[English] 日本語
Yorodumi
- PDB-7cxc: Structure of mouse Galectin-3 CRD point mutant (V160A) in complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cxc
TitleStructure of mouse Galectin-3 CRD point mutant (V160A) in complex with TD-139 belonging to P121 space group.
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN / beta-galactose binding protein / CARBOHYDRATE / TD-139
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 / negative regulation of endocytosis / IgE binding / 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 / negative regulation of endocytosis / IgE binding / 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 / extracellular matrix organization / neutrophil chemotaxis / 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
Chem-TD2 / Galectin-3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsKumar, A.
CitationJournal: Glycobiology / Year: 2021
Title: Molecular mechanism of interspecies differences in the binding affinity of TD139 to Galectin-3.
Authors: Kumar, A. / Paul, M. / Panda, M. / Jayaram, S. / Kalidindi, N. / Sale, H. / Vetrichelvan, M. / Gupta, A. / Mathur, A. / Beno, B. / Regueiro-Ren, A. / Cheng, D. / Ramarao, M. / Ghosh, K.
History
DepositionSep 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 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
B: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5204
Polymers37,2222
Non-polymers1,2972
Water4,648258
1
A: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2602
Polymers18,6111
Non-polymers6491
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2602
Polymers18,6111
Non-polymers6491
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.513, 58.286, 68.085
Angle α, β, γ (deg.)90.000, 103.560, 90.000
Int Tables number4
Space group name H-MP1211

-
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: 18611.191 Da / Num. of mol.: 2 / Fragment: Carbohydrate Recognition Domain / Mutation: V160A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lgals3 / Production host: Escherichia coli (E. coli) / References: UniProt: P16110
#2: Chemical ChemComp-TD2 / 3-deoxy-3-[4-(3-fluorophenyl)-1H-1,2,3-triazol-1-yl]-beta-D-galactopyranosyl 3-deoxy-3-[4-(3-fluorophenyl)-1H-1,2,3-triazol-1-yl]-1-thio-beta-D-galactopyranoside


Mass: 648.635 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H30F2N6O8S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 1.84 Å3/Da / Density % sol: 33.16 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 24-35% PEG 4000/6000, 0.1M Tris (pH 7.5 to pH 8.5), 0.4M NaSCN

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12713 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Dec 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12713 Å / Relative weight: 1
ReflectionResolution: 1.4→58.29 Å / Num. obs: 53247 / % possible obs: 77.7 % / Redundancy: 3.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.029 / Rrim(I) all: 0.053 / Net I/σ(I): 16.9 / Num. measured all: 244146
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.14-1.220.159501524990.9530.1510.22417.6
3.6-58.293.20.045928328890.9840.0320.05528.790.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.5.29data scaling
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CXB

7cxb


Resolution: 1.4→43.74 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.527 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.014 / ESU R Free: 0.013 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1782 2566 5 %RANDOM
Rwork0.1442 ---
obs0.1459 48248 95.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.31 Å2 / Biso mean: 14.564 Å2 / Biso min: 3.97 Å2
Baniso -1Baniso -2Baniso -3
1--3.85 Å2-0 Å22.2 Å2
2--2.78 Å20 Å2
3---1.07 Å2
Refinement stepCycle: final / Resolution: 1.4→43.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2126 0 300 258 2684
Biso mean--9.44 24.4 -
Num. residues----274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0132418
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172269
X-RAY DIFFRACTIONr_angle_refined_deg2.0231.7563312
X-RAY DIFFRACTIONr_angle_other_deg0.761.6435124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9425284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.30221.933119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.05315356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0941516
X-RAY DIFFRACTIONr_chiral_restr0.1270.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023242
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02602
X-RAY DIFFRACTIONr_rigid_bond_restr4.29734687
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.182 160 -
Rwork0.122 3604 -
all-3764 -
obs--95.36 %

+
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