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- PDB-5jkc: Crystal structure of human IZUMO1-JUNO complex (crystal form 1) -

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Basic information

Entry
Database: PDB / ID: 5jkc
TitleCrystal structure of human IZUMO1-JUNO complex (crystal form 1)
Components
  • Izumo sperm-egg fusion protein 1
  • Sperm-egg fusion protein Juno
KeywordsCELL ADHESION / fertilization / IZUMO1 / JUNO
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 / Post-translational modification: synthesis of GPI-anchored proteins / binding of sperm to zona pellucida / heterotypic cell-cell adhesion ...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 / Post-translational modification: synthesis of GPI-anchored proteins / binding of sperm to zona pellucida / heterotypic cell-cell adhesion / microvillus membrane / single fertilization / acrosomal vesicle / signaling receptor activity / cell adhesion / receptor ligand activity / signaling receptor binding / external side of plasma membrane / endoplasmic reticulum membrane / protein homodimerization activity / extracellular region / identical protein binding / 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 / Folate receptor / Folate receptor-like / Folate receptor family / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Sperm-egg fusion protein Juno / Izumo sperm-egg fusion protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsOhto, U. / Ishida, H. / Shimizu, T.
CitationJournal: Nature / Year: 2016
Title: Structure of IZUMO1-JUNO reveals sperm-oocyte recognition during mammalian fertilization
Authors: Ohto, U. / Ishida, H. / Krayukhina, E. / Uchiyama, S. / Inoue, N. / Shimizu, T.
History
DepositionApr 26, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / citation ...chem_comp / citation / diffrn_source / pdbx_struct_oper_list
Item: _chem_comp.type / _citation.journal_id_CSD ..._chem_comp.type / _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 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 1.5Oct 23, 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: Izumo sperm-egg fusion protein 1
B: Sperm-egg fusion protein Juno
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0705
Polymers53,5922
Non-polymers4783
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-12 kcal/mol
Surface area21940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.188, 144.750, 141.880
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 Izumo sperm-egg fusion protein 1 / Oocyte binding/fusion factor / OBF / Sperm-specific protein izumo


Mass: 28163.326 Da / Num. of mol.: 1 / Fragment: UNP residues 22-255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IZUMO1 / Production host: Drosophila (fruit flies) / References: UniProt: Q8IYV9
#2: Protein Sperm-egg fusion protein Juno / Folate receptor 4 / Folate receptor delta / FR-delta / IZUMO1 receptor protein JUNO


Mass: 25428.842 Da / Num. of mol.: 1 / Fragment: UNP residues 20-228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IZUMO1R, FOLR4, JUNO / Production host: Drosophila (fruit flies) / References: UniProt: A6ND01
#3: 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
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 3.12 Å3/Da / Density % sol: 60.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 8-12% PEG4000, 0.2 M Li2SO4, 0.1 M MES-NaOH pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 15228 / % possible obs: 100 % / Redundancy: 6.5 % / Net I/σ(I): 34.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JK9, 5JKA

5jk9

5jka


Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.942 / SU B: 46.739 / SU ML: 0.379 / Cross valid method: THROUGHOUT / ESU R: 2.175 / ESU R Free: 0.379 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25941 787 5.2 %RANDOM
Rwork0.22547 ---
obs0.2273 14419 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 105.131 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å2-0 Å2
2--2.42 Å20 Å2
3----3.15 Å2
Refinement stepCycle: 1 / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3488 0 29 5 3522
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193630
X-RAY DIFFRACTIONr_bond_other_d0.0020.023310
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.9474931
X-RAY DIFFRACTIONr_angle_other_deg1.03737664
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9265430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13924.32169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.10615607
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5121518
X-RAY DIFFRACTIONr_chiral_restr0.0950.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214046
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02838
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1597.6161732
X-RAY DIFFRACTIONr_mcbond_other3.1597.6141731
X-RAY DIFFRACTIONr_mcangle_it5.24711.4122158
X-RAY DIFFRACTIONr_mcangle_other5.24611.4142159
X-RAY DIFFRACTIONr_scbond_it3.1017.9811897
X-RAY DIFFRACTIONr_scbond_other3.17.9821898
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.29111.8372774
X-RAY DIFFRACTIONr_long_range_B_refined11.36171.98814953
X-RAY DIFFRACTIONr_long_range_B_other11.3671.99114954
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.903→2.979 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 59 -
Rwork0.382 1023 -
obs--98.54 %
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)
10.55470.6152-0.50853.89420.10780.66510.0108-0.1785-0.1936-0.1607-0.3148-0.0822-0.09650.09060.3040.264-0.1103-0.08790.2132-0.03160.24491.871-35.911522.3744
23.183-1.61660.95682.3602-0.7381.3799-0.0985-0.3097-0.08020.12640.0030.0076-0.1021-0.65820.09540.01160.044-0.02150.4286-0.15090.198-22.127-25.91177.8949
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 254
2X-RAY DIFFRACTION2B18 - 230

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