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- PDB-9myl: Fertilization IZUMO1 Protein Ectodomain in Complex with Anti-sper... -

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Basic information

Entry
Database: PDB / ID: 9myl
TitleFertilization IZUMO1 Protein Ectodomain in Complex with Anti-sperm Antibody OBF13
Components
  • (Anti-sperm antibody OBF13 ...) x 2
  • Izumo sperm-egg fusion protein 1
KeywordsCELL ADHESION / Fertilization / Anti-sperm antibody / IZUMO1 / Infertility / Contraception
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
PROLINE / Izumo sperm-egg fusion protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.177 Å
AuthorsTang, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)R00HD104924 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Allosteric inhibition of the IZUMO1-JUNO fertilization complex by the naturally occurring antisperm antibody OBF13.
Authors: Lu, Y. / Ikawa, M. / Tang, S.
History
DepositionJan 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Izumo sperm-egg fusion protein 1
D: Izumo sperm-egg fusion protein 1
H: Anti-sperm antibody OBF13 heavy chain
L: Anti-sperm antibody OBF13 light chain
A: Anti-sperm antibody OBF13 heavy chain
B: Anti-sperm antibody OBF13 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,57212
Polymers148,8296
Non-polymers7446
Water00
1
C: Izumo sperm-egg fusion protein 1
H: Anti-sperm antibody OBF13 heavy chain
L: Anti-sperm antibody OBF13 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7866
Polymers74,4143
Non-polymers3723
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-41 kcal/mol
Surface area30240 Å2
MethodPISA
2
D: Izumo sperm-egg fusion protein 1
A: Anti-sperm antibody OBF13 heavy chain
B: Anti-sperm antibody OBF13 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7866
Polymers74,4143
Non-polymers3723
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-39 kcal/mol
Surface area29520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.069, 83.208, 92.605
Angle α, β, γ (deg.)82.85, 89.72, 71.40
Int Tables number1
Space group name H-MP1

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Components

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Antibody , 2 types, 4 molecules HALB

#2: Antibody Anti-sperm antibody OBF13 heavy chain


Mass: 23307.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#3: Antibody Anti-sperm antibody OBF13 light chain


Mass: 23587.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 4 molecules CD

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


Mass: 27519.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Izumo1 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q9D9J7
#4: 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: obtained synthetically / 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 , 2 types, 4 molecules

#5: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl

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Details

Has ligand of interestN
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: 3.95 Å3/Da / Density % sol: 68.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 200 mM L-Proline, 100 mM HEPES pH 7.4, 9% PEG 3,350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 16, 2021
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.177→40.062 Å / Num. obs: 34758 / % possible obs: 90.72 % / Redundancy: 2.2 % / CC1/2: 0.994 / Net I/σ(I): 5.9
Reflection shellResolution: 3.18→3.27 Å / Num. unique obs: 2932 / CC1/2: 0.929

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.177→40.062 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 31.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2633 1683 4.84 %
Rwork0.2119 --
obs0.2145 34758 90.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.177→40.062 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9150 0 44 0 9194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069425
X-RAY DIFFRACTIONf_angle_d1.03212877
X-RAY DIFFRACTIONf_dihedral_angle_d10.5933088
X-RAY DIFFRACTIONf_chiral_restr0.0451484
X-RAY DIFFRACTIONf_plane_restr0.0031659
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1772-3.27070.37011390.31522793X-RAY DIFFRACTION93
3.2707-3.37620.37111440.29222787X-RAY DIFFRACTION92
3.3762-3.49680.31571140.27142803X-RAY DIFFRACTION91
3.4968-3.63670.31441240.25952744X-RAY DIFFRACTION89
3.6367-3.80210.32841360.2552561X-RAY DIFFRACTION84
3.8021-4.00240.2711360.23382829X-RAY DIFFRACTION92
4.0024-4.25290.25221630.19872786X-RAY DIFFRACTION92
4.2529-4.58080.2011510.18212772X-RAY DIFFRACTION92
4.5808-5.0410.24171310.17112649X-RAY DIFFRACTION87
5.041-5.76860.29481310.19672885X-RAY DIFFRACTION94
5.7686-7.26070.25941580.23482726X-RAY DIFFRACTION91
7.2607-40.0620.22841560.18062740X-RAY DIFFRACTION91

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