrix that surrounds the ovum of animals. The egg coat provides structural support and can play an essential role in oogenesis, fertilization and early development.
	GO:2000344	positive regulation of acrosome reaction	Any process that activates or increases the frequency, rate or extent of the acrosome reaction.
	GO:0032570	response to progesterone	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a progesterone stimulus.
	GO:0033574	response to testosterone	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a testosterone stimulus.
	GO:0007338	single fertilization	The union of male and female gametes to form a zygote.
cellular component
	GO:0045177	apical part of cell	The region of a polarized cell that forms a tip or is distal to a base. For example, in a polarized epithelial cell, the apical region has an exposed surface and lies opposite to the basal lamina that separates the epithelium from other tissue.
	GO:0005623	cell	The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
	GO:0031012	extracellular matrix	A structure lying external to one or more cells, which provides structural support for cells or tissues.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0005578	proteinaceous extracellular matrix	A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

Asymmetric/Biological 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
		A2G	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FLC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GAL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly C:375 - Pro C:376	[ RasMol ]
		Gly D:375 - Pro D:376	[ RasMol ]
		Ser A:240 - Pro A:241	[ RasMol ]
		Ser B:240 - Pro B:241	[ RasMol ]
		Thr A:266 - Pro A:267	[ RasMol ]
		Thr B:266 - Pro B:267	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites 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)

Access by PDB/NDB ID
	3nk3
		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
	ZP3_CHICK \| P79762
		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

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
	ZP3_CHICK \| P79762
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	ZP3_CHICK \| P79762	:	3nk4

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

SS Bonds (12, 12)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (17, 17)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File