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- PDB-5jka: Crystal structure of human JUNO (crystal form 1) -

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Basic information

Entry
Database: PDB / ID: 5jka
TitleCrystal structure of human JUNO (crystal form 1)
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: 2 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 6, 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
B: Sperm-egg fusion protein Juno
A: Sperm-egg fusion protein Juno
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7136
Polymers50,8582
Non-polymers8554
Water2,684149
1
B: Sperm-egg fusion protein Juno
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2133
Polymers25,4291
Non-polymers7842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-1 kcal/mol
Surface area10540 Å2
MethodPISA
2
A: Sperm-egg fusion protein Juno
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5003
Polymers25,4291
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area10230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.920, 81.038, 235.084
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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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.: 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
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.43 Å3/Da / Density % sol: 49.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG3350, 0.24 M malonate pH 7.0

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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: Feb 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 33749 / % possible obs: 99.2 % / Redundancy: 12.3 % / Net I/σ(I): 26.6

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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: 4KMY

4kmy


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 8.581 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.146 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21782 1674 5 %RANDOM
Rwork0.19749 ---
obs0.19855 32072 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.833 Å2
Baniso -1Baniso -2Baniso -3
1-3.65 Å20 Å2-0 Å2
2---0.92 Å20 Å2
3----2.72 Å2
Refinement stepCycle: 1 / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3236 0 53 149 3438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193418
X-RAY DIFFRACTIONr_bond_other_d0.0030.023005
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.9424662
X-RAY DIFFRACTIONr_angle_other_deg1.0136969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2385395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41923.832167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.12115527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7241520
X-RAY DIFFRACTIONr_chiral_restr0.0890.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213824
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02834
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_it2.3663.0361592
X-RAY DIFFRACTIONr_mcbond_other2.3643.0331591
X-RAY DIFFRACTIONr_mcangle_it3.5354.531983
X-RAY DIFFRACTIONr_mcangle_other3.5344.5331984
X-RAY DIFFRACTIONr_scbond_it2.8573.3921826
X-RAY DIFFRACTIONr_scbond_other2.8573.3941827
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3934.9532680
X-RAY DIFFRACTIONr_long_range_B_refined6.94229.2114415
X-RAY DIFFRACTIONr_long_range_B_other6.94129.21314416
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 118 -
Rwork0.284 2125 -
obs--90.66 %
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)
10.1466-0.1967-0.10860.599-0.1341.3115-0.016-0.0656-0.0161-0.06310.0365-0.0123-0.0149-0.0456-0.02050.05110.01460.01560.0657-0.00060.1285-10.88024.6076-44.9665
20.6661-0.63470.31390.844-0.55890.8889-0.2615-0.2910.00940.18040.362-0.0222-0.125-0.0923-0.10050.14850.10420.00830.2716-0.05730.0299-6.9097-2.2306-13.3699
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 231
2X-RAY DIFFRACTION2B20 - 231

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