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- PDB-5b5k: Crystal structure of Izumo1, the mammalian sperm ligand for egg Juno -

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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 / protein complex involved in cell-cell adhesion / syncytium formation by plasma membrane fusion / sperm-egg recognition / protein binding involved in heterotypic cell-cell adhesion / fusion of sperm to egg plasma membrane involved in single fertilization / acrosomal membrane / acrosomal vesicle / cell adhesion / receptor ligand activity ...Acrosome Reaction and Sperm:Oocyte Membrane Binding / protein complex involved in cell-cell adhesion / syncytium formation by plasma membrane fusion / sperm-egg recognition / protein binding involved in heterotypic cell-cell adhesion / fusion of sperm to egg plasma membrane involved in single fertilization / acrosomal membrane / acrosomal vesicle / cell adhesion / receptor ligand activity / signaling receptor binding / endoplasmic reticulum membrane / protein homodimerization activity / membrane / 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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
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: 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

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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

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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 )

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