[English] 日本語
Yorodumi
- PDB-5jkb: Crystal structure of human JUNO (crystal form 2) -

+
Open data


ID or keywords:

Loading...

-
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 / external side of plasma membrane / signaling receptor binding / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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: 0 / Refine code: 0

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

-
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 / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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