[English] 日本語
Yorodumi
- PDB-5nfa: Structure of Galectin-3 CRD in complex with compound 3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nfa
TitleStructure of Galectin-3 CRD in complex with compound 3
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN / Galectin-3 CRD / cation-Pi interactions
Function / homology
Function and homology information


negative regulation of NK T cell activation / 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 / RUNX2 regulates genes involved in differentiation of myeloid cells / regulation of T cell apoptotic process / mononuclear cell migration / receptor ligand inhibitor activity / positive regulation of mononuclear cell migration / negative regulation of endocytosis ...negative regulation of NK T cell activation / 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 / RUNX2 regulates genes involved in differentiation of myeloid cells / regulation of T cell apoptotic process / mononuclear cell migration / receptor ligand inhibitor activity / positive regulation of mononuclear cell migration / negative regulation of endocytosis / IgE binding / eosinophil chemotaxis / regulation of extrinsic apoptotic signaling pathway via death domain receptors / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / signaling receptor inhibitor activity / negative regulation of T cell receptor signaling pathway / protein phosphatase inhibitor activity / positive chemotaxis / positive regulation of calcium ion import / chemoattractant activity / macrophage chemotaxis / monocyte chemotaxis / regulation of T cell proliferation / Advanced glycosylation endproduct receptor signaling / immunological synapse / ficolin-1-rich granule membrane / laminin binding / neutrophil chemotaxis / epithelial cell differentiation / RNA splicing / secretory granule membrane / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein localization to plasma membrane / spliceosomal complex / positive regulation of protein-containing complex assembly / molecular condensate scaffold activity / mRNA processing / : / carbohydrate binding / protein phosphatase binding / mitochondrial inner membrane / innate immune response / Neutrophil degranulation / cell surface / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsRonin, C. / Atmanene, C. / Gautier, F.M. / Djedaini Pilard, F. / Teletchea, S. / Ciesielski, F. / Vivat Hannah, V. / Grandjean, C.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Biophysical and structural characterization of mono/di-arylated lactosamine derivatives interaction with human galectin-3.
Authors: Atmanene, C. / Ronin, C. / Teletchea, S. / Gautier, F.M. / Djedaini-Pilard, F. / Ciesielski, F. / Vivat, V. / Grandjean, C.
History
DepositionMar 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: pdbx_database_related
Item: _pdbx_database_related.db_id / _pdbx_database_related.details
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0032
Polymers16,4591
Non-polymers5451
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.800, 58.150, 63.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
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 / Galactoside-binding protein / GALBP / IgE-binding protein / L-31 / Laminin-binding protein / Lectin L-29 / Mac-2 antigen


Mass: 16458.844 Da / Num. of mol.: 1 / Fragment: UNP residues 106-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS3, MAC2 / Production host: Escherichia coli (E. coli) / References: UniProt: P17931
#2: Polysaccharide 3-O-[(3-methoxyphenyl)methyl]-beta-D-galactopyranose-(1-4)-N-acetyl-2-(acetylamino)-2-deoxy-beta-D- ...3-O-[(3-methoxyphenyl)methyl]-beta-D-galactopyranose-(1-4)-N-acetyl-2-(acetylamino)-2-deoxy-beta-D-glucopyranosylamine


Type: oligosaccharide / Mass: 544.549 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1b_1-5_1*NCC/3=O_2*NCC/3=O][a2112h-1b_1-5_3*OC(C^EC^EC^EC^ZC^ZC^E$4)/6OC]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp1NAc2NAc]{[(4+1)][b-D-Galp]{[(3+1)][<C8O1>]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 27.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM Tris HCl pH7.5; 30-34% PEG4000; 100mM MgCl2; 400mM NaSCN; 8mM beta-mercaptoethanol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 18804 / % possible obs: 99.2 % / Redundancy: 6.1 % / Rsym value: 0.038 / Net I/σ(I): 28.3
Reflection shellResolution: 1.59→1.68 Å / Rsym value: 0.128

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3zsl

3zsl


Resolution: 1.59→42.75 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.253 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.076 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16943 941 5 %RANDOM
Rwork0.14258 ---
obs0.14392 17863 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.869 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å20 Å2
2---0.57 Å20 Å2
3----0.45 Å2
Refinement stepCycle: 1 / Resolution: 1.59→42.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1108 0 38 146 1292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191272
X-RAY DIFFRACTIONr_bond_other_d0.0010.021250
X-RAY DIFFRACTIONr_angle_refined_deg2.2991.9841749
X-RAY DIFFRACTIONr_angle_other_deg0.97832888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0625166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.65324.03262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35615219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.231510
X-RAY DIFFRACTIONr_chiral_restr0.1490.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211451
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02309
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_it1.4761.263586
X-RAY DIFFRACTIONr_mcbond_other1.461.26585
X-RAY DIFFRACTIONr_mcangle_it2.1351.892739
X-RAY DIFFRACTIONr_mcangle_other2.1411.894740
X-RAY DIFFRACTIONr_scbond_it2.7981.62686
X-RAY DIFFRACTIONr_scbond_other2.7961.623687
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1632.319998
X-RAY DIFFRACTIONr_long_range_B_refined5.98511.8151382
X-RAY DIFFRACTIONr_long_range_B_other5.73511.1321320
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.586→1.627 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.182 67 -
Rwork0.146 1258 -
obs--97.28 %

+
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