[English] 日本語
Yorodumi
- PDB-8rdc: Galectin-1 in complex with thiogalactoside derivative -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8rdc
TitleGalectin-1 in complex with thiogalactoside derivative
ComponentsGalectin-1
KeywordsSUGAR BINDING PROTEIN / galectin / ligand / thiogalactoside derivative
Function / homology
Function and homology information


galectin complex / lactose binding / negative regulation of T-helper 17 cell lineage commitment / myoblast differentiation / plasma cell differentiation / laminin binding / T cell costimulation / Post-translational protein phosphorylation / cell-cell adhesion / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) ...galectin complex / lactose binding / negative regulation of T-helper 17 cell lineage commitment / myoblast differentiation / plasma cell differentiation / laminin binding / T cell costimulation / Post-translational protein phosphorylation / cell-cell adhesion / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of inflammatory response / : / regulation of apoptotic process / positive regulation of viral entry into host cell / positive regulation of canonical NF-kappaB signal transduction / positive regulation of apoptotic process / receptor ligand activity / endoplasmic reticulum lumen / apoptotic process / extracellular space / RNA binding / extracellular exosome / extracellular region / 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. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHakansson, M. / Diehl, C. / Peterson, K. / Zetterberg, F. / Nilsson, U.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Galectin-1 in complex with thiogalactoside derivative
Authors: Hakansson, M. / Diehl, C. / Petersn, K. / Nilsson, U.
History
DepositionDec 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Galectin-1
B: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,69011
Polymers29,9182
Non-polymers1,7729
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-38 kcal/mol
Surface area11580 Å2
Unit cell
Length a, b, c (Å)52.995, 70.035, 99.508
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Galectin-1 / Gal-1 / 14 kDa laminin-binding protein / HLBP14 / 14 kDa lectin / Beta-galactoside-binding lectin L- ...Gal-1 / 14 kDa laminin-binding protein / HLBP14 / 14 kDa lectin / Beta-galactoside-binding lectin L-14-I / Galaptin / HBL / HPL / Lactose-binding lectin 1 / Lectin galactoside-binding soluble 1 / Putative MAPK-activating protein PM12 / S-Lac lectin 1


Mass: 14959.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 841 and GOL are not part of the sequence / Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09382
#2: Chemical ChemComp-YNO / 5-bromanyl-3-[(2~{R},3~{R},4~{S},5~{R},6~{R})-4-[4-(4-chloranyl-1,3-thiazol-2-yl)-1,2,3-triazol-1-yl]-6-(hydroxymethyl)-3-methoxy-5-oxidanyl-oxan-2-yl]sulfanyl-pyridine-2-carbonitrile


Mass: 559.844 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H16BrClN6O4S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.59 %
Crystal growTemperature: 291 K / Method: evaporation
Details: 30% PEG 3350, 0.1 M Tris/HCl pH 8.0, 0.2 M Li2SO4, 1 % beta mercapthoethanol, seeded

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.7→52.99 Å / Num. obs: 268479 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.999 / Net I/σ(I): 13.6
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 13804 / CC1/2: 0.666

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→46.82 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.214 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20002 2113 5.1 %RANDOM
Rwork0.17241 ---
obs0.17378 39359 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.952 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.7→46.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2118 0 60 183 2361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132327
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172076
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.6573155
X-RAY DIFFRACTIONr_angle_other_deg1.331.5994849
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7575291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.45523.12125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29515348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8331514
X-RAY DIFFRACTIONr_chiral_restr0.0670.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022796
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02482
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4612.3451107
X-RAY DIFFRACTIONr_mcbond_other1.4532.3431106
X-RAY DIFFRACTIONr_mcangle_it2.3473.51390
X-RAY DIFFRACTIONr_mcangle_other2.3463.5021391
X-RAY DIFFRACTIONr_scbond_it2.2622.6761220
X-RAY DIFFRACTIONr_scbond_other2.2572.6261213
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3353.8151745
X-RAY DIFFRACTIONr_long_range_B_refined6.81128.6032307
X-RAY DIFFRACTIONr_long_range_B_other6.40627.8272266
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 4162 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 139 -
Rwork0.264 2870 -
obs--99.87 %
Refinement TLS params.

S31: -0.0307 Å ° / 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 °)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)
11.71040.3640.04570.94590.29260.737-0.05060.02190.0314-0.03060.04240.0066-0.01470.00820.01320.0028-0.00960.00770.01150.06373.167-15.734-6.849
20.70770.01070.56411.5072-1.22683.083-0.0404-0.05050.0004-0.00210.30840.0709-0.4048-0.26790.03930.0029-0.03430.09630.06880.1364-17.265-0.879-20.393
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 601
2X-RAY DIFFRACTION2B1 - 601

+
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