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- PDB-5f4e: Crystal structure of the human sperm Izumo1 and egg Juno complex -

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Basic information

Entry
Database: PDB / ID: 5f4e
TitleCrystal structure of the human sperm Izumo1 and egg Juno complex
Components
  • Izumo sperm-egg fusion protein 1
  • Sperm-egg fusion protein Juno
KeywordsCELL ADHESION / glycoprotein / membrane-bound / cysteine-rich / complex
Function / homology
Function and homology information


Acrosome Reaction and Sperm:Oocyte Membrane Binding / protein complex involved in cell-cell adhesion / 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 / heterotypic cell-cell adhesion / microvillus membrane / single fertilization ...Acrosome Reaction and Sperm:Oocyte Membrane Binding / protein complex involved in cell-cell adhesion / 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 / heterotypic cell-cell adhesion / microvillus membrane / single fertilization / acrosomal vesicle / signaling receptor activity / cell adhesion / external side of plasma membrane / signaling receptor binding / 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 / molecular replacement / Resolution: 2.4 Å
AuthorsAydin, H. / Sultana, A. / Lee, J.E.
CitationJournal: Nature / Year: 2016
Title: Molecular architecture of the human sperm IZUMO1 and egg JUNO fertilization complex.
Authors: Aydin, H. / Sultana, A. / Li, S. / Thavalingam, A. / Lee, J.E.
History
DepositionDec 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Jul 6, 2016Group: Database references
Revision 1.3Jul 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 1.4Sep 27, 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 30, 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)52,0645
Polymers51,7152
Non-polymers3493
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-21 kcal/mol
Surface area21550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.000, 55.800, 81.600
Angle α, β, γ (deg.)90.00, 103.60, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-113-

TRP

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 27139.160 Da / Num. of mol.: 1 / Fragment: UNP residues 22-254
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IZUMO1 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q8IYV9
#2: Protein Sperm-egg fusion protein Juno / Folate receptor 4 / Folate receptor delta / FR-delta / IZUMO1 receptor protein JUNO


Mass: 24575.932 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 melanogaster (fruit fly) / References: UniProt: A6ND01

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Sugars , 1 types, 1 molecules

#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.: 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

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Non-polymers , 3 types, 27 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.22 Å3/Da / Density % sol: 61.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES [pH 6.5], 20% (w/v) PEG 4000 and 0.6 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.77 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 24, 2015
RadiationMonochromator: ACCEL/BRUKER double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77 Å / Relative weight: 1
ReflectionResolution: 2.4→47.962 Å / Num. obs: 25587 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 49.43 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.03 / Net I/σ(I): 14.4 / Num. measured all: 184910
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.4-2.497.20.6792.81899826240.9540.2799.8
8.98-47.966.60.05533.634695260.9960.02399.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.5.8data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LRH

4lrh


Resolution: 2.4→47.962 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2217 1254 4.92 %
Rwork0.1801 --
obs0.1822 25503 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→47.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3458 0 21 25 3504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013637
X-RAY DIFFRACTIONf_angle_d1.1834928
X-RAY DIFFRACTIONf_dihedral_angle_d15.2311307
X-RAY DIFFRACTIONf_chiral_restr0.048524
X-RAY DIFFRACTIONf_plane_restr0.006631
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.49620.34551410.28322613X-RAY DIFFRACTION99
2.4962-2.60980.32161260.24372708X-RAY DIFFRACTION100
2.6098-2.74730.30751270.2252663X-RAY DIFFRACTION99
2.7473-2.91950.28291410.232693X-RAY DIFFRACTION100
2.9195-3.14480.29351260.22372693X-RAY DIFFRACTION100
3.1448-3.46120.26631400.19842686X-RAY DIFFRACTION100
3.4612-3.96190.21041390.17082707X-RAY DIFFRACTION100
3.9619-4.99070.16741400.13652728X-RAY DIFFRACTION100
4.9907-47.97150.19571740.16522758X-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)
13.7772-0.00180.8233.9791-0.91955.8431-0.057-0.39570.73790.4277-0.18730.2586-0.5552-0.60650.19770.68230.0208-0.18710.5828-0.07320.5224-16.144137.693795.6955
22.3542-1.5839-2.56512.835-0.38515.28020.1334-0.9903-1.11630.21040.01210.28310.3923-0.6066-0.03580.8248-0.1558-0.25850.70330.11810.8397-16.637927.878895.6414
39.58460.8032-0.19315.08823.29672.32760.58931.2191-2.1813-0.5142-0.4322-0.53971.05070.5486-0.28130.8936-0.0314-0.24630.7344-0.06290.81116.065324.119992.9719
43.6204-3.89113.42475.2621-2.67874.1968-0.23690.06890.4183-0.7003-0.20640.1842-0.50370.06190.34760.9341-0.0348-0.21880.56190.02130.557-9.691139.04287.1416
58.3159-1.77313.66792.0512-0.8882.8425-0.3250.7357-0.0563-0.47780.07430.0864-0.34660.3660.18790.6482-0.0993-0.05130.4540.03840.42122.202530.027592.0457
65.85634.8711-6.39165.6156-4.07177.9477-0.6533-0.2688-0.4623-1.056-0.2519-0.7744-0.02921.29270.73290.6825-0.30320.04081.02560.22780.953137.577231.468492.933
75.95113.1658-1.7933.09390.36833.93820.1489-0.45980.7374-0.11320.00470.0519-0.08310.5017-0.10370.7612-0.2977-0.0970.97990.18530.953239.298940.929998.5303
84.95123.0649-0.79312.5184-0.45166.0033-0.2898-2.12751.07260.5094-0.24670.24030.53640.61040.5660.6827-0.27480.17651.09830.11970.870732.894934.9712103.5915
98.19581.7667-2.86215.8341-2.71854.27070.5612-2.0565-1.0067-1.1905-0.5124-0.4230.00031.7257-0.09530.6624-0.14060.10511.01590.04910.823443.670235.020893.4688
108.81930.9233-4.48677.6332-1.05758.9259-0.20420.3184-0.69450.1211-0.5406-1.15071.09781.3840.88450.53220.1275-0.02660.51110.09910.831631.88886.9967117.4141
116.13830.9802-0.04573.79710.90767.7673-0.02060.28860.7213-1.1435-0.1173-1.1401-0.86571.17880.00270.532-0.13890.07270.61880.12620.734429.259622.9424113.2382
123.4462-1.23411.54876.8797-1.84875.53240.05250.7769-0.1416-0.4556-0.1228-0.49920.18360.76420.0790.3787-0.02750.05470.47180.04220.393220.825115.815110.3015
137.9971-5.64872.29079.3155-4.11466.68810.19250.3889-1.1258-0.10410.0237-0.30811.63260.2162-0.38930.6796-0.0155-0.05260.4765-0.07990.681219.8835-0.2181118.8689
145.57240.16710.37935.013-0.10618.32150.29980.4157-0.6319-0.41710.17310.28131.2856-0.6946-0.36020.6065-0.1139-0.1530.48340.09590.55284.703814.8701108.6139
158.5484-0.38362.85436.8344-2.14952.2028-0.01120.2386-0.3679-0.40620.08940.09040.3678-0.4326-0.25930.5231-0.0063-0.02060.51540.06420.561310.687811.4646120.55
167.4764-2.19330.03466.7857-5.60435.1397-0.17920.00220.48870.1791-0.2712-0.3001-0.30310.51510.42690.6465-0.015-0.13580.5108-0.06690.416822.627713.5194128.5535
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 65 )
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 79 )
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 103 )
5X-RAY DIFFRACTION5chain 'A' and (resid 104 through 160 )
6X-RAY DIFFRACTION6chain 'A' and (resid 161 through 173 )
7X-RAY DIFFRACTION7chain 'A' and (resid 174 through 228 )
8X-RAY DIFFRACTION8chain 'A' and (resid 229 through 243 )
9X-RAY DIFFRACTION9chain 'A' and (resid 244 through 254 )
10X-RAY DIFFRACTION10chain 'B' and (resid 20 through 39 )
11X-RAY DIFFRACTION11chain 'B' and (resid 40 through 50 )
12X-RAY DIFFRACTION12chain 'B' and (resid 51 through 109 )
13X-RAY DIFFRACTION13chain 'B' and (resid 110 through 132 )
14X-RAY DIFFRACTION14chain 'B' and (resid 133 through 181 )
15X-RAY DIFFRACTION15chain 'B' and (resid 182 through 201 )
16X-RAY DIFFRACTION16chain 'B' and (resid 202 through 233 )

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