[English] 日本語
Yorodumi
- PDB-6gf8: Molecular basis of egg coat filament cross-linking: structure of ... -

+
Open data


ID or keywords:

Loading...

-
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 / 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: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
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 / 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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more