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- PDB-6gf6: Molecular basis of egg coat filament cross-linking: high-resoluti... -

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Basic information

Entry
Database: PDB / ID: 6gf6
TitleMolecular basis of egg coat filament cross-linking: high-resolution structure of the partially deglycosylated ZP1 ZP-N1 domain homodimer
ComponentsZona pellucida sperm-binding protein 1,Zona pellucida sperm-binding protein 1
KeywordsCELL ADHESION / Zona pellucida / ZP1 / ZP-N domain / ZP module / ZP domain / egg coat filament cross-linking / egg coat penetration by sperm
Function / homology
Function and homology information


egg coat / structural constituent of egg coat / acrosin binding / prevention of polyspermy / binding of sperm to zona pellucida / collagen-containing extracellular matrix / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Trefoil (P-type) domain / P-type trefoil domain / P-type trefoil domain superfamily / P-type 'Trefoil' domain profile. / P or trefoil or TFF domain / Zona pellucida domain, conserved site / Zona pellucida, ZP-C domain / ZP domain signature. / Zona pellucida-like domain / Zona pellucida (ZP) domain ...Trefoil (P-type) domain / P-type trefoil domain / P-type trefoil domain superfamily / P-type 'Trefoil' domain profile. / P or trefoil or TFF domain / 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 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNishimura, K. / Jovine, L.
Funding support Sweden, 4items
OrganizationGrant numberCountry
Swedish Research Council2012-5093 Sweden
Swedish Research Council2016-03999 Sweden
European Molecular Biology OrganizationEMBO Young Investigator Programme
European Research CouncilERC 260759
Citation
Journal: Nat Commun / Year: 2019
Title: Molecular basis of egg coat cross-linking sheds light on ZP1-associated female infertility.
Authors: Nishimura, K. / Dioguardi, E. / Nishio, S. / Villa, A. / Han, L. / Matsuda, T. / Jovine, L.
#1: Journal: J. Mol. Biol. / Year: 1985
Title: Mouse egg extracellular coat is a matrix of interconnected filaments possessing a structural repeat.
Authors: Greve, J.M. / Wassarman, P.M.
#2: Journal: Development / Year: 1999
Title: Abnormal zonae pellucidae in mice lacking ZP1 result in early embryonic loss.
Authors: Rankin, T. / Talbot, P. / Lee, E. / Dean, J.
#3: Journal: Biol. Reprod. / Year: 2001
Title: Morphological and biochemical changes of isolated chicken egg-envelope during sperm penetration: degradation of the 97-kilodalton glycoprotein is involved in sperm-driven hole formation on the egg-envelope.
Authors: Takeuchi, Y. / Cho, R. / Iwata, Y. / Nishimura, K. / Kato, T. / Aoki, N. / Kitajima, K. / Matsuda, T.
#4: Journal: Biochem. J. / Year: 2004
Title: A newly identified zona pellucida glycoprotein, ZPD, and dimeric ZP1 of chicken egg envelope are involved in sperm activation on sperm-egg interaction.
Authors: Okumura, H. / Kohno, Y. / Iwata, Y. / Mori, H. / Aoki, N. / Sato, C. / Kitajima, K. / Nadano, D. / Matsuda, T.
#5: Journal: N. Engl. J. Med. / Year: 2014
Title: Mutant ZP1 in familial infertility.
Authors: Huang, H.L. / Lv, C. / Zhao, Y.C. / Li, W. / He, X.M. / Li, P. / Sha, A.G. / Tian, X. / Papasian, C.J. / Deng, H.W. / Lu, G.X. / Xiao, H.M.
#6: Journal: FEBS Open Bio / Year: 2015
Title: Identification of distinctive interdomain interactions among ZP-N, ZP-C and other domains of zona pellucida glycoproteins underlying association of chicken egg-coat matrix.
Authors: Okumura, H. / Sato, T. / Sakuma, R. / Fukushima, H. / Matsuda, T. / Ujita, M.
History
DepositionApr 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Jul 24, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / refine / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _refine.pdbx_diffrn_id / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 1,Zona pellucida sperm-binding protein 1
B: Zona pellucida sperm-binding protein 1,Zona pellucida sperm-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5055
Polymers30,9712
Non-polymers5353
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, Dimer in non-reducing SDS-PAGE, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-7 kcal/mol
Surface area12340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.980, 75.980, 101.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Zona pellucida sperm-binding protein 1,Zona pellucida sperm-binding protein 1


Mass: 15485.485 Da / Num. of mol.: 2 / Mutation: N121Q, G140H(6), G149S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: ZP1 / Plasmid: pJ609 / Details (production host): ATUM/DNA2.0 / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: A0A140JXP0
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: isolated from a natural source / 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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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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: 2.08 Å3/Da / Density % sol: 40.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.6 M LiCl, 0.1 M tri-sodium citrate pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.771 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.771 Å / Relative weight: 1
ReflectionResolution: 2.3→37.99 Å / Num. obs: 13550 / % possible obs: 98 % / Redundancy: 19.7 % / Biso Wilson estimate: 42.41 Å2 / CC1/2: 1 / Rpim(I) all: 0.026 / Rrim(I) all: 0.116 / Net I/σ(I): 22.2
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1422 / CC1/2: 0.55 / Rpim(I) all: 0.495 / Rrim(I) all: 1.498 / % possible all: 84.6

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Processing

Software
NameVersionClassification
PHENIX(dev_3409: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Partially refined model derived from SAD phasing of a gold derivative

Resolution: 2.3→36.966 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2292 1349 9.96 %
Rwork0.1922 --
obs0.1958 13546 97.98 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→36.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1704 0 34 88 1826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051788
X-RAY DIFFRACTIONf_angle_d0.7382421
X-RAY DIFFRACTIONf_dihedral_angle_d15.1751049
X-RAY DIFFRACTIONf_chiral_restr0.049264
X-RAY DIFFRACTIONf_plane_restr0.005311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.40470.31911370.29511282X-RAY DIFFRACTION84
2.4047-2.53150.27681900.24711480X-RAY DIFFRACTION99
2.5315-2.69010.27561690.23061536X-RAY DIFFRACTION100
2.6901-2.89770.23351680.21331522X-RAY DIFFRACTION100
2.8977-3.18910.25611580.20621556X-RAY DIFFRACTION100
3.1891-3.65030.21981710.18581552X-RAY DIFFRACTION100
3.6503-4.59760.19281720.1571583X-RAY DIFFRACTION100
4.5976-36.97050.21971840.17831686X-RAY DIFFRACTION100
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)
12.1942-0.5556-0.26342.80850.46391.5790.02970.0890.0250.0071-0.00960.2003-0.0749-0.22670.00050.39340.01150.01930.2350.02420.32-17.9024-26.669214.7079
23.97140.8263-1.15280.4476-1.04563.88710.0342-0.1750.09940.2373-0.12370.0724-0.13960.6130.00010.3727-0.02830.00460.46450.00480.3377.5554-32.643212.5431
30.01660.01890.00060.0275-0.0009-0.00070.14220.3482-0.5717-0.01050.19080.38390.2680.032301.2676-0.0160.10260.7493-0.17620.9009-1.6188-60.128526.5105
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resi 22:127 or resi 900)
2X-RAY DIFFRACTION2chain B and (resi 25:127 or resi 900)
3X-RAY DIFFRACTION3chain B and (resi 128:134)

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