3EF7

ZP-N domain of mammalian sperm receptor ZP3 (crystal form III)

• PDB DOI: https://doi.org/10.2210/pdb3EF7/pdb

• Classification: CELL ADHESION
• Organism(s): Escherichia coli K-12, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-09-08 Released: 2008-12-02 
• Deposition Author(s): Monne, M., Jovine, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.256 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 107.59 kDa 
• Atom Count: 7,311 
• Modelled Residue Count: 934 
• Deposited Residue Count: 962 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein, LINKER, Zona pellucida protein 3	A, B	481	Escherichia coli K-12, Mus musculus This entity is chimeric	Mutation(s): 5  Gene Names: ZP3, ZP-3, ZPC
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for P10761 (Mus musculus) Explore P10761  Go to UniProtKB:  P10761
UniProt Groups	P10761P0AEX9

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth A], G [auth A], J [auth A], K [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	H [auth A], I [auth A], T [auth B], U [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	C, D	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.256 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.2	α = 90
b = 98.58	β = 90
c = 143.68	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-02 
Deposition Author(s): Monne, M., Jovine, L.

Revision History  

• Version 1.0: 2008-12-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.2: 2017-06-28
  Changes: Source and taxonomy
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2021-11-10
  Changes: Database references, Structure summary
• Version 2.2: 2023-11-01
  Changes: Data collection, Refinement description