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- PDB-5f4v: Crystal structure of the human sperm Izumo1 residues 22-268 -

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Basic information

Entry
Database: PDB / ID: 5f4v
TitleCrystal structure of the human sperm Izumo1 residues 22-268
ComponentsIzumo sperm-egg fusion protein 1
KeywordsCELL ADHESION / glycoprotein / membrane-bound / cysteine-rich / adhesion / fusion
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 / heterotypic cell-cell adhesion / single fertilization / acrosomal vesicle / cell adhesion ...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 / heterotypic cell-cell adhesion / single fertilization / acrosomal vesicle / cell adhesion / signaling receptor binding / endoplasmic reticulum membrane / protein homodimerization activity / membrane / identical protein binding / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Izumo sperm-egg fusion protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 1.3Dec 28, 2016Group: Structure summary
Revision 1.4Jul 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 / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 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

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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)29,0012
Polymers28,7801
Non-polymers2211
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.300, 121.300, 53.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-412-

HOH

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Components

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


Mass: 28780.166 Da / Num. of mol.: 1 / Fragment: UNP residues 22-268
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: 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 / N-Acetylglucosamine


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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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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: 2.83 Å3/Da / Density % sol: 56.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.085 M HEPES sodium salt (pH 7.5), 8.5% (v/v) isopropanol, 17% (w/v) PEG 4000 and 15% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.9→47.603 Å / Num. obs: 6484 / % possible obs: 100 % / Redundancy: 5.8 % / Biso Wilson estimate: 49.33 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.055 / Net I/σ(I): 12.9 / Num. measured all: 37350
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.9-3.085.80.5263.7597910260.8890.239100
8.7-47.65.70.04133.213512380.9980.01999.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.5.8data scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F4E
Resolution: 2.9→47.603 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 24.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2318 367 5.66 %
Rwork0.1882 --
obs0.1907 6482 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→47.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 14 13 1849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121873
X-RAY DIFFRACTIONf_angle_d1.272534
X-RAY DIFFRACTIONf_dihedral_angle_d15.444670
X-RAY DIFFRACTIONf_chiral_restr0.055289
X-RAY DIFFRACTIONf_plane_restr0.006320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9002-3.31980.29661240.23052024X-RAY DIFFRACTION100
3.3198-4.18220.23281140.18952060X-RAY DIFFRACTION100
4.1822-47.6090.20641290.17072031X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.8702-0.34851.39981.2099-1.12451.6804-0.07560.1544-0.4615-0.09550.17420.3675-0.015-0.3273-0.13180.34860.0051-0.01990.34140.00650.335443.564945.837439.6646
23.3071-1.6931.0592.2791-0.72392.37140.0777-0.2670.02040.2388-0.03390.21630.0777-0.1476-0.07620.3198-0.02810.02410.2641-0.03430.25540.973153.36345.2007
31.5719-0.0638-0.62933.3587-0.85080.96780.0950.10750.27950.05760.0570.2423-0.1929-0.0751-0.14340.3199-0.0322-0.02840.37930.01170.263832.724485.387725.2586
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 76 )
2X-RAY DIFFRACTION2chain 'A' and (resid 77 through 132 )
3X-RAY DIFFRACTION3chain 'A' and (resid 133 through 256 )

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