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Basic information

Entry
Database: PDB / ID: 6gf8
TitleMolecular basis of egg coat filament cross-linking: structure of the glycosylated 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 / MOLECULAR REPLACEMENT / Resolution: 3.1 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity_src_gen / pdbx_database_related / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_atcc / _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_related.db_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Jan 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)32,4398
Polymers30,9712
Non-polymers1,4686
Water00
1
A: Zona pellucida sperm-binding protein 1,Zona pellucida sperm-binding protein 1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)32,5858
Polymers30,9712
Non-polymers1,6146
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3560 Å2
ΔGint-38 kcal/mol
Surface area11950 Å2
MethodPISA
2
B: Zona pellucida sperm-binding protein 1,Zona pellucida sperm-binding protein 1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)32,2928
Polymers30,9712
Non-polymers1,3216
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area2960 Å2
ΔGint-39 kcal/mol
Surface area12260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.774, 125.734, 105.001
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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,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): HEK293T / Production host: Homo sapiens (human) / References: UniProt: A0A140JXP0
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}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: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H14O2 / Comment: precipitant*YM
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: 4.23 Å3/Da / Density % sol: 70.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 29% (V/V) MPD, 0.1 M MES PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.1→42.74 Å / Num. obs: 11119 / % possible obs: 99.1 % / Redundancy: 4.1 % / Biso Wilson estimate: 103.69 Å2 / CC1/2: 1 / Rpim(I) all: 0.043 / Rrim(I) all: 0.093 / Net I/σ(I): 9.5
Reflection shellResolution: 3.1→3.24 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1 / Num. unique obs: 1328 / CC1/2: 0.65 / Rpim(I) all: 0.52 / Rrim(I) all: 1.114 / % possible all: 96.9

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Processing

Software
NameClassification
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Monomer 6GF6

6gf6


Resolution: 3.1→24.725 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.83
RfactorNum. reflection% reflection
Rfree0.2352 1070 9.66 %
Rwork0.2104 --
obs0.2127 11079 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→24.725 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1638 0 98 0 1736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041780
X-RAY DIFFRACTIONf_angle_d0.6572412
X-RAY DIFFRACTIONf_dihedral_angle_d14.8591026
X-RAY DIFFRACTIONf_chiral_restr0.046270
X-RAY DIFFRACTIONf_plane_restr0.004298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1001-3.24090.38331220.35321197X-RAY DIFFRACTION96
3.2409-3.41140.381280.33151235X-RAY DIFFRACTION99
3.4114-3.62450.32261390.29241242X-RAY DIFFRACTION100
3.6245-3.90340.24561550.22451216X-RAY DIFFRACTION99
3.9034-4.29430.22981200.19321266X-RAY DIFFRACTION99
4.2943-4.91150.20391420.16861245X-RAY DIFFRACTION99
4.9115-6.1720.21751260.19751276X-RAY DIFFRACTION99
6.172-24.72540.21151380.19471332X-RAY DIFFRACTION99
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)
14.87272.86670.01448.91790.98418.3884-0.57240.324-0.4615-1.2970.33730.2925-0.1987-0.08050.00011.2428-0.2496-0.01391.23230.01021.292125.86265.4361-13.3653
25.93271.8380.11614.08150.40637.1640.4189-0.99840.0580.4551-0.3845-0.0334-0.20170.1908-0.00021.2754-0.21190.01011.2204-0.00571.14494.4766-26.5701-12.9753
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resi 25:127 or resi 201:203)
2X-RAY DIFFRACTION2chain B and (resi 23:127 or resi 201:203)

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