[English] 日本語
Yorodumi
- PDB-5b5k: Crystal structure of Izumo1, the mammalian sperm ligand for egg Juno -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5b5k
TitleCrystal structure of Izumo1, the mammalian sperm ligand for egg Juno
ComponentsIzumo sperm-egg fusion protein 1
KeywordsCELL ADHESION / FERTILIZATION / EGG RECEPTOR / GAMETE ADHESION / SPERM-EGG MEMBRANE FUSION
Function / homology
Function and homology information


Acrosome Reaction and Sperm:Oocyte Membrane Binding / sperm-egg recognition / protein binding involved in heterotypic cell-cell adhesion / fusion of sperm to egg plasma membrane involved in single fertilization / acrosomal membrane / heterotypic cell-cell adhesion / single fertilization / acrosomal vesicle / membrane => GO:0016020 / cell adhesion ...Acrosome Reaction and Sperm:Oocyte Membrane Binding / sperm-egg recognition / protein binding involved in heterotypic cell-cell adhesion / fusion of sperm to egg plasma membrane involved in single fertilization / acrosomal membrane / heterotypic cell-cell adhesion / single fertilization / acrosomal vesicle / membrane => GO:0016020 / cell adhesion / signaling receptor binding / protein homodimerization activity / identical protein binding / plasma membrane
Similarity search - Function
Izumo sperm-egg fusion protein / Izumo protein, immunoglobulin domain / Izumo sperm-egg fusion protein 1 / Izumo sperm-egg fusion, Ig domain-associated / Izumo-like Immunoglobulin domain / Immunoglobulin-like domain superfamily
Similarity search - Domain/homology
Izumo sperm-egg fusion protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNishimura, K. / Han, L. / 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
EMBO Young Investigator
European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013)ERC 260759
Citation
Journal: Curr.Biol. / Year: 2016
Title: The structure of sperm Izumo1 reveals unexpected similarities with Plasmodium invasion proteins.
Authors: Nishimura, K. / Han, L. / Bianchi, E. / Wright, G.J. / de Sanctis, D. / Jovine, L.
#1: Journal: Curr. Biol. / Year: 2016
Title: Divergent evolution of vitamin B9 binding underlies Juno-mediated adhesion of mammalian gametes.
Authors: Han, L. / Nishimura, K. / Sadat Al Hosseini, H. / Bianchi, E. / Wright, G.J. / Jovine, L.
#2: Journal: Nature / Year: 2014
Title: Juno is the egg Izumo receptor and is essential for mammalian fertilization.
Authors: Bianchi, E. / Doe, B. / Goulding, D. / Wright, G.J.
#3: Journal: Nature / Year: 2005
Title: The immunoglobulin superfamily protein Izumo is required for sperm to fuse with eggs.
Authors: Inoue, N. / Ikawa, M. / Isotani, A. / Okabe, M.
History
DepositionMay 11, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 2023Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Izumo sperm-egg fusion protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7923
Polymers27,3321
Non-polymers4602
Water50428
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.280, 103.280, 139.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

-
Components

#1: Protein Izumo sperm-egg fusion protein 1 / Oocyte binding/fusion factor / OBF / Sperm-specific protein izumo


Mass: 27332.318 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 22-257
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Izumo1 / Plasmid: pHLsec / Cell line (production host): HEK-293S / Production host: Homo sapiens (human) / References: UniProt: Q9D9J7
#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.: 1
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-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.47 Å3/Da / Density % sol: 64.6 % / Description: Square plate
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6 / Details: 0.2 M Ammonium formate pH 6.6, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.5→43.84 Å / Num. obs: 13389 / % possible obs: 100 % / Redundancy: 12.6 % / Biso Wilson estimate: 59.2 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1948 / Net I/σ(I): 12.13
Reflection shellResolution: 2.5→2.589 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.2296 / Mean I/σ(I) obs: 1.13 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDS20151015data reduction
XDS20151015data scaling
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JK9

5jk9


Resolution: 2.5→43.84 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.93
RfactorNum. reflection% reflection
Rfree0.2807 670 5.01 %
Rwork0.2565 --
obs0.2577 13384 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→43.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1932 0 0 28 1960
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041978
X-RAY DIFFRACTIONf_angle_d0.8092679
X-RAY DIFFRACTIONf_dihedral_angle_d12.0331203
X-RAY DIFFRACTIONf_chiral_restr0.051299
X-RAY DIFFRACTIONf_plane_restr0.004335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.6930.40541300.37112473X-RAY DIFFRACTION100
2.693-2.9640.32861330.34782509X-RAY DIFFRACTION100
2.964-3.39270.36691320.31382509X-RAY DIFFRACTION100
3.3927-4.27390.28011330.24372543X-RAY DIFFRACTION100
4.2739-43.84690.2221420.20832680X-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)
14.4150.1886-3.61330.03-0.04813.16520.1326-0.1940.03720.0556-0.0412-0.0229-0.07460.21910.00030.5918-0.0048-0.01190.5528-0.00520.60930.531841.829532.5578
23.108-0.5549-0.5832.4521-0.38482.093-0.04810.0193-0.09440.08450.02330.34530.0828-0.17370.00010.6185-0.0755-0.0220.562-0.00250.5399-5.882342.020757.5589
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 22 through 160 )
2X-RAY DIFFRACTION2chain A and (resid 161 through 256 )

+
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://pdbjlvh1.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