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- PDB-5jkb: Crystal structure of human JUNO (crystal form 2) -

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Basic information

Entry
Database: PDB / ID: 5jkb
TitleCrystal structure of human JUNO (crystal form 2)
ComponentsSperm-egg fusion protein Juno
KeywordsCELL ADHESION / fertilization / IZUMO1 / JUNO
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 / signaling receptor binding / external side of plasma membrane / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.23 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: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)101,8578
Polymers101,7154
Non-polymers1424
Water00
1
A: Sperm-egg fusion protein Juno
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4642
Polymers25,4291
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area9990 Å2
MethodPISA
2
B: Sperm-egg fusion protein Juno
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4642
Polymers25,4291
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area10090 Å2
MethodPISA
3
C: Sperm-egg fusion protein Juno
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4642
Polymers25,4291
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area9930 Å2
MethodPISA
4
D: Sperm-egg fusion protein Juno
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4642
Polymers25,4291
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area9940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.770, 88.579, 108.132
Angle α, β, γ (deg.)90.00, 96.88, 90.00
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROGLUGLUAA18 - 2293 - 214
21PROPROGLUGLUBB18 - 2293 - 214
12GLYGLYSERSERAA20 - 2285 - 213
22GLYGLYSERSERCC20 - 2285 - 213
13GLYGLYSERSERAA20 - 2285 - 213
23GLYGLYSERSERDD20 - 2285 - 213
14GLYGLYSERSERBB20 - 2285 - 213
24GLYGLYSERSERCC20 - 2285 - 213
15GLYGLYSERSERBB20 - 2285 - 213
25GLYGLYSERSERDD20 - 2285 - 213
16GLYGLYGLUGLUCC20 - 2295 - 214
26GLYGLYGLUGLUDD20 - 2295 - 214

NCS ensembles :
ID
1
2
3
4
5
6

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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: 25428.842 Da / Num. of mol.: 4
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
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
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: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 3% (w/v) PEG4000, 5% 2-propanol, 0.1 M HEPES-NaOH pH 7.5

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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: Nov 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.23→44.3 Å / Num. obs: 14574 / % possible obs: 99.4 % / Redundancy: 3.4 % / Net I/σ(I): 8

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JKA

5jka


Resolution: 3.23→44.3 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.885 / SU B: 64.762 / SU ML: 0.464 / Cross valid method: THROUGHOUT / ESU R Free: 0.54 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24053 730 5 %RANDOM
Rwork0.21649 ---
obs0.21773 13842 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 72.264 Å2
Baniso -1Baniso -2Baniso -3
1--1.72 Å2-0 Å21.49 Å2
2--0.76 Å2-0 Å2
3---0.59 Å2
Refinement stepCycle: 1 / Resolution: 3.23→44.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6410 0 4 0 6414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196664
X-RAY DIFFRACTIONr_bond_other_d0.0060.025874
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.9239080
X-RAY DIFFRACTIONr_angle_other_deg1.223313606
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9375784
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.05623.879330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.662151042
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1881540
X-RAY DIFFRACTIONr_chiral_restr0.0870.2880
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217552
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021640
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_it2.3515.0033160
X-RAY DIFFRACTIONr_mcbond_other2.3435.0023159
X-RAY DIFFRACTIONr_mcangle_it4.0077.4983936
X-RAY DIFFRACTIONr_mcangle_other4.0067.4993937
X-RAY DIFFRACTIONr_scbond_it2.5985.2793504
X-RAY DIFFRACTIONr_scbond_other2.5945.2773502
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4427.7985144
X-RAY DIFFRACTIONr_long_range_B_refined8.9447.39327715
X-RAY DIFFRACTIONr_long_range_B_other8.9447.39327715
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)
11A232280.06
12B232280.06
21A230480.04
22C230480.04
31A230260.04
32D230260.04
41B230800.05
42C230800.05
51B230600.05
52D230600.05
61C233240.01
62D233240.01
LS refinement shellResolution: 3.23→3.314 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 44 -
Rwork0.323 1026 -
obs--99.81 %
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)
12.54220.39510.61990.54930.85682.36920.09550.14930.04930.0785-0.12650.0798-0.0460.04370.03110.12330.0203-0.02930.2116-0.0620.077634.1167-0.45281.8659
22.2906-0.0508-0.93750.6138-0.77022.0823-0.04710.20210.0037-0.00790.0882-0.12180.0368-0.136-0.04110.1457-0.00840.00730.3011-0.06180.082410.278-32.5205-10.0961
32.0471-0.7263-1.12792.4723-0.70231.501-0.1646-0.1742-0.2077-0.07630.0062-0.1012-0.01990.03640.15840.12020.02580.08490.1846-0.12880.213639.9338-41.7631-18.0474
43.40950.1407-0.72912.24271.23220.91340.178-0.18790.1195-0.0611-0.0493-0.0157-0.05980.0556-0.12860.0913-0.00120.01360.1531-0.12160.215365.1092-35.8969-32.2426
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 229
2X-RAY DIFFRACTION2B18 - 229
3X-RAY DIFFRACTION3C20 - 229
4X-RAY DIFFRACTION4D20 - 229

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