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- PDB-5f4q: Crystal structure of the human egg surface protein Juno -

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Basic information

Entry
Database: PDB / ID: 5f4q
TitleCrystal structure of the human egg surface protein Juno
ComponentsSperm-egg fusion protein Juno
KeywordsCELL ADHESION / glycoprotein / membrane-bound / cysteine-rich / receptor
Function / homology
Function and homology information


sperm-egg recognition / fusion of sperm to egg plasma membrane involved in single fertilization / Post-translational modification: synthesis of GPI-anchored proteins / microvillus membrane / single fertilization / signaling receptor activity / cell adhesion / external side of plasma membrane / signaling receptor binding / extracellular region / plasma membrane
Similarity search - Function
Folate receptor / Folate receptor-like / Folate receptor family
Similarity search - Domain/homology
Sperm-egg fusion protein Juno
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sperm-egg fusion protein Juno
B: Sperm-egg fusion protein Juno
C: Sperm-egg fusion protein Juno
D: Sperm-egg fusion protein Juno
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,60715
Polymers98,3044
Non-polymers1,30311
Water21,5461196
1
A: Sperm-egg fusion protein Juno
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9254
Polymers24,5761
Non-polymers3493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sperm-egg fusion protein Juno
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8333
Polymers24,5761
Non-polymers2572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sperm-egg fusion protein Juno
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9254
Polymers24,5761
Non-polymers3493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Sperm-egg fusion protein Juno
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9254
Polymers24,5761
Non-polymers3493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.150, 73.150, 163.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
Sperm-egg fusion protein Juno / Folate receptor 4 / Folate receptor delta / FR-delta / IZUMO1 receptor protein JUNO


Mass: 24575.932 Da / Num. of mol.: 4 / 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 melanogaster (fruit fly) / References: UniProt: A6ND01
#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.: 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
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1196 / Source method: isolated from a natural source / Formula: H2O
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: 2.24 Å3/Da / Density % sol: 45.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.02 M magnesium chloride, 0.1 M HEPES sodium salt [pH 7.5], 22% (w/v) Polyacrylic acid 5100

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Jul 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.5
ReflectionResolution: 1.8→43.68 Å / Num. obs: 79079 / % possible obs: 100 % / Redundancy: 8.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.044 / Net I/σ(I): 17.5 / Num. measured all: 640808
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.8-1.847.60.73533461845400.8980.28499.8
9.18-43.687.40.02562.6458661710.0199.2

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.5.8data scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F4E

5f4e


Resolution: 1.8→43.68 Å / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.45 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2266 2022 2.57 %
Rwork0.1962 --
obs0.1985 78621 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→43.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6293 0 78 1196 7567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086637
X-RAY DIFFRACTIONf_angle_d1.0859069
X-RAY DIFFRACTIONf_dihedral_angle_d10.8683964
X-RAY DIFFRACTIONf_chiral_restr0.065912
X-RAY DIFFRACTIONf_plane_restr0.0081170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8003-1.84530.28011460.23835506X-RAY DIFFRACTION97
1.8453-1.89520.35551420.32175386X-RAY DIFFRACTION96
1.8952-1.9510.35251420.28935492X-RAY DIFFRACTION97
1.951-2.01390.26391470.21975452X-RAY DIFFRACTION97
2.0139-2.08590.23381460.19065497X-RAY DIFFRACTION97
2.0859-2.16940.28211450.18295466X-RAY DIFFRACTION97
2.1694-2.26810.34071390.26155417X-RAY DIFFRACTION96
2.2681-2.38770.24711390.20095312X-RAY DIFFRACTION95
2.3877-2.53730.22431450.17635510X-RAY DIFFRACTION97
2.5373-2.73310.23191440.17465481X-RAY DIFFRACTION97
2.7331-3.0080.20111450.16635506X-RAY DIFFRACTION97
3.008-3.44310.21571410.1635517X-RAY DIFFRACTION98
3.4431-4.33690.1661480.15915483X-RAY DIFFRACTION97
4.3369-37.48220.2051470.20035555X-RAY DIFFRACTION97
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)
11.10050.39670.1351.82820.06731.4167-0.0252-0.0118-0.0078-0.1911-0.0028-0.0307-0.077-0.03490.00590.0912-0.01210.02080.068-0.00460.086519.606919.728-10.9392
21.5111.12180.52031.6167-1.39274.37960.0630.0225-0.21050.0986-0.1752-0.36710.03330.60250.08950.1138-0.0274-0.04860.19340.03720.174735.412422.41851.2708
31.41090.04521.23072.2109-0.93473.64450.06780.0519-0.0745-0.15420.05730.1918-0.02930.033-0.15290.1861-0.00430.0110.0638-0.00260.098218.083831.4042-12.775
40.8879-0.044-0.47511.21810.08820.80380.02380.04160.0333-0.2557-0.0367-0.0258-0.10050.01890.00330.1932-0.0055-0.01660.0771-0.00280.085554.695956.7857-12.0983
51.8234-0.1166-1.39531.0021.40572.95990.03470.07150.0352-0.0153-0.05910.0910.0252-0.20630.04140.1204-0.0102-0.01630.05860.00330.105147.846345.5907-10.6025
61.34190.12230.14423.76971.01610.73950.2240.17960.5866-0.668-0.28310.219-1.0425-0.70320.11430.35760.0798-0.0420.263-0.00370.362934.895759.3221-6.0337
71.75130.0799-1.00530.65730.12592.7506-0.09420.0693-0.09160.0578-0.05740.33090.1743-0.44290.14440.1379-0.02550.05010.2193-0.05590.174536.886947.99741.35
82.7644-0.4425-1.20291.64381.29553.2109-0.07280.0560.0041-0.05480.01710.07960.092-0.09760.03580.1414-0.0175-0.00170.06620.00730.073951.453241.234-12.2326
90.9045-0.6478-1.71652.27251.79374.1416-0.04590.05260.0094-0.20460.283-0.266-0.24130.3705-0.25350.1268-0.01160.02920.11120.0250.159260.899541.2141-21.5043
100.5531-0.24190.68671.33520.34191.6486-0.0065-0.0114-0.01480.3066-0.00060.03840.11660.0036-0.0020.1589-0.01640.01370.0842-0.00050.092717.004354.639-18.1906
113.74120.99261.66211.38951.15921.985-0.0833-0.1559-0.0372-0.0047-0.06070.1222-0.1533-0.13260.14630.14340.02810.01270.073-0.00420.09675.047862.3399-30.8777
121.17870.10661.47192.51781.18122.59060.09250.1345-0.02730.07960.0008-0.05950.07660.1502-0.07590.1316-0.00330.02960.08310.00080.084618.327368.5427-16.0896
132.1073-0.69670.47860.7802-0.60450.51630.0265-0.18340.13790.5436-0.0942-0.0277-0.0194-0.0360.04990.34430.0076-0.02480.1058-0.00060.121853.940818.9238-8.3349
142.08391.6751-0.38571.8457-1.37673.3179-0.00350.30560.1309-0.16520.20660.5049-0.0604-0.4209-0.21390.1517-0.0285-0.01680.12540.04930.194546.649420.7384-22.8538
151.4882-0.7019-1.47410.37780.51363.00010.02120.1165-0.0666-0.0483-0.01960.05230.02610.00980.01970.1298-0.00190.00220.067-0.00250.085157.887822.75-26.6945
160.809-0.0924-1.0721.3704-0.6831.8827-0.0288-0.10720.0860.23490.0882-0.07270.16120.1565-0.05850.20810.008-0.02680.0873-0.00760.109158.429113.3413-18.6539
172.59270.0012-1.1770.9982-0.74182.4676-0.0214-0.0189-0.0686-0.1269-0.1095-0.19680.39490.34750.13790.20270.05860.01980.17970.03290.098968.077510.697-32.7057
181.678-0.9610.04280.816-0.00753.03590.09390.1419-0.2263-0.1062-0.1076-0.11120.5180.19360.05130.15990.05350.05390.11710.01860.16865.91148.0923-23.7898
190.68950.3829-0.17411.573-0.68540.27880.02560.10710.0127-0.41310.0077-0.07710.21330.0907-0.03450.24910.00390.01260.0826-0.0040.095153.55972.5384-20.4971
201.03570.9333-1.34571.7332-0.2422.8037-0.13250.21980.11860.13230.1290.2397-0.3132-0.4223-0.01330.2580.0068-0.01970.1350.00470.093449.05084.81-12.3264
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 142 )
2X-RAY DIFFRACTION2chain 'A' and (resid 143 through 181 )
3X-RAY DIFFRACTION3chain 'A' and (resid 182 through 228 )
4X-RAY DIFFRACTION4chain 'B' and (resid 20 through 99 )
5X-RAY DIFFRACTION5chain 'B' and (resid 100 through 153 )
6X-RAY DIFFRACTION6chain 'B' and (resid 154 through 163 )
7X-RAY DIFFRACTION7chain 'B' and (resid 164 through 181 )
8X-RAY DIFFRACTION8chain 'B' and (resid 182 through 211 )
9X-RAY DIFFRACTION9chain 'B' and (resid 212 through 232 )
10X-RAY DIFFRACTION10chain 'C' and (resid 22 through 132 )
11X-RAY DIFFRACTION11chain 'C' and (resid 133 through 181 )
12X-RAY DIFFRACTION12chain 'C' and (resid 182 through 232 )
13X-RAY DIFFRACTION13chain 'D' and (resid 20 through 39 )
14X-RAY DIFFRACTION14chain 'D' and (resid 40 through 50 )
15X-RAY DIFFRACTION15chain 'D' and (resid 51 through 83 )
16X-RAY DIFFRACTION16chain 'D' and (resid 84 through 132 )
17X-RAY DIFFRACTION17chain 'D' and (resid 133 through 181 )
18X-RAY DIFFRACTION18chain 'D' and (resid 182 through 193 )
19X-RAY DIFFRACTION19chain 'D' and (resid 194 through 211 )
20X-RAY DIFFRACTION20chain 'D' and (resid 212 through 232 )

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