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- PDB-6gf7: Molecular basis of egg coat filament cross-linking: Zn-SAD struct... -

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Basic information

Entry
Database: PDB / ID: 6gf7
TitleMolecular basis of egg coat filament cross-linking: Zn-SAD 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 / single fertilization / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
: / Zona pellucida sperm-binding proteins 1/4, Ig-like 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 / ZP domain signature. ...: / Zona pellucida sperm-binding proteins 1/4, Ig-like 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 / 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 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 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 / diffrn_source
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 / _diffrn_source.pdbx_synchrotron_site
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 / pdbx_struct_conn_angle / refine / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _refine.pdbx_diffrn_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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)32,00213
Polymers30,9712
Non-polymers1,03111
Water43224
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 area2470 Å2
ΔGint-249 kcal/mol
Surface area12210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.410, 75.410, 100.780
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 genetically manipulated 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.02 Å3/Da / Density % sol: 39.18 %
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: Diamond / Beamline: I03 / Wavelength: 1.2825 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2825 Å / Relative weight: 1
ReflectionResolution: 2.7→53.323 Å / Num. obs: 15254 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 70.95 Å2 / CC1/2: 1 / Rpim(I) all: 0.041 / Rrim(I) all: 0.103 / Net I/σ(I): 12.4
Reflection shellResolution: 2.7→2.82 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1896 / CC1/2: 0.51 / Rpim(I) all: 0.852 / Rrim(I) all: 1.627 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(dev_3409: ???)refinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.7→53.323 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.97 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2718 1528 10.02 %
Rwork0.2218 --
obs0.227 15247 99.88 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→53.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1638 0 37 24 1699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041730
X-RAY DIFFRACTIONf_angle_d0.7232349
X-RAY DIFFRACTIONf_dihedral_angle_d9.9291015
X-RAY DIFFRACTIONf_chiral_restr0.049257
X-RAY DIFFRACTIONf_plane_restr0.004302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.8230.43091880.36961703X-RAY DIFFRACTION99
2.823-2.97180.35091940.32731720X-RAY DIFFRACTION100
2.9718-3.1580.35691870.26541727X-RAY DIFFRACTION100
3.158-3.40180.28741910.2531718X-RAY DIFFRACTION100
3.4018-3.74410.26881860.21511715X-RAY DIFFRACTION100
3.7441-4.28560.26721950.20171713X-RAY DIFFRACTION100
4.2856-5.39860.20971930.18151710X-RAY DIFFRACTION100
5.3986-53.33330.27451940.21411713X-RAY DIFFRACTION100

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