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- PDB-4no4: Crystal Structure of Galectin-1 L11A mutant -

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Basic information

Entry
Database: PDB / ID: 4no4
TitleCrystal Structure of Galectin-1 L11A mutant
ComponentsGalectin-1
KeywordsAPOPTOSIS / beta barrel / lactose binding protein / lactose
Function / homology
Function and homology information


positive regulation of erythrocyte aggregation / Post-translational protein phosphorylation / 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 / response to isolation stress / negative regulation of cell-substrate adhesion ...positive regulation of erythrocyte aggregation / Post-translational protein phosphorylation / 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 / response to isolation stress / negative regulation of cell-substrate adhesion / response to axon injury / laminin binding / T cell costimulation / cellular response to glucose stimulus / cell-cell adhesion / positive regulation of inflammatory response / negative regulation of neuron projection development / carbohydrate binding / positive regulation of viral entry into host cell / positive regulation of apoptotic process / receptor ligand activity / response to xenobiotic stimulus / apoptotic process / cell surface / extracellular space / identical protein binding / plasma membrane / 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-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.399 Å
AuthorsDessau, M.
CitationJournal: To be Published
Title: Crystal Structure of Galectin-1 L11A mutant
Authors: Dessau, M. / Segev, O.
History
DepositionNov 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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 / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / 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.occupancy / _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.id / _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_asym_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.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)91,06923
Polymers88,1976
Non-polymers2,87117
Water23,2211289
1
A: Galectin-1
C: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,50510
Polymers29,3992
Non-polymers1,1068
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Galectin-1
hetero molecules

B: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2686
Polymers29,3992
Non-polymers8694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
3
D: Galectin-1
E: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2726
Polymers29,3992
Non-polymers8734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: Galectin-1
hetero molecules

F: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3168
Polymers29,3992
Non-polymers9176
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)112.520, 193.830, 108.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-433-

HOH

21E-432-

HOH

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Components

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Protein / Sugars , 2 types, 12 molecules ABCDEF

#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 / RL 14.5 / S-Lac lectin 1


Mass: 14699.545 Da / Num. of mol.: 6 / Mutation: L11A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Lgals1 / Production host: Escherichia coli (E. coli) / References: UniProt: P11762
#2: Polysaccharide
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 6
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

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Non-polymers , 4 types, 1300 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1289 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 62.98 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG 4K, ammonium sulfate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 1, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 443997 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellHighest resolution: 1.4 Å / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIXdev_1593refinement
SHARPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
RefinementMethod to determine structure: SAD / Resolution: 1.399→28.969 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU ML: 0.15 / σ(F): 1.35 / Phase error: 22.98 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rfree0.1971 11363 5.01 %
Rwork0.1877 --
obs0.1882 226809 98.19 %
all-215489 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.714 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.399→28.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6180 0 187 1289 7656
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016608
X-RAY DIFFRACTIONf_angle_d1.4798978
X-RAY DIFFRACTIONf_dihedral_angle_d13.2012385
X-RAY DIFFRACTIONf_chiral_restr0.0741004
X-RAY DIFFRACTIONf_plane_restr0.0071189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3991-1.4150.30943540.31946648X-RAY DIFFRACTION92
1.415-1.43170.32533930.30417122X-RAY DIFFRACTION98
1.4317-1.44910.2923820.28957101X-RAY DIFFRACTION98
1.4491-1.46750.27923870.28677151X-RAY DIFFRACTION98
1.4675-1.48680.27583850.27237192X-RAY DIFFRACTION99
1.4868-1.50720.28553450.2687171X-RAY DIFFRACTION99
1.5072-1.52870.26323670.25257199X-RAY DIFFRACTION99
1.5287-1.55150.24893570.23697174X-RAY DIFFRACTION99
1.5515-1.57580.2553850.2317240X-RAY DIFFRACTION99
1.5758-1.60160.23653820.22487189X-RAY DIFFRACTION99
1.6016-1.62920.23753980.21697169X-RAY DIFFRACTION99
1.6292-1.65880.23313890.20947247X-RAY DIFFRACTION99
1.6588-1.69070.20673960.20657150X-RAY DIFFRACTION99
1.6907-1.72520.2213850.21047236X-RAY DIFFRACTION99
1.7252-1.76270.21553740.20497247X-RAY DIFFRACTION99
1.7627-1.80370.2213880.19027247X-RAY DIFFRACTION99
1.8037-1.84880.18013820.17927229X-RAY DIFFRACTION100
1.8488-1.89880.18094080.18057289X-RAY DIFFRACTION100
1.8988-1.95470.19753800.18067231X-RAY DIFFRACTION100
1.9547-2.01780.18683930.1697288X-RAY DIFFRACTION100
2.0178-2.08990.19613970.17597287X-RAY DIFFRACTION100
2.0899-2.17350.17773470.16547320X-RAY DIFFRACTION100
2.1735-2.27240.18993920.17127310X-RAY DIFFRACTION100
2.2724-2.39210.17844080.17427317X-RAY DIFFRACTION100
2.3921-2.54190.17933680.16747331X-RAY DIFFRACTION100
2.5419-2.73810.1673830.17027361X-RAY DIFFRACTION100
2.7381-3.01330.17653860.16897344X-RAY DIFFRACTION100
3.0133-3.44880.16313520.15987261X-RAY DIFFRACTION98
3.4488-4.34270.17543860.16016875X-RAY DIFFRACTION92
4.3427-28.97540.21793140.21526520X-RAY DIFFRACTION85
Refinement TLS params.Method: refined / Origin x: 21.1583 Å / Origin y: 29.9525 Å / Origin z: 36.553 Å
111213212223313233
T0.1372 Å2-0.0214 Å20.0037 Å2-0.1728 Å20.0073 Å2--0.1859 Å2
L-0.011 °20.0321 °2-0.0034 °2-0.1352 °2-0.0623 °2--0.2488 °2
S-0.0101 Å °0.0012 Å °-0.0029 Å °-0.0088 Å °0.0021 Å °-0.0063 Å °0.0451 Å °0.0226 Å °-0.005 Å °
Refinement TLS groupSelection details: all

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