[English] 日本語
Yorodumi
- PDB-8iu1: Crystal structure of mouse Galectin-3 in complex with small molec... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8iu1
TitleCrystal structure of mouse Galectin-3 in complex with small molecule inhibitor
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN / Fibrosis / Galactose
Function / homology
Function and homology information


negative regulation of cell proliferation in bone marrow / advanced glycation end-product receptor activity / positive regulation of serotonin secretion / negative regulation of immunological synapse formation / disaccharide binding / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / cornified envelope / IgE binding / negative regulation of endocytosis / Fc-gamma receptor I complex binding ...negative regulation of cell proliferation in bone marrow / advanced glycation end-product receptor activity / positive regulation of serotonin secretion / negative regulation of immunological synapse formation / disaccharide binding / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / cornified envelope / IgE binding / negative regulation of endocytosis / Fc-gamma receptor I complex binding / eosinophil chemotaxis / monosaccharide binding / negative regulation of T cell receptor signaling pathway / positive chemotaxis / positive regulation of calcium ion import / macrophage chemotaxis / monocyte chemotaxis / glial cell projection / immunological synapse / laminin binding / Neutrophil degranulation / RNA splicing / neutrophil chemotaxis / extracellular matrix organization / extracellular matrix / skeletal system development / negative regulation of extrinsic apoptotic signaling pathway / spliceosomal complex / mRNA processing / positive regulation of angiogenesis / collagen-containing extracellular matrix / cell differentiation / external side of plasma membrane / innate immune response / positive regulation of cell population proliferation / negative regulation of apoptotic process / cell surface / extracellular space / extracellular region / nucleus / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsJinal, S. / Amit, K. / Ghosh, K.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Discovery and Exploration of Monosaccharide Linked Dimers to Target Fibrosis
Authors: Swidorski, J.J. / Beno, B.B. / Liu, C. / Yoon, D. / Ghosh, K. / Sale, H. / Shah, D. / Acharya, K. / Yanchunas, J. / Ellsworth, B. / Cheng, D. / Regueiro-Ren, A.
History
DepositionMar 23, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0603
Polymers16,4551
Non-polymers6052
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60 Å2
ΔGint-4 kcal/mol
Surface area7320 Å2
Unit cell
Length a, b, c (Å)110.670, 110.670, 110.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-302-

MG

21A-474-

HOH

31A-498-

HOH

-
Components

#1: Protein 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 / IgE-binding protein / L-34 galactoside-binding lectin / Laminin-binding protein / Lectin L-29 / Mac-2 antigen


Mass: 16454.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Lgals3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P16110
#2: Chemical ChemComp-QB2 / 2-[(2R,3R,4S,5R,6R)-2-(3,4-dichlorophenyl)sulfanyl-6-(hydroxymethyl)-5-oxidanyl-4-[4-[3,4,5-tris(fluoranyl)phenyl]-1,2,3-triazol-1-yl]oxan-3-yl]oxyethanoic acid


Mass: 580.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H18Cl2F3N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.43 Å3/Da / Density % sol: 64.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 32% PEG 4000, 0.1M TRIS(8.0), 0.4M NASCN, 0.1M MGCL2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.0332 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.97→35 Å / Num. obs: 16076 / % possible obs: 99.9 % / Redundancy: 20.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.6
Reflection shellResolution: 1.97→2.02 Å / Rmerge(I) obs: 0.038

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
REFMAC5.8.0049refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→35 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.409 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.215 754 4.7 %RANDOM
Rwork0.173 ---
obs0.175 15322 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.74 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.97→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1103 0 38 98 1239
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.021168
X-RAY DIFFRACTIONr_bond_other_d00.0118
X-RAY DIFFRACTIONr_angle_refined_deg2.3761.981586
X-RAY DIFFRACTIONr_angle_other_deg0.829340
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8335137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97123.79358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.12915191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3081510
X-RAY DIFFRACTIONr_chiral_restr0.1820.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211003
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027
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_it5.1475.102552
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.7167.579687
X-RAY DIFFRACTIONr_mcangle_other5.7137.578688
X-RAY DIFFRACTIONr_scbond_it7.0275.565614
X-RAY DIFFRACTIONr_scbond_other7.0215.564615
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.648.146900
X-RAY DIFFRACTIONr_long_range_B_refined10.30743.3381661
X-RAY DIFFRACTIONr_long_range_B_other10.26543.1241638
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.97→2.02 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 56 -
Rwork0.316 1119 -
obs--100 %

+
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