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- PDB-9mym: Fertilization IZUMO1 Protein Ectodomain -

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Basic information

Entry
Database: PDB / ID: 9mym
TitleFertilization IZUMO1 Protein Ectodomain
ComponentsIzumo 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
alpha-L-fucopyranose / DI(HYDROXYETHYL)ETHER / Izumo sperm-egg fusion protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.843 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,36710
Polymers27,1941
Non-polymers1,1739
Water5,855325
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.454, 103.454, 139.297
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-1504-

PEG

21A-1508-

CA

31A-1509-

CA

41A-1641-

HOH

51A-1760-

HOH

61A-1796-

HOH

71A-1878-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 27194.172 Da / Num. of mol.: 1
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

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Sugars , 2 types, 3 molecules

#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.: 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
#3: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 331 molecules

#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O

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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: 3.43 Å3/Da / Density % sol: 64.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 200 mM CaCl2, 100 nM HEPES pH 7.5, 28% PPG P400

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 22, 2021
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.84→36.58 Å / Num. obs: 32920 / % possible obs: 99.98 % / Redundancy: 20 % / CC1/2: 1 / Net I/σ(I): 27.5
Reflection shellResolution: 1.84→1.9 Å / Num. unique obs: 2921 / CC1/2: 0.79

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.843→36.577 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1907 1591 4.83 %
Rwork0.1695 --
obs0.1706 32920 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.843→36.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1883 0 71 325 2279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182111
X-RAY DIFFRACTIONf_angle_d1.6342858
X-RAY DIFFRACTIONf_dihedral_angle_d15.524784
X-RAY DIFFRACTIONf_chiral_restr0.104325
X-RAY DIFFRACTIONf_plane_restr0.007363
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.843-1.90230.30021240.24822797X-RAY DIFFRACTION100
1.9023-1.97030.23521450.20032805X-RAY DIFFRACTION100
1.9703-2.04920.21841580.18192800X-RAY DIFFRACTION100
2.0492-2.14240.22941620.17232805X-RAY DIFFRACTION100
2.1424-2.25540.20421190.16252829X-RAY DIFFRACTION100
2.2554-2.39670.18541240.16472845X-RAY DIFFRACTION100
2.3967-2.58170.20111430.16782832X-RAY DIFFRACTION100
2.5817-2.84140.18981750.17692814X-RAY DIFFRACTION100
2.8414-3.25230.17131080.16832907X-RAY DIFFRACTION100
3.2523-4.09670.17011460.15292888X-RAY DIFFRACTION100
4.0967-36.5770.18691870.17173007X-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)
14.82140.2222.45681.14940.39442.571-0.1394-0.02860.344-0.01250.04470.0802-0.1433-0.07270.16790.22840.00040.01790.19050.00180.2935-38.0322-36.3224-46.4909
25.867-1.3635-3.34370.45850.79332.06060.0339-2.5693-1.35651.07120.28230.51571.28050.67660.07090.815-0.1048-0.02520.96240.13040.5755-33.2863-45.5579-24.5255
35.01350.95392.90191.32291.17953.3250.1030.28-0.33650.04270.1901-0.16440.04710.384-0.27640.2188-0.0060.01130.1759-0.00140.2794-27.3985-44.0234-44.2076
48.14341.25528.25080.84330.90986.45430.4254-0.2588-0.51670.2821-0.0305-0.09360.4124-0.2698-0.37350.2963-0.0138-0.03260.26490.0060.3109-32.983-49.1381-38.2489
56.6833-1.67195.38950.6333-1.83125.8642-0.1603-0.59840.11520.1840.12210.1192-0.2492-0.44960.04940.2279-0.0166-0.0120.2563-0.01070.2176-19.1228-38.8418-21.3762
62.8618-3.44080.55674.5507-0.78022.1374-0.4208-0.0893-0.28040.14790.1847-0.3210.16030.33760.09440.2325-0.0179-0.0180.3024-0.05850.22866.8285-48.2076-11.0218
73.8326-1.61271.92263.1018-0.66431.7041-0.06850.20140.03640.0539-0.0111-0.3981-0.18010.35050.08720.2296-0.04850.00180.28740.00580.21145.5873-40.2408-12.0539
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 63 )
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 76 )
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 103 )
4X-RAY DIFFRACTION4chain 'A' and (resid 104 through 132 )
5X-RAY DIFFRACTION5chain 'A' and (resid 133 through 160 )
6X-RAY DIFFRACTION6chain 'A' and (resid 161 through 181 )
7X-RAY DIFFRACTION7chain 'A' and (resid 182 through 256 )

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