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- PDB-5jk9: Crystal structure of human IZUMO1 -

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Basic information

Entry
Database: PDB / ID: 5jk9
TitleCrystal structure of human IZUMO1
ComponentsIzumo sperm-egg fusion protein 1
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 / 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 / MIR / Resolution: 2.1 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

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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: Izumo sperm-egg fusion protein 1
C: Izumo sperm-egg fusion protein 1
D: Izumo sperm-egg fusion protein 1
E: Izumo sperm-egg fusion protein 1
F: Izumo sperm-egg fusion protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,30712
Polymers168,9806
Non-polymers1,3276
Water9,674537
1
A: Izumo sperm-egg fusion protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3852
Polymers28,1631
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Izumo sperm-egg fusion protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3852
Polymers28,1631
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Izumo sperm-egg fusion protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3852
Polymers28,1631
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Izumo sperm-egg fusion protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3852
Polymers28,1631
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Izumo sperm-egg fusion protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3852
Polymers28,1631
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Izumo sperm-egg fusion protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3852
Polymers28,1631
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.936, 75.067, 108.885
Angle α, β, γ (deg.)77.65, 79.11, 70.66
Int Tables number1
Space group name H-MP1

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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.: 6 / 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: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
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.: 537 / 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: 2.87 Å3/Da / Density % sol: 57.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 12-15% (w/v) PEG6000, 0.1 M sodium citrate pH 5.6

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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: Dec 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 106951 / % possible obs: 97.6 % / Redundancy: 3.5 % / Net I/σ(I): 21.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
autoSHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 9.503 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.169 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23057 5249 4.9 %RANDOM
Rwork0.19431 ---
obs0.19615 101240 97.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 48.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å21.63 Å2-1.38 Å2
2--0.32 Å20.7 Å2
3---0.81 Å2
Refinement stepCycle: 1 / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11088 0 84 537 11709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01911462
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210778
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.96115519
X-RAY DIFFRACTIONr_angle_other_deg0.97324951
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.05451382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85724.892511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.861152063
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5341546
X-RAY DIFFRACTIONr_chiral_restr0.0930.21707
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212674
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022504
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_it4.433.5765552
X-RAY DIFFRACTIONr_mcbond_other4.4293.5765551
X-RAY DIFFRACTIONr_mcangle_it5.955.3366923
X-RAY DIFFRACTIONr_mcangle_other5.9495.3366924
X-RAY DIFFRACTIONr_scbond_it6.1834.3435910
X-RAY DIFFRACTIONr_scbond_other6.1824.3435911
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.0096.2258596
X-RAY DIFFRACTIONr_long_range_B_refined10.83534.45646557
X-RAY DIFFRACTIONr_long_range_B_other10.83934.41646245
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.103→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 371 -
Rwork0.28 7007 -
obs--91.2 %
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)
10.7608-0.28590.49630.2538-0.17280.3260.0182-0.0102-0.0063-0.0297-0.0167-0.03630.0045-0.019-0.00150.04820.01550.0420.1116-0.01390.0479-0.37730.6094-0.314
20.8259-0.6755-0.16270.69710.06780.0649-0.0056-0.0921-0.05290.00740.02670.0672-0.00720.0411-0.02110.0148-0.00140.02140.0976-0.03160.0969-21.0974-5.27034.1644
30.5828-0.46680.42390.402-0.26630.58790.01820.01080.0353-0.0015-0.0136-0.0635-0.0414-0.0424-0.00460.0899-0.0084-0.05130.0381-0.00980.084916.911322.477636.5357
40.8087-0.50740.36660.3841-0.33170.43430.02190.0550.0892-0.02670.0194-0.0196-0.02870.0055-0.04130.1039-0.0145-0.00050.09010.01750.04128.1843-32.8963-18.5843
50.4571-0.82750.07252.235-0.58610.2948-0.0662-0.0481-0.0522-0.03970.1520.21720.0561-0.0516-0.08580.1865-0.0395-0.10070.01930.03510.0728.031512.681653.0843
60.2299-0.12910.18850.365-0.55210.8822-0.07240.0170.0576-0.0511-0.135-0.13180.07780.14130.20740.05550.0183-0.00330.11290.04260.0793-12.8761-17.110852.9774
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 258
2X-RAY DIFFRACTION2B19 - 255
3X-RAY DIFFRACTION3C18 - 254
4X-RAY DIFFRACTION4D18 - 250
5X-RAY DIFFRACTION5E19 - 254
6X-RAY DIFFRACTION6F19 - 256

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