[English] 日本語
Yorodumi
- PDB-4lbq: Crystal structure of mouse galectin-1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lbq
TitleCrystal structure of mouse galectin-1
Components(Galectin-1) x 3
KeywordsSUGAR BINDING PROTEIN / beta-sandwich / beta-galactosides binding / regulator of immunity / Secreted / extracellular space / extracellular matrix
Function / homology
Function and homology information


galectin complex / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / negative regulation of T-helper 17 cell lineage commitment / galactose binding / myoblast differentiation / plasma cell differentiation / heterophilic cell-cell adhesion / T cell costimulation / cell-cell adhesion ...galectin complex / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / negative regulation of T-helper 17 cell lineage commitment / galactose binding / myoblast differentiation / plasma cell differentiation / heterophilic cell-cell adhesion / T cell costimulation / cell-cell adhesion / positive regulation of inflammatory response / : / carbohydrate binding / positive regulation of viral entry into host cell / positive regulation of apoptotic process / receptor ligand activity / apoptotic process / extracellular space / extracellular region / plasma membrane / 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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRustiguel, J.K. / Trabuco, A.C. / Del Cistia Andrade, C. / Stowell, S.R. / Cummings, R.D. / Dias-Baruffi, M. / Nonato, M.C.
CitationJournal: To be Published
Title: Crystal structure of mouse galectin-1
Authors: Rustiguel, J.K. / Trabuco, A.C. / Del Cistia Andrade, C. / Stowell, S.R. / Cummings, R.D. / Dias-Baruffi, M. / Nonato, M.C.
History
DepositionJun 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,9488
Polymers59,5794
Non-polymers3684
Water4,360242
1
A: Galectin-1
D: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9984
Polymers29,8142
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-5 kcal/mol
Surface area11790 Å2
MethodPISA
2
B: Galectin-1
C: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9504
Polymers29,7662
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-8 kcal/mol
Surface area11910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.040, 38.200, 130.180
Angle α, β, γ (deg.)90.00, 112.71, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Galectin-1 / Gal-1 / 14 kDa lectin / Beta-galactoside-binding lectin L-14-I / Galaptin / Lactose-binding lectin ...Gal-1 / 14 kDa lectin / Beta-galactoside-binding lectin L-14-I / Galaptin / Lactose-binding lectin 1 / Lectin galactoside-binding soluble 1 / S-Lac lectin 1


Mass: 14898.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gbp, Lgals1 / Plasmid: pET29a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P16045
#2: Protein Galectin-1 / Gal-1 / 14 kDa lectin / Beta-galactoside-binding lectin L-14-I / Galaptin / Lactose-binding lectin ...Gal-1 / 14 kDa lectin / Beta-galactoside-binding lectin L-14-I / Galaptin / Lactose-binding lectin 1 / Lectin galactoside-binding soluble 1 / S-Lac lectin 1


Mass: 14882.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gbp, Lgals1 / Plasmid: pET29a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P16045
#3: Protein Galectin-1 / Gal-1 / 14 kDa lectin / Beta-galactoside-binding lectin L-14-I / Galaptin / Lactose-binding lectin ...Gal-1 / 14 kDa lectin / Beta-galactoside-binding lectin L-14-I / Galaptin / Lactose-binding lectin 1 / Lectin galactoside-binding soluble 1 / S-Lac lectin 1


Mass: 14914.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gbp, Lgals1 / Plasmid: pET29a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P16045
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 20% PEG 3350, 0.2 M ammonium fluoride, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 26, 2010
Details: Collimating mirror, Si(111) double-crystal monochromator and toroidal bendable mirror
RadiationMonochromator: Si(111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 2.4→35.752 Å / Num. obs: 19975 / % possible obs: 99.88 % / Observed criterion σ(F): 1.35 / Observed criterion σ(I): 1.7 / Redundancy: 3.8 % / Biso Wilson estimate: 34.6 Å2 / Rmerge(I) obs: 0.444 / Rsym value: 0.444 / Net I/σ(I): 4.5
Reflection shellResolution: 2.4→2.5267 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 2.5 / Num. unique all: 39013 / Rsym value: 0.444 / % possible all: 99.88

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M2M

3m2m


Resolution: 2.4→35.75 Å / SU ML: 0.3 / Isotropic thermal model: overall / σ(F): 1.35 / σ(I): 1.7 / Phase error: 24.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2382 1018 5.1 %Random
Rwork0.1858 ---
obs0.1884 19975 99.88 %-
all-39013 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→35.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3936 0 24 242 4202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044106
X-RAY DIFFRACTIONf_angle_d0.8625581
X-RAY DIFFRACTIONf_dihedral_angle_d13.341453
X-RAY DIFFRACTIONf_chiral_restr0.033617
X-RAY DIFFRACTIONf_plane_restr0.004751
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.52670.30971560.25652658X-RAY DIFFRACTION100
2.5267-2.68490.29341440.23722663X-RAY DIFFRACTION100
2.6849-2.89210.29911600.22562681X-RAY DIFFRACTION100
2.8921-3.1830.30061370.21442694X-RAY DIFFRACTION100
3.183-3.64320.22941330.17632709X-RAY DIFFRACTION100
3.6432-4.58850.20231430.14472726X-RAY DIFFRACTION100
4.5885-35.75620.19111450.17232826X-RAY DIFFRACTION100
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)
13.2377-2.09623.85657.9998-3.61026.004-0.1920.3310.06670.041-0.0592-0.6322-0.2686-0.08020.48020.3340.17610.06380.38050.0560.4134-33.07548.3936134.5274
24.76870.5012-1.6743.57071.02152.9976-0.3824-0.1346-1.03650.09560.0652-0.06350.5606-0.12240.22080.32010.11840.03910.32020.08590.5538-44.0659-3.4628137.3731
33.98170.0882-0.51563.21911.93332.3785-0.0599-0.2784-0.2918-0.0082-0.07010.36550.0761-0.29880.11560.27670.0809-0.0160.33030.05720.3433-49.24426.5694140.6805
43.57013.4481-0.67787.91960.27021.9216-0.04460.03650.0925-0.20220.04620.58590.12170.0447-0.07540.34270.059-0.00310.38340.04610.3219-45.53966.7774128.2272
56.5622-2.01670.32894.96620.61612.32250.06330.34660.2819-0.3303-0.31630.1471-0.4558-0.14720.24140.40550.0932-0.01330.34790.07510.2916-43.664916.0656133.0737
63.47712.36750.0672.27131.04082.84070.23180.2456-0.74780.5434-0.2270.62220.2104-0.4215-0.140.2524-0.01770.00940.40960.02840.4207-39.24642.5502141.9259
78.18885.1573-6.23133.4739-4.80398.72160.35540.4510.4857-0.49830.10290.7298-0.3268-0.663-0.2630.42290.1434-0.02010.35670.02110.3766-36.0524-1.4466132.0554
86.00643.8427-5.08537.6417-3.89464.2954-0.1817-0.1295-0.4575-0.51550.1701-0.69980.52280.19580.30920.36470.0366-0.02510.4358-0.02030.3878-24.959115.4242166.3663
94.6610.40371.09421.8727-0.00970.9219-0.08530.2140.5107-0.06970.118-0.1595-0.1365-0.06540.00480.26720.08170.01890.41010.04040.4056-30.791424.8972162.3193
104.56461.43821.57334.90712.21033.1867-0.0239-0.1390.89-0.3581-0.18150.4204-0.5552-0.46720.20440.3810.11680.03750.47230.05630.5798-38.562428.1095161.8794
112.52411.895-0.513.6951-0.54271.71330.25860.14110.60930.77840.1270.4903-0.278-0.2997-0.37130.37420.08060.0430.4167-0.05930.3948-34.921923.8494173.1056
127.85053.0736-0.55813.48060.45471.98630.1348-0.08360.61160.0934-0.01080.422-0.1217-0.1109-0.12990.25060.10880.01410.37820.0310.3434-28.099419.6564165.5168
137.57975.7984-3.72414.4924-3.12047.9377-0.0622-0.0005-0.1609-0.4792-0.0902-1.11530.0221-0.01640.31670.27340.07220.08280.37680.10.5867-13.80219.83159.538
144.4621-1.7112.42163.8695-2.38782.4350.1879-0.08610.39671.196-0.40610.1186-0.576-0.0943-0.08460.45550.09010.12680.3798-0.03410.4723-11.20517.589171.734
153.108-0.9668-0.20172.6059-2.25486.40720.07810.0816-0.3603-0.13-0.26820.04340.10650.57820.22870.20890.0271-0.02660.3756-0.03460.3681-7.6468.637163.097
165.0254-0.5582-0.02280.86962.01653.7-0.0257-0.043-0.4260.12750.1348-0.31120.69790.98790.01650.3860.1233-0.04150.4090.07430.4326-0.4025.959166.615
174.8792-1.0786-0.54092.44081.68874.60160.29740.18580.959-0.15450.1304-0.3632-0.30150.8952-0.38270.2853-0.00570.03220.3773-0.00030.4846-1.51719.287162.282
186.3253-4.5151-1.46685.46431.74778.18450.083-0.3347-0.27940.2175-0.04290.10080.0213-0.2844-0.09260.19340.0059-0.03330.32460.01380.3167-14.07115.242167.455
194.7861-3.20080.61843.4632-2.00263.566-0.2967-0.2365-0.54550.63160.2882-0.2064-0.194-0.17930.02950.24530.1007-0.02160.40520.03270.5339-27.429-4.571139.392
205.66830.3183-2.44936.6688-3.9443.21140.04530.83930.3924-0.8961-0.4642-0.26030.54070.60490.04280.47450.2037-0.00810.69990.13670.5231-23.792-1.011125.916
216.2709-2.34651.75031.88350.11321.17780.09120.16030.83080.0348-0.1151-0.2891-0.36480.2881-0.21590.30910.10460.03510.39190.04960.4199-15.4480.765136.257
224.3019-1.06151.50783.1743-0.41024.99790.01020.3654-0.1186-0.3480.1949-0.1061-0.26830.65510.03030.33110.07310.03630.5218-0.0080.4571-9.718-2.902133.989
233.2943-0.0682-0.4743.4041-0.6024.20650.2624-0.4106-0.58090.08070.1790.79880.12830.1443-0.17190.34190.10370.02110.4444-0.03630.5077-19.945-10.962133.902
247.9197-2.20324.0595.9619-3.38943.01910.24741.0507-0.7757-0.5408-0.1622-0.41030.98770.71050.15390.34790.13990.03470.5589-0.11460.5868-14.369-12.613130.492
257.7471-3.94512.73032.3625-1.43993.6652-0.2441-0.3178-0.01230.27240.2440.0683-0.1949-0.1733-0.02110.32480.0997-0.00690.45710.05490.4934-22.584-2.825137.81
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 3:16)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 17:32)
3X-RAY DIFFRACTION3CHAIN A AND (RESID 33:84)
4X-RAY DIFFRACTION4CHAIN A AND (RESID 85:105)
5X-RAY DIFFRACTION5CHAIN A AND (RESID 106:119)
6X-RAY DIFFRACTION6CHAIN A AND (RESID 120:126)
7X-RAY DIFFRACTION7CHAIN A AND (RESID 127:135)
8X-RAY DIFFRACTION8CHAIN B AND (RESID 3:16)
9X-RAY DIFFRACTION9CHAIN B AND (RESID 17:49)
10X-RAY DIFFRACTION10CHAIN B AND (RESID 50:84)
11X-RAY DIFFRACTION11CHAIN B AND (RESID 85:110)
12X-RAY DIFFRACTION12CHAIN B AND (RESID 111:135)
13X-RAY DIFFRACTION13CHAIN C AND (RESID 3:16)
14X-RAY DIFFRACTION14CHAIN C AND (RESID 17:24)
15X-RAY DIFFRACTION15CHAIN C AND (RESID 25:49)
16X-RAY DIFFRACTION16CHAIN C AND (RESID 50:84)
17X-RAY DIFFRACTION17CHAIN C AND (RESID 85:119)
18X-RAY DIFFRACTION18CHAIN C AND (RESID 120:135)
19X-RAY DIFFRACTION19CHAIN D AND (RESID 3:18)
20X-RAY DIFFRACTION20CHAIN D AND (RESID 19:24)
21X-RAY DIFFRACTION21CHAIN D AND (RESID 25:49)
22X-RAY DIFFRACTION22CHAIN D AND (RESID 50:84)
23X-RAY DIFFRACTION23CHAIN D AND (RESID 85:100)
24X-RAY DIFFRACTION24CHAIN D AND (RESID 101:110)
25X-RAY DIFFRACTION25CHAIN D AND (RESID 111:135)

+
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