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- PDB-6eym: Neutron crystal structure of perdeuterated galectin-3C in complex... -

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Basic information

Entry
Database: PDB / ID: 6eym
TitleNeutron crystal structure of perdeuterated galectin-3C in complex with lactose
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN / galectin / hydrogen bonding / molecular recognition / perdeuteration
Function / homology
Function and homology information


negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / RUNX2 regulates genes involved in differentiation of myeloid cells / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / regulation of T cell apoptotic process / mononuclear cell migration / IgE binding / positive regulation of mononuclear cell migration / negative regulation of endocytosis / eosinophil chemotaxis ...negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / RUNX2 regulates genes involved in differentiation of myeloid cells / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / regulation of T cell apoptotic process / mononuclear cell migration / IgE binding / positive regulation of mononuclear cell migration / negative regulation of endocytosis / eosinophil chemotaxis / regulation of extrinsic apoptotic signaling pathway via death domain receptors / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / protein phosphatase inhibitor activity / negative regulation of T cell receptor signaling pathway / positive chemotaxis / macrophage chemotaxis / regulation of T cell proliferation / positive regulation of calcium ion import / chemoattractant activity / monocyte chemotaxis / Advanced glycosylation endproduct receptor signaling / ficolin-1-rich granule membrane / immunological synapse / laminin binding / spliceosomal complex / molecular condensate scaffold activity / 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 / positive regulation of protein-containing complex assembly / mRNA processing / carbohydrate binding / collagen-containing extracellular matrix / protein phosphatase binding / mitochondrial inner membrane / innate immune response / Neutrophil degranulation / cell surface / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / 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
beta-lactose / Galectin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / SYNCHROTRON / NUCLEAR REACTOR / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsManzoni, F. / Coates, L. / Blakeley, M.P. / Oksanen, E. / Logan, D.T.
Funding support Sweden, 1items
OrganizationGrant numberCountry
European Spallation Source Sweden
Citation
Journal: J. Med. Chem. / Year: 2018
Title: Elucidation of Hydrogen Bonding Patterns in Ligand-Free, Lactose- and Glycerol-Bound Galectin-3C by Neutron Crystallography to Guide Drug Design.
Authors: Manzoni, F. / Wallerstein, J. / Schrader, T.E. / Ostermann, A. / Coates, L. / Akke, M. / Blakeley, M.P. / Oksanen, E. / Logan, D.T.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Perdeuteration, crystallization, data collection and comparison of five neutron diffraction data sets of complexes of human galectin-3C.
Authors: Manzoni, F. / Saraboji, K. / Sprenger, J. / Kumar, R. / Noresson, A.L. / Nilsson, U.J. / Leffler, H. / Fisher, S.Z. / Schrader, T.E. / Ostermann, A. / Coates, L. / Blakeley, M.P. / Oksanen, E. / Logan, D.T.
History
DepositionNov 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: Data collection / Experimental preparation / Category: diffrn_source / exptl
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _exptl.crystals_number
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / 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_molecule_features / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0432
Polymers15,7011
Non-polymers3421
Water1,982110
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint1 kcal/mol
Surface area7340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.010, 58.360, 63.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 15701.049 Da / Num. of mol.: 1 / Fragment: UNP residues 113-250
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 beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION2
NEUTRON DIFFRACTION2

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Sample preparation

Crystal
IDDensity Matthews3/Da)Density % sol (%)Description
12.1944The crystal dimensions were 1.74 x 1.14 x 0.91 mm (1.8 mm3). This was the crystal used to collect data at LADI-III.
22.1944The crystal measured approximately 1.8 mm3. This was the crystal used to collect data at MaNDi.
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2951vapor diffusion, sitting drop7.512-15% PEG 4000 OR PEG 3000, 0.1M MGCL2, 0.015M BETA MERCAPTOETHANOL, 0.1M TRIS-DCL, PD 7.9, 0.4M NASCN. All dissolved in D2O. Crystal grown in a 15 + 15 microlitre sitting drops that was first equilibrated for 1 week. A crystal grown at 20-28% PEG was introduced. The drop was fed with fresh protein by adding 3-4 micro litres of protein with 10 mM lactose every 3-4 days for 3 months. For details see Manzoni et al. (2016).
2932vapor diffusion7.512-15% PEG 4000 OR PEG 3000, 0.1M MGCL2, 0.015M BETA MERCAPTOETHANOL, 0.1M TRIS-DCL, PD 7.9, 0.4M NASCN. All dissolved in D2O. Crystal grown in a 15 + 15 microlitre sitting drops that was first equilibrated for 1 week. A crystal grown at 20-28% PEG was introduced. The drop was fed with fresh protein by adding 3-4 micro litres of protein with 10 mM lactose every 3-4 days for 3 months. For details see Manzoni et al. (2016).

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
22981
32981
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONMAX II I911-311
NUCLEAR REACTORILL LADI III23.35-4.35
SPALLATION SOURCEORNL Spallation Neutron Source MANDI32.0-4.0
Detector
TypeIDDetectorDateDetails
MARMOSAIC 325 mm CCD1CCDMay 31, 2015FOCUSING MIRRORS
LADI III2IMAGE PLATEDec 15, 2014
ORNL ANGER CAMERA3AREA DETECTORMay 15, 2015
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI(111) DOUBLE CRYSTALSINGLE WAVELENGTHMx-ray1
2LAUELneutron2
3LAUELneutron3
Radiation wavelength
IDWavelength (Å)Relative weight
111
23.351
34.351
421
541
Reflection

Entry-ID: 6EYM

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsDiffraction-IDNet I/σ(I)Rpim(I) all
1.07-406135499.46.610.032124.7
1.7-281548595.8130.209222.20.052
1.7-281374187.1100.162212.40.044
1.6-191548581.34.40.155312.20.066
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible allNum. unique obsRpim(I) all
1.07-1.10.8172.10.772196.8
1.7-1.84.90.3343.9287.921720.139
1.7-1.84.90.2087266.514900.076
1.6-1.661.70.2072.4354.610220.15

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
LAUEGENdata reduction
LSCALEdata scaling
SCALAdata scaling
Mantiddata reduction
XPREPdata scaling
PHENIXphasing
Refinement

SU ML: 0.07 / Cross valid method: THROUGHOUT / Method to determine structure: FOURIER SYNTHESIS / Phase error: 10.82 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 3ZSJ

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDDetailsR Free selection details
1.7-28NEUTRON DIFFRACTION0.2110.1680.17769151945.0696.22NEUTRON DATA.
1.1-32X-RAY DIFFRACTION0.1250.107281556662599.41RANDOM
Refinement stepCycle: LAST / Resolution: 1.7→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1104 0 23 110 1237
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0112736
NEUTRON DIFFRACTIONf_angle_d1.7354717
NEUTRON DIFFRACTIONf_dihedral_angle_d13.887721
NEUTRON DIFFRACTIONf_chiral_restr0.117198
NEUTRON DIFFRACTIONf_plane_restr0.009397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.1190.19381460.17482627X-RAY DIFFRACTION98
1.119-1.13930.21861270.1572606X-RAY DIFFRACTION99
1.1393-1.16120.1471460.15182651X-RAY DIFFRACTION99
1.1612-1.18490.17221440.13772626X-RAY DIFFRACTION100
1.1849-1.21070.16791420.13062677X-RAY DIFFRACTION100
1.2107-1.23890.15311340.12092671X-RAY DIFFRACTION100
1.2389-1.26990.16551430.10972680X-RAY DIFFRACTION100
1.2699-1.30420.12011470.10072650X-RAY DIFFRACTION100
1.3042-1.34260.11981270.09992686X-RAY DIFFRACTION100
1.3426-1.38590.10181230.09342698X-RAY DIFFRACTION100
1.3859-1.43540.12771470.08772667X-RAY DIFFRACTION100
1.4354-1.49290.11131370.07822705X-RAY DIFFRACTION100
1.4929-1.56080.10571370.08012687X-RAY DIFFRACTION100
1.5608-1.64310.09711290.08172712X-RAY DIFFRACTION100
1.6431-1.74610.10711460.08342702X-RAY DIFFRACTION100
1.7461-1.88090.1151500.08792716X-RAY DIFFRACTION100
1.8809-2.07010.09621500.08852712X-RAY DIFFRACTION100
2.0701-2.36960.13171180.10232767X-RAY DIFFRACTION100
2.3696-2.98510.15971600.12982759X-RAY DIFFRACTION100
2.9851-320.13211620.11982847X-RAY DIFFRACTION98
1.7001-1.83130.32821350.25262643NEUTRON DIFFRACTION90
1.8313-2.01560.20411620.17772812NEUTRON DIFFRACTION96
2.0156-2.30710.18751330.1392920NEUTRON DIFFRACTION98
2.3071-2.90620.21831650.14422943NEUTRON DIFFRACTION99
2.9062-280.18181740.16183108NEUTRON DIFFRACTION99

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