[English] 日本語
Yorodumi
- PDB-3wlu: Crystal Structure of human galectin-9 NCRD with Selenolactose -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wlu
TitleCrystal Structure of human galectin-9 NCRD with Selenolactose
ComponentsGalectin-9
KeywordsSUGAR BINDING PROTEIN / selenolactose / beta sandwich / galectin / carbohydrate binding
Function / homology
Function and homology information


positive regulation of activated T cell autonomous cell death / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response / Interleukin-2 family signaling / positive regulation of dendritic cell apoptotic process / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / natural killer cell tolerance induction / negative regulation of mast cell degranulation / positive regulation of dendritic cell chemotaxis / positive regulation of dendritic cell differentiation / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway ...positive regulation of activated T cell autonomous cell death / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response / Interleukin-2 family signaling / positive regulation of dendritic cell apoptotic process / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / natural killer cell tolerance induction / negative regulation of mast cell degranulation / positive regulation of dendritic cell chemotaxis / positive regulation of dendritic cell differentiation / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / positive regulation of transforming growth factor beta production / galactoside binding / galactose binding / negative regulation of natural killer cell mediated cytotoxicity / disaccharide binding / positive regulation of interleukin-13 production / negative regulation of chemokine production / positive regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of monocyte chemotactic protein-1 production / positive regulation of interleukin-4 production / p38MAPK cascade / negative regulation of activated T cell proliferation / positive regulation of interleukin-10 production / negative regulation of tumor necrosis factor production / negative regulation of type II interferon production / maternal process involved in female pregnancy / ERK1 and ERK2 cascade / positive regulation of interleukin-12 production / response to interleukin-1 / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / female pregnancy / cellular response to virus / cellular response to type II interferon / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of interleukin-6 production / positive regulation of type II interferon production / chemotaxis / positive regulation of tumor necrosis factor production / positive regulation of NF-kappaB transcription factor activity / carbohydrate binding / collagen-containing extracellular matrix / positive regulation of canonical NF-kappaB signal transduction / response to lipopolysaccharide / positive regulation of ERK1 and ERK2 cascade / positive regulation of viral entry into host cell / inflammatory response / negative regulation of gene expression / positive regulation of gene expression / enzyme binding / extracellular space / nucleus / 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-LSE / Galectin-9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsMakyio, H. / Suzuki, T. / Ando, H. / Yamada, Y. / Ishida, H. / Kiso, M. / Wakatsuki, S. / Kato, R.
CitationJournal: Bioorg.Med.Chem. / Year: 2014
Title: Expanded potential of seleno-carbohydrates as a molecular tool for X-ray structural determination of a carbohydrate-protein complex with single/multi-wavelength anomalous dispersion phasing
Authors: Suzuki, T. / Makyio, H. / Ando, H. / Komura, N. / Menjo, M. / Yamada, Y. / Imamura, A. / Ishida, H. / Wakatsuki, S. / Kato, R. / Kiso, M.
History
DepositionNov 14, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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-9
B: Galectin-9
C: Galectin-9
D: Galectin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7658
Polymers63,6874
Non-polymers2,0784
Water15,655869
1
A: Galectin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4412
Polymers15,9221
Non-polymers5201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Galectin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4412
Polymers15,9221
Non-polymers5201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Galectin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4412
Polymers15,9221
Non-polymers5201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Galectin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4412
Polymers15,9221
Non-polymers5201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.732, 68.167, 224.156
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a monomer. There are 4 biological units in the asymmetric unit (chains A,B,C and D)

-
Components

#1: Protein
Galectin-9 / Gal-9 / Ecalectin / Tumor antigen HOM-HD-21


Mass: 15921.826 Da / Num. of mol.: 4 / Fragment: ligand binding domain, UNP residues 5-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS9 / Plasmid: pGEX4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O00182
#2: Chemical
ChemComp-LSE / 2-(trimethylsilyl)ethyl 4-O-beta-D-galactopyranosyl-6-Se-methyl-6-seleno-beta-D-glucopyranoside


Mass: 519.518 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H36O10SeSi
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 869 / 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: 2.14 Å3/Da / Density % sol: 42.61 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.5
Details: PEG 6000, 100mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.97889 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 31, 2011
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97889 Å / Relative weight: 1
ReflectionResolution: 1.4→43.3 Å / Num. all: 109389 / Num. obs: 109285 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 19.3
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.885 / Mean I/σ(I) obs: 3.3 / Num. unique all: 5393 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
REFMAC5.7.0032refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→40 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.895 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.194 5463 5 %RANDOM
Rwork0.17224 ---
obs0.17332 103811 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.248 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2---0.49 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4456 0 120 869 5445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.024708
X-RAY DIFFRACTIONr_bond_other_d0.0010.024292
X-RAY DIFFRACTIONr_angle_refined_deg1.7361.9386396
X-RAY DIFFRACTIONr_angle_other_deg0.8052.9879844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1045564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13623.793232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.84915680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.6381524
X-RAY DIFFRACTIONr_chiral_restr0.1090.2692
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215384
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021232
X-RAY DIFFRACTIONr_mcbond_it0.6930.7912268
X-RAY DIFFRACTIONr_mcbond_other0.6930.792267
X-RAY DIFFRACTIONr_mcangle_it1.0281.1882832
X-RAY DIFFRACTIONr_mcangle_other1.0281.1882833
X-RAY DIFFRACTIONr_scbond_it1.5490.9632440
X-RAY DIFFRACTIONr_scbond_other1.5480.9632441
X-RAY DIFFRACTIONr_scangle_other2.2061.3933565
X-RAY DIFFRACTIONr_long_range_B_refined5.4679.2975743
X-RAY DIFFRACTIONr_long_range_B_other5.4669.2975744
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 424 -
Rwork0.288 7548 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.82240.13910.30571.12630.16671.78960.0113-0.0125-0.02520.0064-0.00590.07750.0254-0.0218-0.00550.02930.00380.01450.01060.00310.028139.41818.5316153.287
20.79130.10680.1411.1648-0.13412.2635-0.016-0.0117-0.01640.0032-0.0812-0.07230.02360.14290.09720.00190.0020.00770.0140.01340.045322.999623.1463125.1234
30.95270.29530.09171.1981-0.51221.80690.0052-0.0209-0.00860.0151-0.0559-0.0723-0.00270.11740.05070.0126-0.00830.00260.01350.00190.022720.762256.0242125.3283
40.97710.08470.04851.1025-0.01761.97410.00020.02140.06870.0373-0.01280.0494-0.0199-0.01860.01260.0124-0.0030.01290.0103-0.00380.020438.193751.4827154.043
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 148
2X-RAY DIFFRACTION2B7 - 148
3X-RAY DIFFRACTION3C7 - 148
4X-RAY DIFFRACTION4D7 - 148

+
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://pdbjlc1.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