[English] 日本語
Yorodumi
- PDB-7rgz: Crystal structure of human galectin-3 CRD in complex with Methyl ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rgz
TitleCrystal structure of human galectin-3 CRD in complex with Methyl 2-O-(2-nitro-4-fluoro)-benzoyl-3-O-toluoyl-b-D-talopyranoside
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN / Carbohydrates-binding protein
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 / cytosol / cytoplasm
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
Chem-5A4 / Galectin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.485 Å
AuthorsCollins, P.M. / Kishor, C. / Blanchard, H.
CitationJournal: J.Med.Chem. / Year: 2022
Title: Novel Selective Galectin-3 Antagonists Are Cytotoxic to Acute Lymphoblastic Leukemia.
Authors: Bum-Erdene, K. / Collins, P.M. / Hugo, M.W. / Tarighat, S.S. / Fei, F. / Kishor, C. / Leffler, H. / Nilsson, U.J. / Groffen, J. / Grice, I.D. / Heisterkamp, N. / Blanchard, H.
History
DepositionJul 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2854
Polymers15,7351
Non-polymers5503
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.258, 58.220, 62.723
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 15735.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS3, MAC2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P17931
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-5A4 / methyl 2-O-(4-fluoro-2-nitrobenzoyl)-3-O-(4-methylbenzoyl)-beta-D-talopyranoside


Mass: 479.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H22FNO10 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.09 Å3/Da / Density % sol: 41.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 31% PEG 6000, 100mM MgCl2, 8mM beta mercaptoethanol, 100mM Tris-HCL, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.48→42.67 Å / Num. obs: 19942 / % possible obs: 87.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 14.8
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 156

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NMO

2nmo


Resolution: 1.485→29.127 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.839 / SU ML: 0.064 / Cross valid method: FREE R-VALUE / ESU R: 0.09 / ESU R Free: 0.091
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2151 997 5.012 %
Rwork0.1799 18895 -
all0.182 --
obs-19892 87.983 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.462 Å2
Baniso -1Baniso -2Baniso -3
1-0.005 Å2-0 Å2-0 Å2
2---0.012 Å20 Å2
3---0.007 Å2
Refinement stepCycle: LAST / Resolution: 1.485→29.127 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1109 0 36 181 1326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131213
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171163
X-RAY DIFFRACTIONr_angle_refined_deg1.7381.6381652
X-RAY DIFFRACTIONr_angle_other_deg1.3471.6092666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3785145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.77221.54971
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.59715205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3491511
X-RAY DIFFRACTIONr_chiral_restr0.0810.2154
X-RAY DIFFRACTIONr_chiral_restr_other0.0150.23
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021476
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02302
X-RAY DIFFRACTIONr_nbd_refined0.210.2157
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.21018
X-RAY DIFFRACTIONr_nbtor_refined0.1640.2573
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.2601
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.295
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2320.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0930.24
X-RAY DIFFRACTIONr_nbd_other0.1750.226
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1280.216
X-RAY DIFFRACTIONr_mcbond_it1.251.558571
X-RAY DIFFRACTIONr_mcbond_other1.2451.556570
X-RAY DIFFRACTIONr_mcangle_it1.7082.333719
X-RAY DIFFRACTIONr_mcangle_other1.7082.336720
X-RAY DIFFRACTIONr_scbond_it2.1571.888642
X-RAY DIFFRACTIONr_scbond_other2.111.878639
X-RAY DIFFRACTIONr_scangle_it3.2212.746933
X-RAY DIFFRACTIONr_scangle_other3.1752.746933
X-RAY DIFFRACTIONr_lrange_it4.47919.9371259
X-RAY DIFFRACTIONr_lrange_other4.47919.9661260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.485-1.5230.403160.326321X-RAY DIFFRACTION20.1917
1.523-1.5650.263380.263773X-RAY DIFFRACTION51.2966
1.565-1.610.303680.2831092X-RAY DIFFRACTION74.6461
1.61-1.660.299600.2611308X-RAY DIFFRACTION90.2375
1.66-1.7140.293800.2391366X-RAY DIFFRACTION97.1774
1.714-1.7740.263790.2031318X-RAY DIFFRACTION100
1.774-1.8410.211710.1971320X-RAY DIFFRACTION99.9282
1.841-1.9160.239810.2031224X-RAY DIFFRACTION99.847
1.916-2.0010.235640.1891224X-RAY DIFFRACTION99.9224
2.001-2.0980.208430.1831173X-RAY DIFFRACTION99.8358
2.098-2.2120.197470.1791101X-RAY DIFFRACTION99.6528
2.212-2.3450.226490.1741069X-RAY DIFFRACTION99.8214
2.345-2.5070.21610.159981X-RAY DIFFRACTION100
2.507-2.7070.239430.172924X-RAY DIFFRACTION99.8967
2.707-2.9640.23540.187848X-RAY DIFFRACTION100
2.964-3.3120.19330.171809X-RAY DIFFRACTION99.8814
3.312-3.820.158390.148684X-RAY DIFFRACTION100
3.82-4.6690.116220.116608X-RAY DIFFRACTION99.8415
4.669-6.5640.198340.165474X-RAY DIFFRACTION100

+
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