[English] 日本語
Yorodumi
- PDB-5f4e: Crystal structure of the human sperm Izumo1 and egg Juno complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5f4e
TitleCrystal structure of the human sperm Izumo1 and egg Juno complex
Components
  • Izumo sperm-egg fusion protein 1
  • Sperm-egg fusion protein Juno
KeywordsCELL ADHESION / glycoprotein / membrane-bound / cysteine-rich / complex
Function / homology
Function and homology information


Acrosome Reaction and Sperm:Oocyte Membrane Binding / protein complex involved in cell-cell adhesion / sperm-egg recognition / protein binding involved in heterotypic cell-cell adhesion / fusion of sperm to egg plasma membrane involved in single fertilization / acrosomal membrane / Post-translational modification: synthesis of GPI-anchored proteins / heterotypic cell-cell adhesion / microvillus membrane / single fertilization ...Acrosome Reaction and Sperm:Oocyte Membrane Binding / protein complex involved in cell-cell adhesion / sperm-egg recognition / protein binding involved in heterotypic cell-cell adhesion / fusion of sperm to egg plasma membrane involved in single fertilization / acrosomal membrane / Post-translational modification: synthesis of GPI-anchored proteins / heterotypic cell-cell adhesion / microvillus membrane / single fertilization / acrosomal vesicle / signaling receptor activity / cell adhesion / external side of plasma membrane / signaling receptor binding / endoplasmic reticulum membrane / protein homodimerization activity / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Izumo sperm-egg fusion protein / Izumo protein, immunoglobulin domain / Izumo sperm-egg fusion protein 1 / Izumo sperm-egg fusion, Ig domain-associated / Izumo-like Immunoglobulin domain / Folate receptor / Folate receptor-like / Folate receptor family / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Sperm-egg fusion protein Juno / Izumo sperm-egg fusion protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Izumo sperm-egg fusion protein 1
B: Sperm-egg fusion protein Juno
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0645
Polymers51,7152
Non-polymers3493
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-21 kcal/mol
Surface area21550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.000, 55.800, 81.600
Angle α, β, γ (deg.)90.00, 103.60, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-113-

TRP

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Izumo sperm-egg fusion protein 1 / Oocyte binding/fusion factor / OBF / Sperm-specific protein izumo


Mass: 27139.160 Da / Num. of mol.: 1 / Fragment: UNP residues 22-254
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IZUMO1 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q8IYV9
#2: 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.: 1 / 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

-
Sugars , 1 types, 1 molecules

#3: 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.: 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

-
Non-polymers , 3 types, 27 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES [pH 6.5], 20% (w/v) PEG 4000 and 0.6 M NaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.77 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 24, 2015
RadiationMonochromator: ACCEL/BRUKER double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77 Å / Relative weight: 1
ReflectionResolution: 2.4→47.962 Å / Num. obs: 25587 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 49.43 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.03 / Net I/σ(I): 14.4 / Num. measured all: 184910
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
2.4-2.497.20.6792.81899826240.9540.2799.8
8.98-47.966.60.05533.634695260.9960.02399.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.5.8data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LRH

4lrh


Resolution: 2.4→47.962 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2217 1254 4.92 %
Rwork0.1801 --
obs0.1822 25503 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→47.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3458 0 21 25 3504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013637
X-RAY DIFFRACTIONf_angle_d1.1834928
X-RAY DIFFRACTIONf_dihedral_angle_d15.2311307
X-RAY DIFFRACTIONf_chiral_restr0.048524
X-RAY DIFFRACTIONf_plane_restr0.006631
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.49620.34551410.28322613X-RAY DIFFRACTION99
2.4962-2.60980.32161260.24372708X-RAY DIFFRACTION100
2.6098-2.74730.30751270.2252663X-RAY DIFFRACTION99
2.7473-2.91950.28291410.232693X-RAY DIFFRACTION100
2.9195-3.14480.29351260.22372693X-RAY DIFFRACTION100
3.1448-3.46120.26631400.19842686X-RAY DIFFRACTION100
3.4612-3.96190.21041390.17082707X-RAY DIFFRACTION100
3.9619-4.99070.16741400.13652728X-RAY DIFFRACTION100
4.9907-47.97150.19571740.16522758X-RAY DIFFRACTION100
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)
13.7772-0.00180.8233.9791-0.91955.8431-0.057-0.39570.73790.4277-0.18730.2586-0.5552-0.60650.19770.68230.0208-0.18710.5828-0.07320.5224-16.144137.693795.6955
22.3542-1.5839-2.56512.835-0.38515.28020.1334-0.9903-1.11630.21040.01210.28310.3923-0.6066-0.03580.8248-0.1558-0.25850.70330.11810.8397-16.637927.878895.6414
39.58460.8032-0.19315.08823.29672.32760.58931.2191-2.1813-0.5142-0.4322-0.53971.05070.5486-0.28130.8936-0.0314-0.24630.7344-0.06290.81116.065324.119992.9719
43.6204-3.89113.42475.2621-2.67874.1968-0.23690.06890.4183-0.7003-0.20640.1842-0.50370.06190.34760.9341-0.0348-0.21880.56190.02130.557-9.691139.04287.1416
58.3159-1.77313.66792.0512-0.8882.8425-0.3250.7357-0.0563-0.47780.07430.0864-0.34660.3660.18790.6482-0.0993-0.05130.4540.03840.42122.202530.027592.0457
65.85634.8711-6.39165.6156-4.07177.9477-0.6533-0.2688-0.4623-1.056-0.2519-0.7744-0.02921.29270.73290.6825-0.30320.04081.02560.22780.953137.577231.468492.933
75.95113.1658-1.7933.09390.36833.93820.1489-0.45980.7374-0.11320.00470.0519-0.08310.5017-0.10370.7612-0.2977-0.0970.97990.18530.953239.298940.929998.5303
84.95123.0649-0.79312.5184-0.45166.0033-0.2898-2.12751.07260.5094-0.24670.24030.53640.61040.5660.6827-0.27480.17651.09830.11970.870732.894934.9712103.5915
98.19581.7667-2.86215.8341-2.71854.27070.5612-2.0565-1.0067-1.1905-0.5124-0.4230.00031.7257-0.09530.6624-0.14060.10511.01590.04910.823443.670235.020893.4688
108.81930.9233-4.48677.6332-1.05758.9259-0.20420.3184-0.69450.1211-0.5406-1.15071.09781.3840.88450.53220.1275-0.02660.51110.09910.831631.88886.9967117.4141
116.13830.9802-0.04573.79710.90767.7673-0.02060.28860.7213-1.1435-0.1173-1.1401-0.86571.17880.00270.532-0.13890.07270.61880.12620.734429.259622.9424113.2382
123.4462-1.23411.54876.8797-1.84875.53240.05250.7769-0.1416-0.4556-0.1228-0.49920.18360.76420.0790.3787-0.02750.05470.47180.04220.393220.825115.815110.3015
137.9971-5.64872.29079.3155-4.11466.68810.19250.3889-1.1258-0.10410.0237-0.30811.63260.2162-0.38930.6796-0.0155-0.05260.4765-0.07990.681219.8835-0.2181118.8689
145.57240.16710.37935.013-0.10618.32150.29980.4157-0.6319-0.41710.17310.28131.2856-0.6946-0.36020.6065-0.1139-0.1530.48340.09590.55284.703814.8701108.6139
158.5484-0.38362.85436.8344-2.14952.2028-0.01120.2386-0.3679-0.40620.08940.09040.3678-0.4326-0.25930.5231-0.0063-0.02060.51540.06420.561310.687811.4646120.55
167.4764-2.19330.03466.7857-5.60435.1397-0.17920.00220.48870.1791-0.2712-0.3001-0.30310.51510.42690.6465-0.015-0.13580.5108-0.06690.416822.627713.5194128.5535
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 65 )
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 79 )
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 103 )
5X-RAY DIFFRACTION5chain 'A' and (resid 104 through 160 )
6X-RAY DIFFRACTION6chain 'A' and (resid 161 through 173 )
7X-RAY DIFFRACTION7chain 'A' and (resid 174 through 228 )
8X-RAY DIFFRACTION8chain 'A' and (resid 229 through 243 )
9X-RAY DIFFRACTION9chain 'A' and (resid 244 through 254 )
10X-RAY DIFFRACTION10chain 'B' and (resid 20 through 39 )
11X-RAY DIFFRACTION11chain 'B' and (resid 40 through 50 )
12X-RAY DIFFRACTION12chain 'B' and (resid 51 through 109 )
13X-RAY DIFFRACTION13chain 'B' and (resid 110 through 132 )
14X-RAY DIFFRACTION14chain 'B' and (resid 133 through 181 )
15X-RAY DIFFRACTION15chain 'B' and (resid 182 through 201 )
16X-RAY DIFFRACTION16chain 'B' and (resid 202 through 233 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more