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- PDB-5ejn: Crystal structure of Juno, the mammalian egg receptor for sperm Izumo1 -

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Basic information

Entry
Database: PDB / ID: 5ejn
TitleCrystal structure of Juno, the mammalian egg receptor for sperm Izumo1
ComponentsSperm-egg fusion protein Juno
KeywordsCELL ADHESION / Fertilization / sperm receptor / gamete adhesion / egg-sperm membrane fusion
Function / homology
Function and homology information


Post-translational modification: synthesis of GPI-anchored proteins / sperm-egg recognition / fusion of sperm to egg plasma membrane involved in single fertilization / single fertilization / signaling receptor activity / cell adhesion / signaling receptor binding / membrane / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.703 Å
AuthorsNishimura, K. / Han, L. / Jovine, L.
Funding support Sweden, 6items
OrganizationGrant numberCountry
Karolinska Institutet Sweden
Swedish Research Council2012-5093 Sweden
Goran Gustafsson Foundation for Research in Natural Sciences and Medicine Sweden
Sven and Ebba-Christina Hagberg foundation Sweden
European Molecular Biology Organization
European UnionERC 260759
Citation
Journal: Curr.Biol. / Year: 2016
Title: Divergent evolution of vitamin B9 binding underlies Juno-mediated adhesion of mammalian gametes.
Authors: Han, L. / Nishimura, K. / Sadat Al Hosseini, H. / Bianchi, E. / Wright, G.J. / Jovine, L.
#1: Journal: Nature / Year: 2014
Title: Juno is the egg Izumo receptor and is essential for mammalian fertilization.
Authors: Bianchi, E. / Doe, B. / Goulding, D. / Wright, G.J.
#2: Journal: Philos. Trans. R. Soc. Lond., B, Biol. Sci. / Year: 2015
Title: Cross-species fertilization: the hamster egg receptor, Juno, binds the human sperm ligand, Izumo1.
Authors: Bianchi, E. / Wright, G.J.
#3: Journal: Nature / Year: 2013
Title: Structural basis for molecular recognition of folic acid by folate receptors.
Authors: Chen, C. / Ke, J. / Zhou, X.E. / Yi, W. / Brunzelle, J.S. / Li, J. / Yong, E.L. / Xu, H.E. / Melcher, K.
#4: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2013
Title: Structures of human folate receptors reveal biological trafficking states and diversity in folate and antifolate recognition.
Authors: Wibowo, A.S. / Singh, M. / Reeder, K.M. / Carter, J.J. / Kovach, A.R. / Meng, W. / Ratnam, M. / Zhang, F. / Dann, C.E.
#5: Journal: Cell / Year: 2009
Title: Structure of N-terminal domain of NPC1 reveals distinct subdomains for binding and transfer of cholesterol.
Authors: Kwon, H.J. / Abi-Mosleh, L. / Wang, M.L. / Deisenhofer, J. / Goldstein, J.L. / Brown, M.S. / Infante, R.E.
#6: Journal: EMBO J. / Year: 1997
Title: Crystal structure of chicken riboflavin-binding protein.
Authors: Monaco, H.L.
History
DepositionNov 2, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / struct_conf
Item: _pdbx_audit_support.funding_organization / _struct_conf.beg_auth_comp_id ..._pdbx_audit_support.funding_organization / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_id / _struct_conf.pdbx_PDB_helix_length
Revision 1.2Jul 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 / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 10, 2024Group: 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
Remark 650HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6563
Polymers50,4352
Non-polymers2211
Water0
1
A: Sperm-egg fusion protein Juno


Theoretical massNumber of molelcules
Total (without water)25,2171
Polymers25,2171
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sperm-egg fusion protein Juno
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4392
Polymers25,2171
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.100, 52.200, 87.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Sperm-egg fusion protein Juno / Folate receptor 4 / Folate receptor delta / FR-delta / Folate-binding protein 3 / IZUMO1 receptor protein JUNO


Mass: 25217.330 Da / Num. of mol.: 2 / Fragment: UNP residues 19-221
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Izumo1r, Folbp3, Folr4, Juno / Plasmid: pHLsec3H / Cell line (production host): HEK-293T / Production host: Homo sapiens (human) / References: UniProt: Q9EQF4
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.72 Å3/Da / Density % sol: 28.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG 4000, 0.1 M Tris-HCl pH 8.5, 0.2 M calcium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.49
ReflectionResolution: 2.7→44.83 Å / Num. obs: 9510 / % possible obs: 99.3 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 13.7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.774 / Mean I/σ(I) obs: 1.9 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDS20151015data reduction
PHASER2.6.0phasing
Coot0.8.2model building
XDS20151015data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LRH

4lrh


Resolution: 2.703→44.829 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 39.25 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2482 482 5.07 %Random selection
Rwork0.233 ---
obs0.2294 9510 99.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.703→44.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2796 0 0 0 2796
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032907
X-RAY DIFFRACTIONf_angle_d0.653965
X-RAY DIFFRACTIONf_dihedral_angle_d14.6471074
X-RAY DIFFRACTIONf_chiral_restr0.04399
X-RAY DIFFRACTIONf_plane_restr0.004507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7033-3.09430.32091580.32332984X-RAY DIFFRACTION95
3.0943-3.89820.30031570.26333001X-RAY DIFFRACTION95
3.8982-43.75570.21151620.19473047X-RAY DIFFRACTION94
Refinement TLS params.

S33: -0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.74580.3584-1.81235.70010.81982.8409-0.03340.0353-0.01470.32320.06240.5370.2392-0.40380.89790.02270.06270.79380.06180.772413.0062-1.59395.93
23.7050.64270.66467.04631.07173.71130.08440.06020.1033-0.1681-0.06380.63310.1402-0.36010.52660.02630.04810.75520.07390.76812.704-25.4837.7995
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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