[English] 日本語
Yorodumi
- PDB-5jyj: Crystal structure of mouse JUNO -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jyj
TitleCrystal structure of mouse JUNO
ComponentsSperm-egg fusion protein Juno
KeywordsCELL ADHESION / Fertilization / Folate receptor
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: 2.3 Å
AuthorsKato, K. / Nishimasu, H. / Morita, J. / Ishitani, R. / Nureki, O.
CitationJournal: To Be Published
Title: Crystal structure of the egg IZUMO1 receptor JUNO
Authors: Kato, K. / Satouh, Y. / Nishimasu, H. / Kurabayashi, A. / Morita, J. / Fujihara, Y. / Oji, A. / Ishitani, R. / Ikawa, M. / Nureki, O.
History
DepositionMay 14, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / pdbx_struct_special_symmetry / 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 / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,9112
Polymers24,4871
Non-polymers4241
Water64936
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint6 kcal/mol
Surface area10080 Å2
Unit cell
Length a, b, c (Å)42.396, 54.449, 87.145
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-1136-

HOH

-
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: 24486.629 Da / Num. of mol.: 1 / Fragment: UNP residues 20-221 / Mutation: N73D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Izumo1r, Folbp3, Folr4, Juno / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9EQF4
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.05 Å3/Da / Density % sol: 40.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Ammonium phosphate dibasic, Imidazole, Sodium chloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→46.2 Å / Num. obs: 9442 / % possible obs: 99.7 % / Redundancy: 5.9 % / Net I/σ(I): 11.2

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→46.177 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.61
RfactorNum. reflection% reflection
Rfree0.2332 492 5.21 %
Rwork0.2077 --
obs0.209 9441 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→46.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1561 0 28 36 1625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021684
X-RAY DIFFRACTIONf_angle_d0.582317
X-RAY DIFFRACTIONf_dihedral_angle_d16.1961016
X-RAY DIFFRACTIONf_chiral_restr0.04241
X-RAY DIFFRACTIONf_plane_restr0.005302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.53150.25971260.25212166X-RAY DIFFRACTION100
2.5315-2.89780.24981160.22562207X-RAY DIFFRACTION100
2.8978-3.65070.23611190.20812232X-RAY DIFFRACTION100
3.6507-46.18590.21781310.18962344X-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)
12.12360.90270.89624.1472-0.23472.056-0.2948-0.09830.61550.6588-0.2991-0.6632-0.95670.56360.15750.4369-0.1383-0.22930.4340.03490.443-3.9359-11.5353-9.5073
22.35970.66050.83061.4720.30771.1531-0.12410.8362-0.3746-0.00780.0351-0.3177-0.22650.436-0.4450.2788-0.1768-0.09020.72670.15280.6731-2.2745-10.4416-22.7196
31.8939-1.45250.40056.0319-3.73282.78270.05270.29120.1722-0.0551-0.2453-0.2906-0.16890.46410.25250.1504-0.06720.00430.27290.01340.1992-11.8558-10.6762-20.8838
45.6201-4.20690.24116.6328-1.22272.93560.18760.0336-0.5761-0.14880.0570.10520.00170.3911-0.10650.1079-0.0113-0.00160.2978-0.03960.3238-12.0655-25.1176-15.5686
52.6557-1.18171.39784.4792-1.94023.53830.14140.1862-0.1616-0.1753-0.05340.17160.09690.0987-0.07770.20130.014-0.00780.1809-0.00590.2376-20.0027-11.3333-25.2625
62.3148-2.414-0.01213.3244-1.87824.42610.0113-0.25150.25160.73310.0760.5567-0.7947-0.1050.15590.58590.10560.03050.3249-0.01510.2211-20.1536-13.813-3.793
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 57 )
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 75 )
3X-RAY DIFFRACTION3chain 'A' and (resid 76 through 109 )
4X-RAY DIFFRACTION4chain 'A' and (resid 110 through 126 )
5X-RAY DIFFRACTION5chain 'A' and (resid 127 through 205 )
6X-RAY DIFFRACTION6chain 'A' and (resid 206 through 228 )

+
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://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