[English] 日本語
Yorodumi
- PDB-9ot8: Crystal structure of Galectin-3 bound to FN3con-9 and FN3con-41, ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ot8
TitleCrystal structure of Galectin-3 bound to FN3con-9 and FN3con-41, a cooperative binder that recognises the Galectin-3-FN3con-9 interface
ComponentsFN3con-9 - FN3con-41 fusion,Galectin-3
KeywordsCARBOHYDRATE / Carbohydrate binding Biosensor fibronectin type 3
Function / homology
Function and homology information


negative regulation of NK T cell activation / mononuclear cell migration / negative regulation of immunological synapse formation / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / disaccharide binding / RUNX2 regulates genes involved in differentiation of myeloid cells / regulation of T cell apoptotic process / receptor ligand inhibitor activity / negative regulation of endocytosis / positive regulation of mononuclear cell migration ...negative regulation of NK T cell activation / mononuclear cell migration / negative regulation of immunological synapse formation / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / disaccharide binding / RUNX2 regulates genes involved in differentiation of myeloid cells / regulation of T cell apoptotic process / receptor ligand inhibitor activity / negative regulation of endocytosis / positive regulation of mononuclear cell migration / IgE binding / eosinophil chemotaxis / macrophage chemotaxis / regulation of extrinsic apoptotic signaling pathway via death domain receptors / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / regulation of T cell proliferation / protein phosphatase inhibitor activity / positive chemotaxis / chemoattractant activity / positive regulation of calcium ion import / monocyte chemotaxis / immunological synapse / Advanced glycosylation endproduct receptor signaling / ficolin-1-rich granule membrane / negative regulation of T cell receptor signaling pathway / neutrophil chemotaxis / spliceosomal complex / epithelial cell differentiation / laminin binding / RNA splicing / secretory granule membrane / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein localization to plasma membrane / molecular condensate scaffold activity / positive regulation of protein-containing complex assembly / mRNA processing / carbohydrate binding / protein phosphatase binding / extracellular matrix / mitochondrial inner membrane / innate immune response / Neutrophil degranulation / cell surface / : / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsMutschler, R. / Caputo, A.T. / Guo, Z. / Fiorito, M.M. / Newton, S. / Zhang, X. / Karunathilaka, N. / Duval, C. / Brazel, H. / Abwanka, D. ...Mutschler, R. / Caputo, A.T. / Guo, Z. / Fiorito, M.M. / Newton, S. / Zhang, X. / Karunathilaka, N. / Duval, C. / Brazel, H. / Abwanka, D. / Punyadeera, C. / Alexandrov, K. / Cui, Z.
Funding support Australia, 3items
OrganizationGrant numberCountry
Australian Research Council (ARC)CE200100029 Australia
National Health and Medical Research Council (NHMRC, Australia)APP 2033951 Australia
National Health and Medical Research Council (NHMRC, Australia)APP 2002576 Australia
Citation
Journal: ACS Sens / Year: 2026
Title: Cooperative Binding Domains Enhance Sensitivity and Overcome the Hook Effect in Two-Component Protein Biosensors.
Authors: Mutschler, R. / Caputo, A.T. / Guo, Z. / Fiorito, M.M. / Hayat, I.F. / Newton, S. / Zhang, X. / Karunathilaka, N. / Duval, C. / Brazel, H. / Chan, W. / Kostner, K. / Korczyk, D. / Abankwa, D. ...Authors: Mutschler, R. / Caputo, A.T. / Guo, Z. / Fiorito, M.M. / Hayat, I.F. / Newton, S. / Zhang, X. / Karunathilaka, N. / Duval, C. / Brazel, H. / Chan, W. / Kostner, K. / Korczyk, D. / Abankwa, D.K. / Atherton, J.J. / Coats, A.J.S. / Punyadeera, C. / Alexandrov, K. / Cui, Z.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMay 26, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FN3con-9 - FN3con-41 fusion,Galectin-3


Theoretical massNumber of molelcules
Total (without water)42,0161
Polymers42,0161
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.311, 68.311, 171.805
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-509-

HOH

-
Components

#1: Protein FN3con-9 - FN3con-41 fusion,Galectin-3 / Gal-3 / 35 kDa lectin / Carbohydrate-binding protein 35 / CBP 35 / Galactose-specific lectin 3 / ...Gal-3 / 35 kDa lectin / Carbohydrate-binding protein 35 / CBP 35 / Galactose-specific lectin 3 / Galactoside-binding protein / GALBP / IgE-binding protein / L-31 / Laminin-binding protein / Lectin L-29 / Mac-2 antigen


Mass: 42015.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: a chimeric fusion of three proteins: Galectin-3 and two engineered binding proteins
Source: (gene. exp.) synthetic construct (others), (gene. exp.) Homo sapiens (human)
Gene: LGALS3, MAC2 / Production host: Escherichia coli (E. coli) / References: UniProt: P17931
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 8000, 0.2 M Magnesium acetate, 0.1 M Sodium cacodylate pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.958→68.311 Å / Num. obs: 13843 / % possible obs: 90.7 % / Redundancy: 12.2 % / Biso Wilson estimate: 32.16 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.062 / Net I/σ(I): 9.7
Reflection shellResolution: 1.958→2.284 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 692 / CC1/2: 0.563 / Rpim(I) all: 0.394 / % possible all: 73

-
Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→63.48 Å / SU ML: 0.2604 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.91
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2554 671 4.86 %
Rwork0.2207 13149 -
obs0.2225 13820 45.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.98 Å2
Refinement stepCycle: LAST / Resolution: 1.96→63.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2490 0 0 70 2560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712554
X-RAY DIFFRACTIONf_angle_d0.87413474
X-RAY DIFFRACTIONf_chiral_restr0.053381
X-RAY DIFFRACTIONf_plane_restr0.0193444
X-RAY DIFFRACTIONf_dihedral_angle_d19.3942917
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.110.2585110.3473199X-RAY DIFFRACTION3.57
2.11-2.320.3936350.3577595X-RAY DIFFRACTION10.65
2.32-2.660.3302850.31411717X-RAY DIFFRACTION30.28
2.66-3.350.31352600.26374809X-RAY DIFFRACTION83.92
3.35-63.480.2152800.18815829X-RAY DIFFRACTION96.1

+
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