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- PDB-3ltq: Structure of Interleukin 1B solved by SAD using an inserted Lanth... -

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Basic information

Entry
Database: PDB / ID: 3ltq
TitleStructure of Interleukin 1B solved by SAD using an inserted Lanthanide Binding Tag
ComponentsInterleukin-1 beta
KeywordsCYTOKINE / Lanthanide Binding Tag / LBT / terbium / IL1B / Inflammatory response / Mitogen / Pyrogen / Secreted
Function / homology
Function and homology information


smooth muscle adaptation / positive regulation of T cell mediated immunity / positive regulation of myosin light chain kinase activity / negative regulation of adiponectin secretion / monocyte aggregation / negative regulation of lipid metabolic process / positive regulation of lipid catabolic process / negative regulation of D-glucose transmembrane transport / regulation of nitric-oxide synthase activity / positive regulation of cell adhesion molecule production ...smooth muscle adaptation / positive regulation of T cell mediated immunity / positive regulation of myosin light chain kinase activity / negative regulation of adiponectin secretion / monocyte aggregation / negative regulation of lipid metabolic process / positive regulation of lipid catabolic process / negative regulation of D-glucose transmembrane transport / regulation of nitric-oxide synthase activity / positive regulation of cell adhesion molecule production / hyaluronan biosynthetic process / positive regulation of T-helper 1 cell cytokine production / positive regulation of complement activation / positive regulation of calcidiol 1-monooxygenase activity / sequestering of triglyceride / cellular response to interleukin-17 / positive regulation of RNA biosynthetic process / negative regulation of gap junction assembly / positive regulation of prostaglandin biosynthetic process / positive regulation of immature T cell proliferation in thymus / vascular endothelial growth factor production / positive regulation of prostaglandin secretion / positive regulation of neuroinflammatory response / regulation of defense response to virus by host / fever generation / positive regulation of fever generation / regulation of establishment of endothelial barrier / CLEC7A/inflammasome pathway / Interleukin-1 processing / response to carbohydrate / positive regulation of monocyte chemotactic protein-1 production / interleukin-1 receptor binding / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of heterotypic cell-cell adhesion / negative regulation of synaptic transmission / positive regulation of membrane protein ectodomain proteolysis / regulation of canonical NF-kappaB signal transduction / positive regulation of granulocyte macrophage colony-stimulating factor production / interleukin-1-mediated signaling pathway / positive regulation of p38MAPK cascade / response to ATP / Interleukin-10 signaling / positive regulation of cell division / regulation of neurogenesis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of vascular endothelial growth factor production / ectopic germ cell programmed cell death / Pyroptosis / negative regulation of lipid catabolic process / Purinergic signaling in leishmaniasis infection / positive regulation of epithelial to mesenchymal transition / negative regulation of MAP kinase activity / positive regulation of T cell proliferation / positive regulation of glial cell proliferation / extrinsic apoptotic signaling pathway in absence of ligand / JNK cascade / negative regulation of insulin receptor signaling pathway / neutrophil chemotaxis / embryo implantation / positive regulation of interleukin-2 production / regulation of insulin secretion / positive regulation of mitotic nuclear division / response to interleukin-1 / regulation of ERK1 and ERK2 cascade / positive regulation of protein export from nucleus / secretory granule / cytokine activity / positive regulation of interleukin-8 production / astrocyte activation / positive regulation of JNK cascade / positive regulation of DNA-binding transcription factor activity / positive regulation of MAP kinase activity / cytokine-mediated signaling pathway / negative regulation of neurogenesis / positive regulation of inflammatory response / positive regulation of interleukin-6 production / cellular response to mechanical stimulus / Interleukin-1 signaling / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of type II interferon production / positive regulation of angiogenesis / positive regulation of nitric oxide biosynthetic process / integrin binding / cellular response to xenobiotic stimulus / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / positive regulation of canonical NF-kappaB signal transduction / response to lipopolysaccharide / lysosome / defense response to Gram-positive bacterium / positive regulation of cell migration / inflammatory response / immune response / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / protein domain specific binding / positive regulation of cell population proliferation / positive regulation of gene expression
Similarity search - Function
Interleukin-1 propeptide / Interleukin-1 propeptide / Interleukin-1 conserved site / Interleukin-1 signature. / Interleukin-1 homologues / Interleukin-1 family / Interleukin-1 / 18 / Cytokine IL1/FGF / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) ...Interleukin-1 propeptide / Interleukin-1 propeptide / Interleukin-1 conserved site / Interleukin-1 signature. / Interleukin-1 homologues / Interleukin-1 family / Interleukin-1 / 18 / Cytokine IL1/FGF / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / TERBIUM(III) ION / Interleukin-1 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsPeisach, E. / Allen, K.N.
Citation
Journal: J.Am.Chem.Soc. / Year: 2011
Title: Engineering encodable lanthanide-binding tags into loop regions of proteins.
Authors: Barthelmes, K. / Reynolds, A.M. / Peisach, E. / Jonker, H.R. / DeNunzio, N.J. / Allen, K.N. / Imperiali, B. / Schwalbe, H.
#1: Journal: J.Am.Chem.Soc. / Year: 2007
Title: Double-Lanthanide-Binding Tags for Macromolecular Crystallographic Structure Determination
Authors: Silvaggi, N.R. / Martin, L.J. / Schwalbe, H. / Imperiali, B. / Allen, K.N.
History
DepositionFeb 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 18, 2019Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-1 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8565
Polymers19,4831
Non-polymers3734
Water2,864159
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.584, 120.584, 74.899
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-157-

SO4

21A-157-

SO4

31A-288-

HOH

41A-301-

HOH

51A-304-

HOH

61A-308-

HOH

71A-312-

HOH

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Components

#1: Protein Interleukin-1 beta / IL-1 beta / Catabolin


Mass: 19483.020 Da / Num. of mol.: 1 / Fragment: sequence database residues 117-269
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL1B, IL1F2 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01584
#2: Chemical ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Tb
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsINSERTED LANTHANIDE BINDING TAG

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.03 Å3/Da / Density % sol: 69.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100 mM sodium acetate trihydrate, pH 4.5, 3.0 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 30, 2006
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 19092 / Num. obs: 19092 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.4 % / Biso Wilson estimate: 29.63 Å2 / Rmerge(I) obs: 0.075 / Χ2: 0.942 / Net I/σ(I): 28.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.1-2.1811.70.27418660.81698.9
2.18-2.2611.70.20918500.66398.7
2.26-2.3711.90.21118700.93198.8
2.37-2.4913.30.15318770.78499.3
2.49-2.6514.60.12618820.88599.2
2.65-2.8516.30.10818911.13299.4
2.85-3.1418.60.08719130.77199.4
3.14-3.5919.30.07119310.94899.5
3.59-4.5218.80.06219461.18899.2
4.52-5017.40.0620661.08697.9

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.1 Å / D res low: 31.81 Å / FOM : 0.486 / FOM acentric: 0.544 / FOM centric: 0.233 / Reflection: 18348 / Reflection acentric: 15088 / Reflection centric: 2564
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.6-11.740.4830.6510.22218711372
7.11-8.60.4940.6530.17623715879
6.19-7.110.6020.7490.25627219181
5.56-6.190.5770.7180.18130822778
5.09-5.560.5360.6470.18533325380
4.72-5.090.5120.6150.16335527481
4.42-4.720.5080.5990.15337129476
4.17-4.420.5290.6110.18339331874
3.96-4.170.5130.6050.16942934085
3.78-3.960.5140.5870.16743636173
3.62-3.780.4970.570.17545437079
3.48-3.620.4940.5580.1746539072
3.36-3.480.5160.5730.22447740173
3.24-3.360.5430.6040.23150342377
3.14-3.240.5390.6020.20952544378
3.05-3.140.4780.5250.21753345474
2.96-3.050.470.5230.18253745774
2.89-2.960.5260.5710.26556048468
2.81-2.890.5450.610.20957048373
2.75-2.810.530.5860.22957549267
2.68-2.750.5580.6070.26757850165
2.62-2.680.520.5750.22861052078
2.57-2.620.5230.570.28362052676
2.52-2.570.5170.5670.25961953264
2.47-2.520.4940.5440.25962953564
2.42-2.470.480.5350.30262551161
2.38-2.420.4840.5270.33963553364
2.34-2.380.4710.5070.31265856562
2.3-2.340.460.5080.2967455674
2.26-2.30.4440.4970.37156945246
2.23-2.260.3590.3750.23972764177
2.19-2.230.4130.4450.3264653354
2.16-2.190.3950.4280.31666354063
2.13-2.160.3960.440.370955669
2.1-2.130.3950.4290.31774160963
Phasing dmFOM : 0.7 / FOM acentric: 0.71 / FOM centric: 0.65 / Reflection: 18347 / Reflection acentric: 15784 / Reflection centric: 2563
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6-11.740.920.960.86902578324
3.8-60.930.950.8426192081538
3-3.80.860.880.7531762700476
2.6-30.740.760.5431282739389
2.3-2.60.590.610.4652814744537
2.1-2.30.460.470.3832412942299

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RESOLVE2.15phasing
PHENIX1.6_289refinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
RefinementMethod to determine structure: SAD / Resolution: 2.1→30.432 Å / Occupancy max: 1 / Occupancy min: 0.16 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0.04 / Phase error: 20.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.221 3342 10 %random
Rwork0.192 ---
obs0.195 33433 93.92 %-
all-33433 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.301 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 84.98 Å2 / Biso mean: 37.723 Å2 / Biso min: 13.21 Å2
Baniso -1Baniso -2Baniso -3
1-1.928 Å2-0 Å2-0 Å2
2--1.928 Å20 Å2
3----3.857 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30.432 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1346 0 14 159 1519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081387
X-RAY DIFFRACTIONf_angle_d1.1351869
X-RAY DIFFRACTIONf_chiral_restr0.076199
X-RAY DIFFRACTIONf_plane_restr0.005245
X-RAY DIFFRACTIONf_dihedral_angle_d16.615521
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.1-2.1750.2283280.21529033231323190
2.175-2.2620.2843010.24428203121312188
2.262-2.3650.2453010.21327393040304085
2.365-2.490.233270.19229283255325592
2.49-2.6460.2543440.20730183362336295
2.646-2.850.2353350.20830813416341696
2.85-3.1360.2563460.19931413487348798
3.136-3.5890.1973590.18431253484348498
3.589-4.520.1763490.1531733522352299
4.52-30.4350.2123520.18431633515351598

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