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- PDB-5ii6: Crystal structure of the ZP-N1 domain of mouse sperm receptor ZP2... -

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Basic information

Entry
Database: PDB / ID: 5ii6
TitleCrystal structure of the ZP-N1 domain of mouse sperm receptor ZP2 at 0.95 A resolution
ComponentsZona pellucida sperm-binding protein 2
KeywordsCELL ADHESION / FERTILIZATION / EGG-SPERM INTERACTION / GAMETE RECOGNITION / SPERM RECEPTOR / EGG COAT / ZONA PELLUCIDA / ZP DOMAIN / ZP-N DOMAIN
Function / homology
Function and homology information


Interaction With Cumulus Cells And The Zona Pellucida / acrosin binding / structural constituent of egg coat / egg coat / prevention of polyspermy / binding of sperm to zona pellucida / multivesicular body / : / endoplasmic reticulum / extracellular region ...Interaction With Cumulus Cells And The Zona Pellucida / acrosin binding / structural constituent of egg coat / egg coat / prevention of polyspermy / binding of sperm to zona pellucida / multivesicular body / : / endoplasmic reticulum / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Zona pellucida sperm-binding protein 2, Ig-like domain / Zona pellucida sperm-binding protein 2, Ig-like domain / Zona pellucida sperm-binding protein 2, Ig-like domain / : / : / Zona pellucida domain, conserved site / ZP domain signature. / : / : / ZP-N domain ...Zona pellucida sperm-binding protein 2, Ig-like domain / Zona pellucida sperm-binding protein 2, Ig-like domain / Zona pellucida sperm-binding protein 2, Ig-like domain / : / : / Zona pellucida domain, conserved site / ZP domain signature. / : / : / ZP-N domain / Zona pellucida, ZP-C domain / ZP-C 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: 0.95 Å
AuthorsDioguardi, E. / Han, L. / Nishimura, K. / De Sanctis, D. / Jovine, L.
Funding support Sweden, 6items
OrganizationGrant numberCountry
Karolinska Institutet Sweden
Swedish Research Council2012-5093 Sweden
Goran Gustafsson Foundation for Research in Natural Sciences and Medicine Sweden
Sven and Ebba-Christina Hagberg foundation Sweden
European Molecular Biology Organization
European UnionERC 260759
Citation
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.
#1: 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.
#2: 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.
#3: 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.
#4: 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.
#5: 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.
#6: 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.
#7: 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.
#8: 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.
#9: 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.
History
DepositionMar 1, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 29, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.4Oct 16, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Zona pellucida sperm-binding protein 2


Theoretical massNumber of molelcules
Total (without water)12,9951
Polymers12,9951
Non-polymers00
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.539, 50.013, 51.751
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 12994.641 Da / Num. of mol.: 1 / Fragment: UNP residues 35-138 / Mutation: N83S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Zp2, Zp-2, Zpa / Cell line (production host): HEK-293T / Production host: Homo sapiens (human) / References: UniProt: P20239
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.15 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 30% PEG 200, 5% PEG 3000, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 0.95→31.419 Å / Num. obs: 64506 / % possible obs: 99 % / Redundancy: 2 % / Biso Wilson estimate: 11.02 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.02234 / Net I/σ(I): 13
Reflection shellResolution: 0.95→0.984 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.2419 / Mean I/σ(I) obs: 2.66 / % possible all: 90

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Processing

Software
NameVersionClassification
PHENIX(dev_2386: ???)refinement
DIALSdata reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 0.95→31.419 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 12.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1448 3230 5.01 %Random selection
Rwork0.1267 ---
obs0.1276 64499 98.7 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.95→31.419 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms825 0 0 142 967
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016936
X-RAY DIFFRACTIONf_angle_d1.4581281
X-RAY DIFFRACTIONf_dihedral_angle_d12.059355
X-RAY DIFFRACTIONf_chiral_restr0.113132
X-RAY DIFFRACTIONf_plane_restr0.012171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.95-0.96420.24271230.2352263X-RAY DIFFRACTION84
0.9642-0.97930.22441440.20722449X-RAY DIFFRACTION93
0.9793-0.99530.18081350.18412692X-RAY DIFFRACTION100
0.9953-1.01250.18681210.17092670X-RAY DIFFRACTION100
1.0125-1.03090.17951510.1562619X-RAY DIFFRACTION100
1.0309-1.05070.17521220.14032689X-RAY DIFFRACTION99
1.0507-1.07220.15091360.13112590X-RAY DIFFRACTION97
1.0722-1.09550.13711470.11262670X-RAY DIFFRACTION100
1.0955-1.1210.10791270.10532673X-RAY DIFFRACTION100
1.121-1.1490.11481470.09932669X-RAY DIFFRACTION100
1.149-1.18010.11591520.09522657X-RAY DIFFRACTION100
1.1801-1.21480.11741540.09652639X-RAY DIFFRACTION99
1.2148-1.2540.12291280.10052672X-RAY DIFFRACTION100
1.254-1.29880.10571320.10332699X-RAY DIFFRACTION100
1.2988-1.35080.12641580.10072675X-RAY DIFFRACTION100
1.3508-1.41230.12391620.10182685X-RAY DIFFRACTION100
1.4123-1.48680.12931350.10012669X-RAY DIFFRACTION99
1.4868-1.57990.11921290.10542725X-RAY DIFFRACTION100
1.5799-1.70190.1391450.11262706X-RAY DIFFRACTION100
1.7019-1.87310.12391320.11642743X-RAY DIFFRACTION100
1.8731-2.14410.13361420.11952734X-RAY DIFFRACTION100
2.1441-2.70110.14951610.13362762X-RAY DIFFRACTION100
2.7011-31.43580.17011470.14762919X-RAY DIFFRACTION100

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