[English] 日本語
Yorodumi
- PDB-1a3k: X-RAY CRYSTAL STRUCTURE OF THE HUMAN GALECTIN-3 CARBOHYDRATE RECO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1a3k
TitleX-RAY CRYSTAL STRUCTURE OF THE HUMAN GALECTIN-3 CARBOHYDRATE RECOGNITION DOMAIN (CRD) AT 2.1 ANGSTROM RESOLUTION
ComponentsGALECTIN-3
KeywordsGALECTIN / GALAPTIN / LECTIN / IGE-BINDING PROTEIN
Function / homology
Function and homology information


negative regulation of NK T cell activation / mononuclear cell migration / 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 / receptor ligand inhibitor activity / positive regulation of mononuclear cell migration / negative regulation of endocytosis ...negative regulation of NK T cell activation / mononuclear cell migration / 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 / 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 / signaling receptor inhibitor activity / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / 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 / ficolin-1-rich granule membrane / immunological synapse / laminin binding / epithelial cell differentiation / neutrophil chemotaxis / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MULTIPLE ISOMORPHOUS METHOD / Resolution: 2.1 Å
AuthorsSeetharaman, J. / Kanigsberg, A. / Slaaby, R. / Leffler, H. / Barondes, S.H. / Rini, J.M.
Citation
Journal: J.Biol.Chem. / Year: 1998
Title: X-ray crystal structure of the human galectin-3 carbohydrate recognition domain at 2.1-A resolution.
Authors: Seetharaman, J. / Kanigsberg, A. / Slaaby, R. / Leffler, H. / Barondes, S.H. / Rini, J.M.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Structure of S-Lectin, a Developmentally Regulated Vertebrate Beta-Galactoside-Binding Protein
Authors: Liao, D.I. / Kapadia, G. / Ahmed, H. / Vasta, G.R. / Herzberg, O.
#2: Journal: J.Biol.Chem. / Year: 1993
Title: X-Ray Crystal Structure of the Human Dimeric S-Lac Lectin, L-14-II, in Complex with Lactose at 2.9-A Resolution
Authors: Lobsanov, Y.D. / Gitt, M.A. / Leffler, H. / Barondes, S.H. / Rini, J.M.
History
DepositionJan 22, 1998Processing site: BNL
Revision 1.0Jul 15, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 7, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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)15,9872
Polymers15,6041
Non-polymers3831
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.600, 58.400, 64.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein GALECTIN-3


Mass: 15603.933 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE RECOGNITION DOMAIN (CRD)
Source method: isolated from a genetically manipulated source
Details: THE CRD WAS PRODUCED BY TYPE VII COLLAGENASE (SIGMA) DIGESTION OF THE N-TERMINAL DOMAIN
Source: (gene. exp.) Homo sapiens (human)
Description: THE CRD WAS PRODUCED BY TYPE VII COLLAGENASE (SIGMA) DIGESTION OF THE N-TERMINAL DOMAIN
Production host: Escherichia coli (E. coli) / References: UniProt: P17931
#2: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 48 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: PROTEIN CRYSTALLIZED BY HANGING-DROP VAPOUR DIFFUSION METHOD FROM DROPS CONTAINING EQUAL VOLUMES OF PROTEIN(10-15MG/ML) IN CRYSTALLIZATION BUFFER CONTAINING 1MM LACTOSE OR 30 MM N- ...Details: PROTEIN CRYSTALLIZED BY HANGING-DROP VAPOUR DIFFUSION METHOD FROM DROPS CONTAINING EQUAL VOLUMES OF PROTEIN(10-15MG/ML) IN CRYSTALLIZATION BUFFER CONTAINING 1MM LACTOSE OR 30 MM N-ACETYLLACTOSAMINE AND THE WELL SOLUTION COMPOSED OF 27-30% PEG 4000-6000, 100MM TRIS-HCL PH 8.5, 100 MM MGCL2, AND 8 MM 2-MERCAPTOETHANOL., vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110-15 mg/mlprotein1drop
21 mMlactose1dropcan be replaced by 30mM N-acetyllactosamine
327-35 %PEG40001reservoirto PEG6000
4100 mMTris-HCl1reservoirpH8.5
5100 mM1reservoirMgCl2
68 mM2-mercaptoethanol1reservoir

-
Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Dec 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 7955 / % possible obs: 99 % / Rmerge(I) obs: 0.052
Reflection
*PLUS
Num. measured all: 40093

-
Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementMethod to determine structure: MULTIPLE ISOMORPHOUS METHOD / Resolution: 2.1→5 Å / σ(F): 2
Details: THE STRUCTURE WAS SOLVED BY THE MULTIPLE ISOMORPHOUS REPLACEMENT METHOD. THE MODEL CONSISTS OF THE 137 AMINO ACID RESIDUE CARBOHYDRATE RECOGNITION DOMAIN IN COMPLEX WITH N-ACETYLLACTOSAMINE ...Details: THE STRUCTURE WAS SOLVED BY THE MULTIPLE ISOMORPHOUS REPLACEMENT METHOD. THE MODEL CONSISTS OF THE 137 AMINO ACID RESIDUE CARBOHYDRATE RECOGNITION DOMAIN IN COMPLEX WITH N-ACETYLLACTOSAMINE AND 120 WATER MOLECULES. THIS STRUCTURE REPRESENTS A CRD DETERMINED FROM A GALECTIN WHICH DOES NOT SHOW THE CANONICAL 2-FOLD SYMMETRIC DIMER ORGANIZATION SHOWN BY GALECTINS-1 AND -2. COMPARISON WITH GALECTINS-1 AND -2 PROVIDES AN EXPLANATION FOR THE DIFFERENCES IN CARBOHYDRATE-BINDING SPECIFICITY SHOWN BY GALECTIN-3, AND FOR THE FACT THAT IT FAILS TO FORM DIMERS BY ANALOGOUS CRD-CRD INTERACTIONS.
Rfactor% reflectionSelection details
Rfree0.24 10 %RANDOM
Rwork0.17 --
obs0.17 99 %-
Displacement parametersBiso mean: 20.6 Å2
Refinement stepCycle: LAST / Resolution: 2.1→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1101 0 26 120 1247
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.1→3.13 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rwork0.206 204 -
obs--77 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX_3.1.PROTOPHCSDX_3.1.PRO
X-RAY DIFFRACTION2PARAM3_MOD_3.1.CHOTOPH3_3.1.CHO

+
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