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- PDB-8rkh: Crystal structure of the ZP-N2 and ZP-N3 domains of mouse ZP2 (mZ... -

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Basic information

Entry
Database: PDB / ID: 8rkh
TitleCrystal structure of the ZP-N2 and ZP-N3 domains of mouse ZP2 (mZP2-N2N3)
ComponentsZona pellucida sperm-binding protein 2
KeywordsCELL ADHESION / fertilization / egg-sperm interaction / gamete recognition / sperm receptor / extracellular matrix / egg coat / zona pellucida / glycoprotein / N-glycan / structural protein / ZP-N domain / block to polyspermy / post-fertilization cleavage / ovastacin
Function / homology
Function and homology information


Interaction With Cumulus Cells And The Zona Pellucida / structural constituent of egg coat / egg coat / acrosin binding / prevention of polyspermy / binding of sperm to zona pellucida / multivesicular body / collagen-containing extracellular matrix / endoplasmic reticulum / extracellular region ...Interaction With Cumulus Cells And The Zona Pellucida / structural constituent of egg coat / egg coat / acrosin binding / prevention of polyspermy / binding of sperm to zona pellucida / multivesicular body / collagen-containing extracellular matrix / endoplasmic reticulum / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
: / Zona pellucida domain, conserved site / Zona pellucida, ZP-C domain / ZP domain signature. / Zona pellucida-like domain / Zona pellucida (ZP) domain / ZP domain profile. / Zona pellucida domain
Similarity search - Domain/homology
Zona pellucida sperm-binding protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsFahrenkamp, D. / de Sanctis, D. / Jovine, L.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Swedish Research Council2016-03999 Sweden
Swedish Research Council2020-04936 Sweden
Knut and Alice Wallenberg Foundation2018.0042 Sweden
Citation
Journal: Cell / Year: 2024
Title: ZP2 cleavage blocks polyspermy by modulating the architecture of the egg coat.
Authors: Shunsuke Nishio / Chihiro Emori / Benjamin Wiseman / Dirk Fahrenkamp / Elisa Dioguardi / Sara Zamora-Caballero / Marcel Bokhove / Ling Han / Alena Stsiapanava / Blanca Algarra / Yonggang Lu ...Authors: Shunsuke Nishio / Chihiro Emori / Benjamin Wiseman / Dirk Fahrenkamp / Elisa Dioguardi / Sara Zamora-Caballero / Marcel Bokhove / Ling Han / Alena Stsiapanava / Blanca Algarra / Yonggang Lu / Mayo Kodani / Rachel E Bainbridge / Kayla M Komondor / Anne E Carlson / Michael Landreh / Daniele de Sanctis / Shigeki Yasumasu / Masahito Ikawa / Luca Jovine /
Abstract: Following the fertilization of an egg by a single sperm, the egg coat or zona pellucida (ZP) hardens and polyspermy is irreversibly blocked. These events are associated with the cleavage of the N- ...Following the fertilization of an egg by a single sperm, the egg coat or zona pellucida (ZP) hardens and polyspermy is irreversibly blocked. These events are associated with the cleavage of the N-terminal region (NTR) of glycoprotein ZP2, a major subunit of ZP filaments. ZP2 processing is thought to inactivate sperm binding to the ZP, but its molecular consequences and connection with ZP hardening are unknown. Biochemical and structural studies show that cleavage of ZP2 triggers its oligomerization. Moreover, the structure of a native vertebrate egg coat filament, combined with AlphaFold predictions of human ZP polymers, reveals that two protofilaments consisting of type I (ZP3) and type II (ZP1/ZP2/ZP4) components interlock into a left-handed double helix from which the NTRs of type II subunits protrude. Together, these data suggest that oligomerization of cleaved ZP2 NTRs extensively cross-links ZP filaments, rigidifying the egg coat and making it physically impenetrable to sperm.
#1: Journal: Proc Natl Acad Sci U S A / Year: 1980
Title: Synthesis of zona pellucida proteins by denuded and follicle-enclosed mouse oocytes during culture in vitro.
Authors: Bleil, J.D. / Wassarman, P.M.
#2: Journal: Dev Biol / Year: 1981
Title: Mammalian sperm-egg interaction: fertilization of mouse eggs triggers modification of the major zona pellucida glycoprotein, ZP2.
Authors: Bleil, J.D. / Beall, C.F. / Wassarman, P.M.
#3: Journal: Cell / Year: 1982
Title: Biosynthesis of the major zona pellucida glycoprotein secreted by oocytes during mammalian oogenesis.
Authors: Greve, J.M. / Salzmann, G.S. / Roller, R.J. / Wassarman, P.M.
#4: Journal: Mol Cell Biol / Year: 1990
Title: Oocyte-specific expression of mouse Zp-2: developmental regulation of the zona pellucida genes.
Authors: Liang, L.F. / Chamow, S.M. / Dean, J.
#5: Journal: Development / Year: 2001
Title: Defective zonae pellucidae in Zp2-null mice disrupt folliculogenesis, fertility and development.
Authors: Rankin, T.L. / O'Brien, M. / Lee, E. / Wigglesworth, K. / Eppig, J. / Dean, J.
#6: Journal: J Biol Chem / Year: 2003
Title: Structural characterization of native mouse zona pellucida proteins using mass spectrometry.
Authors: Boja, E.S. / Hoodbhoy, T. / Fales, H.M. / Dean, J.
#7: Journal: Dev Cell / Year: 2003
Title: Fertility and taxon-specific sperm binding persist after replacement of mouse sperm receptors with human homologs.
Authors: Rankin, T.L. / Coleman, J.S. / Epifano, O. / Hoodbhoy, T. / Turner, S.G. / Castle, P.E. / Lee, E. / Gore-Langton, R. / Dean, J.
#8: Journal: Nature / Year: 2008
Title: Crystal structure of the ZP-N domain of ZP3 reveals the core fold of animal egg coats.
Authors: Monne, M. / Han, L. / Schwend, T. / Burendahl, S. / Jovine, L.
#9: Journal: Science / Year: 2010
Title: Gamete recognition in mice depends on the cleavage status of an egg's zona pellucida protein.
Authors: Gahlay, G. / Gauthier, L. / Baibakov, B. / Epifano, O. / Dean, J.
#10: Journal: Cell / Year: 2017
Title: Structural Basis of Egg Coat-Sperm Recognition at Fertilization.
Authors: Raj, I. / Sadat Al Hosseini, H. / Dioguardi, E. / Nishimura, K. / Han, L. / Villa, A. / de Sanctis, D. / Jovine, L.
#11: Journal: Curr Top Dev Biol / Year: 2018
Title: Structure of Zona Pellucida Module Proteins.
Authors: Marcel Bokhove / Luca Jovine /
Abstract: The egg coat, an extracellular matrix made up of glycoprotein filaments, plays a key role in animal fertilization by acting as a gatekeeper for sperm. Egg coat components polymerize using a common ...The egg coat, an extracellular matrix made up of glycoprotein filaments, plays a key role in animal fertilization by acting as a gatekeeper for sperm. Egg coat components polymerize using a common zona pellucida (ZP) "domain" module that consists of two related immunoglobulin-like domains, called ZP-N and ZP-C. The ZP module has also been recognized in a large number of other secreted proteins with different biological functions, whose mutations are linked to severe human diseases. During the last decade, tremendous progress has been made toward understanding the atomic architecture of the ZP module and the structural basis of its polymerization. Moreover, sperm-binding regions at the N-terminus of mollusk and mammalian egg coat subunits were found to consist of domain repeats that also adopt a ZP-N fold. This discovery revealed an unexpected link between invertebrate and vertebrate fertilization and led to the first structure of an egg coat-sperm protein recognition complex. In this review we summarize these exciting findings, discuss their functional implications, and outline future challenges that must be addressed in order to develop a comprehensive view of this family of biomedically important extracellular molecules.
History
DepositionDec 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zona pellucida sperm-binding protein 2
B: Zona pellucida sperm-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9889
Polymers53,3852
Non-polymers2,6037
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, Despite being intact, the ZP-N2 domains of the two molecules in the asymmetric unit of the crystal form an interface similar to that observed in crystals of collagenase-cleaved Xenopus ZP2-N2N3
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint44 kcal/mol
Surface area24950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.010, 54.170, 68.660
Angle α, β, γ (deg.)90.000, 107.984, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 145 through 361)
d_2ens_1(chain "B" and (resid 145 through 303 or resid 306 through 361))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERLEUA1 - 215
d_21ens_1SERALAK3 - 161
d_22ens_1GLYLEUK164 - 219

NCS oper: (Code: givenMatrix: (-0.34738863863, 0.0588576940818, 0.935872269916), (0.184695004705, -0.974183431397, 0.129824486243), (0.919352429152, 0.217950484832, 0.327549533924)Vector: 54. ...NCS oper: (Code: given
Matrix: (-0.34738863863, 0.0588576940818, 0.935872269916), (0.184695004705, -0.974183431397, 0.129824486243), (0.919352429152, 0.217950484832, 0.327549533924)
Vector: 54.5529937856, 66.9929262669, -45.216208584)

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Components

#1: Protein Zona pellucida sperm-binding protein 2 / Zona pellucida glycoprotein 2 / Zp-2 / Zona pellucida protein A


Mass: 26692.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Egg zona pellucida / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Zp2, Zp-2, Zpa / Organ: Ovary / Plasmid: pHLsec2 / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P20239
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c6-d1_d3-e1_d6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 20% (w/v) PEG 3350, 0.2 M Na-nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.91942 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91942 Å / Relative weight: 1
ReflectionResolution: 1.9→43.73 Å / Num. obs: 44849 / % possible obs: 99.2 % / Redundancy: 5.2 % / Biso Wilson estimate: 40.73 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.031 / Rrim(I) all: 0.072 / Net I/σ(I): 12.6
Reflection shellResolution: 1.9→1.98 Å / Redundancy: 5.4 % / Rmerge(I) obs: 2.33 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4926 / CC1/2: 0.49 / CC star: 0.81 / Rpim(I) all: 1.074 / Rrim(I) all: 2.572 / % possible all: 98.5

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSNov 1, 2016 BUILT=20161205data reduction
XSCALENov 1, 2016 BUILT=20161205data scaling
AutoSol1.13_2998phasing
PHENIX1.13_2998model building
Cootmodel building
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: SAD / Resolution: 1.9→43.73 Å / SU ML: 0.306 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.3189
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2479 2223 4.96 %
Rwork0.2141 42588 -
obs0.2157 44811 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.61 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3467 0 170 187 3824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00463723
X-RAY DIFFRACTIONf_angle_d0.79025057
X-RAY DIFFRACTIONf_chiral_restr0.8524619
X-RAY DIFFRACTIONf_plane_restr0.0045624
X-RAY DIFFRACTIONf_dihedral_angle_d12.48081376
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 3.72749037809 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.38251360.3982641X-RAY DIFFRACTION98.58
1.94-1.990.42471350.37592600X-RAY DIFFRACTION98.56
1.99-2.040.42321400.36042628X-RAY DIFFRACTION98.82
2.04-2.090.37631350.33862659X-RAY DIFFRACTION98.8
2.09-2.150.37771380.3092641X-RAY DIFFRACTION99.11
2.15-2.220.32081380.29112619X-RAY DIFFRACTION99.1
2.22-2.30.30561350.27752654X-RAY DIFFRACTION99.18
2.3-2.390.29211430.2662666X-RAY DIFFRACTION99.33
2.39-2.50.32281370.26012663X-RAY DIFFRACTION99.33
2.5-2.630.31420.2492639X-RAY DIFFRACTION99.39
2.63-2.80.27131400.24012668X-RAY DIFFRACTION99.65
2.8-3.020.25391380.24072681X-RAY DIFFRACTION99.44
3.02-3.320.25531430.22852676X-RAY DIFFRACTION99.54
3.32-3.80.24921370.19632679X-RAY DIFFRACTION99.68
3.8-4.790.17691430.15972713X-RAY DIFFRACTION99.48
4.79-43.730.20781430.16982761X-RAY DIFFRACTION99.05
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.948824285490.346577905803-0.6451533974541.209428613430.3820220889934.14643570231-0.154149536427-0.0202400696194-0.101928341656-0.03878932435620.0468013677055-0.05072197006120.2823458958330.2849530214040.1193683295290.3498536047540.007748775510130.01250848285530.3016070795570.01997570222140.34198275318658.277692891230.39053945554.16796167509
25.61700644429-1.004646199740.04980590482471.21051365465-0.1191498352491.22863542447-0.01422006979170.6698378458470.538031035184-0.279387182850.03494693756670.034476057618-0.1936306127510.0790076073647-0.05291959469550.45864058509-0.0860438868335-0.04489099897280.5966545450590.09865286113790.42504168016478.928424885739.3553661643-15.2061509558
35.58085316854-1.23858238563-0.1424959980581.36125796263-0.4343013367872.41652443433-0.0680295350468-0.1901732390050.2756988324550.006888089397720.108177008437-0.0800251791672-0.1176927778840.0624288457491-0.05354383724850.34754759804-0.01660419606190.01694833103660.240478109971-0.02789139141190.33569464799539.601290326148.458005663516.8027993086
42.47024109602-0.448930461518-0.362595863794.137961046370.8988080204992.54024230951-0.0309062455114-0.151018666985-0.2702371760120.25590593282-0.04095815446480.01098364991050.298110416064-0.2149870504420.08536359426840.499660885854-0.03283759776470.01222091035170.4042023100950.06137579215710.43173796601216.296417984740.331690034429.3126413479
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain A and (resi 145:259)AA - D145 - 2591
21chain A and (resi 401:403)A401 - 403
32chain A and (resi 260:365)AA - J260 - 365116
42chain C and (resi 1:6)C1 - 6
53chain B and (resi 143:259)BK - B143 - 2591
63chain B and (resi 401:402)B401 - 402
74chain B and (resi 260:361)BK - B260 - 361118
84chain D and (resi 1:2)D1 - 2

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