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- PDB-5jke: Crystal structure of human IZUMO1-JUNO complex (crystal form 3) -

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Basic information

Entry
Database: PDB / ID: 5jke
TitleCrystal structure of human IZUMO1-JUNO complex (crystal form 3)
Components
  • Izumo sperm-egg fusion protein 1
  • Sperm-egg fusion protein Juno
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 / 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 / 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 / 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 / Resolution: 2.86 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
Revision 1.4Nov 8, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
C: Izumo sperm-egg fusion protein 1
D: Sperm-egg fusion protein Juno
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,33212
Polymers107,1844
Non-polymers1,1488
Water724
1
A: Izumo sperm-egg fusion protein 1
B: Sperm-egg fusion protein Juno
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1666
Polymers53,5922
Non-polymers5744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-42 kcal/mol
Surface area22080 Å2
MethodPISA
2
C: Izumo sperm-egg fusion protein 1
D: Sperm-egg fusion protein Juno
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1666
Polymers53,5922
Non-polymers5744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-15 kcal/mol
Surface area22250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.182, 141.776, 144.861
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGPROPROAA18 - 2541 - 237
21ARGARGPROPROCC18 - 2541 - 237
12PROPROGLUGLUBB18 - 2323 - 217
22PROPROGLUGLUDD18 - 2323 - 217

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ACBD

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


Mass: 28163.326 Da / Num. of mol.: 2 / Fragment: UNP residues 20-255
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: Protein Sperm-egg fusion protein Juno / Folate receptor 4 / Folate receptor delta / FR-delta / IZUMO1 receptor protein JUNO


Mass: 25428.842 Da / Num. of mol.: 2 / 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 (fruit flies) / References: UniProt: A6ND01

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Sugars , 1 types, 4 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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, 8 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.07 Å3/Da / Density % sol: 59.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG4000, 0.2 M Li2SO4, 0.1 M MES-NaOH pH 6.0

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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: Mar 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.86→48.3 Å / Num. obs: 31399 / % possible obs: 100 % / Redundancy: 13.2 % / Net I/σ(I): 28.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JK9, 5JKA

5jk9

5jka


Resolution: 2.86→48.3 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / SU B: 32.653 / SU ML: 0.278 / Cross valid method: THROUGHOUT / ESU R: 1.232 / ESU R Free: 0.337 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23817 1468 4.7 %RANDOM
Rwork0.20265 ---
obs0.20429 29880 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 86.849 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å20 Å2-0 Å2
2---1.49 Å20 Å2
3----0.35 Å2
Refinement stepCycle: 1 / Resolution: 2.86→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6994 0 68 4 7066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197286
X-RAY DIFFRACTIONr_bond_other_d0.0040.026646
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.9499898
X-RAY DIFFRACTIONr_angle_other_deg1.132315388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5935862
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.87224.32338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.46151220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.381536
X-RAY DIFFRACTIONr_chiral_restr0.0890.21034
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218106
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021678
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_it5.6826.9993472
X-RAY DIFFRACTIONr_mcbond_other5.6766.9993471
X-RAY DIFFRACTIONr_mcangle_it8.49910.4934326
X-RAY DIFFRACTIONr_mcangle_other8.50110.4934327
X-RAY DIFFRACTIONr_scbond_it6.4837.6183814
X-RAY DIFFRACTIONr_scbond_other6.4837.6193815
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.76711.1855573
X-RAY DIFFRACTIONr_long_range_B_refined13.53466.57529438
X-RAY DIFFRACTIONr_long_range_B_other13.53466.57629439
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A273360.06
12C273360.06
21B237220.05
22D237220.05
LS refinement shellResolution: 2.86→2.934 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 117 -
Rwork0.339 2185 -
obs--100 %
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)
10.22680.1592-0.09790.1556-0.24571.67680.00840.01820.05190.01150.07570.03730.0522-0.0489-0.08410.1240.02560.09250.122-0.01250.099714.245923.094635.7053
22.0659-1.25670.62150.7943-0.1851.59950.1547-0.03790.1794-0.10450.0314-0.1573-0.1090.0196-0.18610.06430.0122-0.01690.0351-0.07380.199738.89478.836545.1513
30.17890.12260.27070.256-0.19212.8661-0.00250.0805-0.09010.07190.11280.0096-0.24130.1842-0.11030.118-0.0138-0.03650.09720.02830.127817.59149.047136.4084
41.3409-0.9381-1.03591.08380.15071.6081-0.02750.0055-0.2102-0.010.02910.31580.09890.0107-0.00160.0213-0.00090.00440.08380.08190.1758-6.273964.086147.9405
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 254
2X-RAY DIFFRACTION2B18 - 232
3X-RAY DIFFRACTION3C18 - 254
4X-RAY DIFFRACTION4D18 - 232

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