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- PDB-8rkf: Crystal structure of the ZP-N1 and ZP-N2 domains of human ZP2 (hZ... -

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Basic information

Entry
Database: PDB / ID: 8rkf
TitleCrystal structure of the ZP-N1 and ZP-N2 domains of human ZP2 (hZP2-N1N2)
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


structural constituent of egg coat / egg coat / acrosin binding / Interaction With Cumulus Cells And The Zona Pellucida / prevention of polyspermy / binding of sperm to zona pellucida / coreceptor activity / multivesicular body / collagen-containing extracellular matrix / endoplasmic reticulum ...structural constituent of egg coat / egg coat / acrosin binding / Interaction With Cumulus Cells And The Zona Pellucida / prevention of polyspermy / binding of sperm to zona pellucida / coreceptor activity / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsDioguardi, E. / Stsiapanava, A. / 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: J Cell Biol / Year: 2012
Title: Human sperm bind to the N-terminal domain of ZP2 in humanized zonae pellucidae in transgenic mice.
Authors: Baibakov, B. / Boggs, N.A. / Yauger, B. / Baibakov, G. / Dean, J.
#11: Journal: J Cell Biol / Year: 2014
Title: A single domain of the ZP2 zona pellucida protein mediates gamete recognition in mice and humans.
Authors: Avella, M.A. / Baibakov, B. / Dean, J.
#12: 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.
#13: 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)53,5058
Polymers52,1782
Non-polymers1,3276
Water0
1
A: Zona pellucida sperm-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7524
Polymers26,0891
Non-polymers6643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Zona pellucida sperm-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7524
Polymers26,0891
Non-polymers6643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.930, 86.930, 178.680
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 48 through 140 or resid 152...
d_2ens_1(chain "B" and (resid 48 through 123 or resid 130...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ALAALAALAALAAA48 - 14010 - 102
d_12SERSERPROPROAA152 - 165114 - 127
d_13GLUGLUPROPROAA201 - 265163 - 227
d_14NAGNAGNAGNAGAD302
d_21ALAALAASNASNBB48 - 12310 - 85
d_22GLYGLYALAALABB130 - 14092 - 102
d_23SERSERPROPROBB152 - 165114 - 127
d_24GLUGLUPROPROBB201 - 265163 - 227
d_25NAGNAGNAGNAGBG302

NCS oper: (Code: givenMatrix: (-0.526312631245, -0.24678018156, -0.813691929529), (0.25920334969, 0.864843939515, -0.429951838923), (0.809820126757, -0.437200757402, -0.391212039725)Vector: 87. ...NCS oper: (Code: given
Matrix: (-0.526312631245, -0.24678018156, -0.813691929529), (0.25920334969, 0.864843939515, -0.429951838923), (0.809820126757, -0.437200757402, -0.391212039725)
Vector: 87.0820755945, 49.7047768901, 101.494889447)

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Components

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


Mass: 26088.783 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Egg zona pellucida / Source: (gene. exp.) Homo sapiens (human) / Gene: ZP2, ZPA / Organ: Ovary / Plasmid: pHLsec2 / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: Q05996
#2: 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.: 6 / 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
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: 3.69 Å3/Da / Density % sol: 66.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 10-30% (v/v) MPD, 0.1 M MES pH 6.0 or 0.1 M Na-HEPES pH 7.5
PH range: 6.0-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.95378 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95378 Å / Relative weight: 1
ReflectionResolution: 3.2→19.9 Å / Num. obs: 13385 / % possible obs: 99.3 % / Redundancy: 9.7 % / Biso Wilson estimate: 130.16 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.052 / Rrim(I) all: 0.163 / Net I/σ(I): 11.8
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 9.8 % / Rmerge(I) obs: 3.808 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1296 / CC1/2: 0.34 / CC star: 0.71 / Rpim(I) all: 1.275 / Rrim(I) all: 4.018 / % possible all: 99.2

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXmodel building
Cootmodel building
PHENIX1.19.2_4158+SVNrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ZP-N1 domain ensemble from PDB entries 5II6 and D_1292121897

5ii6


Resolution: 3.2→19.87 Å / SU ML: 0.5148 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.3049
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2926 1320 9.87 %
Rwork0.2343 12048 -
obs0.2402 13368 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 147.8 Å2
Refinement stepCycle: LAST / Resolution: 3.2→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3128 0 84 0 3212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00333291
X-RAY DIFFRACTIONf_angle_d0.69164462
X-RAY DIFFRACTIONf_chiral_restr0.0574518
X-RAY DIFFRACTIONf_plane_restr0.0057562
X-RAY DIFFRACTIONf_dihedral_angle_d10.29621195
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.30693424638 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.330.38051400.37311294X-RAY DIFFRACTION99.17
3.33-3.480.39291420.30751327X-RAY DIFFRACTION99.93
3.48-3.660.34751380.29111303X-RAY DIFFRACTION99.86
3.66-3.890.30031430.27361333X-RAY DIFFRACTION100
3.89-4.180.37171460.24191314X-RAY DIFFRACTION100
4.19-4.60.28871490.21871352X-RAY DIFFRACTION100
4.6-5.250.25321480.21331327X-RAY DIFFRACTION100
5.26-6.580.29251530.25611367X-RAY DIFFRACTION100
6.59-19.870.27051610.20141431X-RAY DIFFRACTION99.75
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)
18.40895760514-0.00899085765865-0.3058731222274.20203057834-3.234358570118.450830490840.163977841242-0.545541826690.201991737480.50248557289-0.1968798739070.203135324803-0.359387342014-0.5572620176590.08294648762081.10257461-0.048535772433-0.0842169834041.08034116562-0.040038185591.04123607455-46.761571541216.95102851593.99850928447
23.214158254691.41333861381.075131774124.860700659571.393778315381.642694342130.851960597191-0.165350216306-0.4897611397110.50553159539-1.45359637461-0.6578401931790.3422755584650.5303681328850.4677090747911.1560016772-0.14857758848-0.08582789391321.169258617290.2467094796121.15694652866-37.1000465219-12.649213380310.761693926
37.00267296602-2.054484329962.683018575315.57643397104-2.198706019166.14751913747-0.3772958916610.4172722587450.606562972450.04908452312720.04232627802970.5315654620240.595709249119-0.3024236483130.246402075650.7959210389780.0095018635265-0.06832636038951.097826325550.2075862808230.978218954243-28.0612390093-7.9240956137816.075512307
48.248914678890.148381483182-0.7654130761645.583035376891.011263504596.420707708630.314922986618-1.01964476217-0.003290025717430.746628233601-0.341691000750.2777214952040.1199807301410.344010021482-0.1798978231131.30350377146-0.2603337298890.05285437783721.13848312683-0.009973054690780.902084550071-54.6147511647-21.423070263621.5751799515
53.980232141512.3589377621-0.5388171059385.96533589736-2.470766779283.19198807707-0.5202794828250.409268887045-0.30257813595-0.2217627966370.8069490907470.5097382493220.342651993711-0.705366960182-0.4870338098860.833917762552-0.08857868392290.2407030807571.23190305856-0.2513741718451.11417226935-62.38797896024.8856699533719.8421017024
66.62655512996-1.611726443780.6581230239237.90767828018-0.5163776237237.58931346116-0.1840204754280.3693884536230.6579621504060.1661489394420.168122509626-0.0420077212042-0.104345628817-0.942088315920.07384755512851.03047496104-0.2165964825180.1453218788951.01873773186-0.2393912761830.940158703552-63.35536092419.4953786557428.9308716879
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resi 39:140)A39 - 140
2X-RAY DIFFRACTION1chain A and resi 301A301
3X-RAY DIFFRACTION1chain A and resi 302A302
4X-RAY DIFFRACTION2chain A and (resi 227:270)A227 - 270
5X-RAY DIFFRACTION3chain A and (resi 151:226)A151 - 226
6X-RAY DIFFRACTION3chain A and resi 303A303
7X-RAY DIFFRACTION4chain B and (resi 47:143)B47 - 143
8X-RAY DIFFRACTION4chain B and resi 301B301
9X-RAY DIFFRACTION4chain B and resi 302B302
10X-RAY DIFFRACTION5chain B and (resi 227:265)B227 - 265
11X-RAY DIFFRACTION6chain B and not (resi 150:226)B150 - 226
12X-RAY DIFFRACTION6chain B and resi 303B303

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