[English] 日本語
Yorodumi
- PDB-4bli: Galectin-3c in complex with Bisamido-thiogalactoside derivate 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bli
TitleGalectin-3c in complex with Bisamido-thiogalactoside derivate 1
ComponentsGALECTIN-3
KeywordsIMMUNE SYSTEM / LECTIN / SUGAR 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 / 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
Chem-GMK / Galectin-3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsNoresson, A.L. / Oberg, C.T. / Engstrom, O. / Hakansson, M. / Logan, D.T. / Leffler, H. / Nilsson, U.J.
CitationJournal: To be Published
Title: Controlling Protein Conformation Through Electronic Fine-Tuning of Arginine-Arene Interactions: Synthetic, Structural, and Biological Studies
Authors: Noresson, A.L. / Oberg, C.T. / Engstrom, O. / Hakansson, M. / Logan, D.T. / Leffler, H. / Nilsson, U.J.
History
DepositionMay 3, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GALECTIN-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4402
Polymers15,7351
Non-polymers7051
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.020, 58.050, 62.380
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: 15735.129 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE RECOGNITION DOMAIN, RESIDUES 114-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P17931
#2: Chemical ChemComp-GMK / (3-Deoxy-3-(3-methoxy-benzamido)-b-D-galactopyranosyl)-(3-deoxy-3-(3-methoxy-benzamido)-2-O-sulfo-b-D-galactopyranosyl)-sulfide


Mass: 704.720 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H36N2O15S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.1 Å3/Da / Density % sol: 41 %
Description: RIGID BODY REFINEMENT COULD BE STARTED DIRECTLY FROM MODEL 1A3K WIHOUT DOING MR USING A SPECIFIC PROGRAM.
Crystal growpH: 7.5
Details: 19 MG/ML GALECTIN-3C, 100MM NACL, 0.1 M TRIS/HCL PH 7.5, 29 % PEG 4000, 0.4 M NASCN, 18 MM BETA-MERCAPTOETHANOL, 5 MM COMPOUND GMK

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0379
DetectorType: MARRESEARCH MAR 165 / Detector: CCD / Date: Sep 25, 2008 / Details: MIRRORS
RadiationMonochromator: BENT SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0379 Å / Relative weight: 1
ReflectionResolution: 1.08→30 Å / Num. obs: 56420 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 22.2
Reflection shellResolution: 1.08→1.11 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 10.2 / % possible all: 97.5

-
Processing

Software
NameClassification
SHELXL-97refinement
XDSdata reduction
SHELXLdata scaling
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A3K

1a3k


Resolution: 1.08→30 Å / Num. parameters: 14932 / Num. restraintsaints: 20690 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1416 2820 5.3 %RANDOM
all0.1083 53600 --
obs0.1064 -99.2 %-
Refine analyzeNum. disordered residues: 54 / Occupancy sum hydrogen: 1158 / Occupancy sum non hydrogen: 1432
Refinement stepCycle: LAST / Resolution: 1.08→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1109 0 47 287 1443
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0351
X-RAY DIFFRACTIONs_zero_chiral_vol0.096
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.081
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.04
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.048
X-RAY DIFFRACTIONs_approx_iso_adps0.111

+
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