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

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Entry
Database: PDB / ID: 5jke
TitleCrystal structure of human IZUMO1-JUNO complex (crystal form 3)
DescriptorIzumo sperm-egg fusion protein 1
Sperm-egg fusion protein Juno
KeywordsCELL ADHESION / fertilization / IZUMO1 / JUNO
Specimen sourceHomo sapiens / human
MethodX-ray diffraction (2.86 Å resolution / Molecular replacement)
AuthorsOhto, U. / Ishida, H. / Shimizu, T.
CitationNature, 2016, 534, 566-569

Nature, 2016, 534, 566-569 Yorodumi Papers
Structure of IZUMO1-JUNO reveals sperm-oocyte recognition during mammalian fertilization
Ohto, U. / Ishida, H. / Krayukhina, E. / Uchiyama, S. / Inoue, N. / Shimizu, T.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 26, 2016 / Release: Jun 22, 2016
RevisionDateData content typeGroupProviderType
1.0Jun 22, 2016Structure modelrepositoryInitial release
1.1Jun 29, 2016Structure modelDatabase references

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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
Polyers107,1844
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
Polyers53,5922
Non-polymers5744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)2880
ΔGint (kcal/M)-42
Surface area (Å2)22080
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
Polyers53,5922
Non-polymers5744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)2480
ΔGint (kcal/M)-15
Surface area (Å2)22250
MethodPISA
Unit cell
γ
α
β
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-MP 2 21 21

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Components

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Polypeptide(L) , 2 types, 4 molecules ACBD

#1: Polypeptide(L)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: (gene. exp.) Homo sapiens / References: UniProt: Q8IYV9

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)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: (gene. exp.) Homo sapiens / References: UniProt: A6ND01

Cellular component

Molecular function

Biological process

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Non-polymers , 4 types, 12 molecules

#3: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 4 / Formula: C8H15NO6
#4: ChemicalChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Formula: SO4
#5: ChemicalChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Formula: Cl
#6: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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 / Density percent sol: 59.99
Crystal growTemp: 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 kelvins
SourceSource: SYNCHROTRON / Type: PHOTON FACTORY BEAMLINE AR-NE3A / Synchrotron site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Collection date: Mar 12, 2016
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionD resolution high: 2.86 Å / D resolution low: 48.3 Å / Number obs: 31399 / NetI over sigmaI: 28.5 / Redundancy: 13.2 / Percent possible obs: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JK9, 5JKA
Correlation coeff Fo to Fc: 0.948 / Correlation coeff Fo to Fc free: 0.926 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS / Overall SU B: 32.653 / Overall SU ML: 0.278 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Overall ESU R: 1.232 / Overall ESU R Free: 0.337
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.2 Å
Displacement parametersB iso mean: 86.849 Å2 / Aniso B11: 1.84 Å2 / Aniso B12: 0 Å2 / Aniso B13: - Å2 / Aniso B22: -1.49 Å2 / Aniso B23: 0 Å2 / Aniso B33: -0.35 Å2
Least-squares processR factor R free: 0.23817 / R factor R work: 0.20265 / R factor obs: 0.20429 / Highest resolution: 2.86 Å / Lowest resolution: 48.3 Å / Number reflection R free: 1468 / Number reflection obs: 29880 / Percent reflection R free: 4.7 / Percent reflection obs: 99.96
Refine hist #1Highest resolution: 2.86 Å / Lowest resolution: 48.3 Å
Number of atoms included #1Protein: 6994 / Nucleic acid: 0 / Ligand: 68 / Solvent: 4 / Total: 7066
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197286
X-RAY DIFFRACTIONr_bond_other_d0.0040.0206646
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.9499898
X-RAY DIFFRACTIONr_angle_other_deg1.1323.00015388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5935.000862
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.87224.320338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.46015.0001220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.38015.00036
X-RAY DIFFRACTIONr_chiral_restr0.0890.2001034
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218106
X-RAY DIFFRACTIONr_gen_planes_other0.0040.0201678
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

Dom IDAuth asym IDEns IDNumberRms dev position
1A1273360.06
2C1273360.06
1B2237220.05
2D2237220.05
Refine LS shellHighest resolution: 2.86 Å / R factor R free: 0.356 / R factor R work: 0.339 / Lowest resolution: 2.934 Å / Number reflection R free: 117 / Number reflection R work: 2185 / Total number of bins used: 20 / Percent reflection obs: 1
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
10.22680.1592-0.09790.1556-0.24571.67680.00840.01820.05190.01150.07570.03730.0522-0.0489-0.08410.12400.02560.09250.1220-0.01250.099714.245923.094635.7053
22.0659-1.25670.62150.7943-0.18501.59950.1547-0.03790.1794-0.10450.0314-0.1573-0.10900.0196-0.18610.06430.0122-0.01690.0351-0.07380.199738.89478.836545.1513
30.17890.12260.27070.2560-0.19212.8661-0.00250.0805-0.09010.07190.11280.0096-0.24130.1842-0.11030.1180-0.0138-0.03650.09720.02830.127817.591049.047136.4084
41.3409-0.9381-1.03591.08380.15071.6081-0.02750.0055-0.2102-0.01000.02910.31580.09890.0107-0.00160.0213-0.00090.00440.08380.08190.1758-6.273964.086147.9405
Refine TLS group

Beg auth seq ID: 18 / Refine ID: X-RAY DIFFRACTION

IDBeg auth asym IDEnd auth asym IDEnd auth seq IDRefine TLS ID
1AA2541
2BB2322
3CC2543
4DD2324

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