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- PDB-4gai: Crystal structure of EBI-005, a chimera of human IL-1beta and IL-1Ra -

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Basic information

Entry
Database: PDB / ID: 4gai
TitleCrystal structure of EBI-005, a chimera of human IL-1beta and IL-1Ra
ComponentsEBI-005
KeywordsSIGNALING PROTEIN / IL-1beta / IL-1Ra / IL-1R1 / IL-1 signaling / Beta-trefoil
Function / homology
Function and homology information


positive regulation of T cell mediated immunity / negative regulation of adiponectin secretion / negative regulation of lipid metabolic process / smooth muscle adaptation / positive regulation of lipid catabolic process / positive regulation of cell adhesion molecule production / regulation of nitric-oxide synthase activity / negative regulation of D-glucose transmembrane transport / positive regulation of T-helper 1 cell cytokine production / hyaluronan biosynthetic process ...positive regulation of T cell mediated immunity / negative regulation of adiponectin secretion / negative regulation of lipid metabolic process / smooth muscle adaptation / positive regulation of lipid catabolic process / positive regulation of cell adhesion molecule production / regulation of nitric-oxide synthase activity / negative regulation of D-glucose transmembrane transport / positive regulation of T-helper 1 cell cytokine production / hyaluronan biosynthetic process / positive regulation of complement activation / positive regulation of RNA biosynthetic process / cellular response to interleukin-17 / monocyte aggregation / positive regulation of tight junction disassembly / negative regulation of gap junction assembly / positive regulation of prostaglandin secretion / positive regulation of immature T cell proliferation in thymus / vascular endothelial growth factor production / positive regulation of prostaglandin biosynthetic process / positive regulation of fever generation / positive regulation of platelet-derived growth factor receptor signaling pathway / regulation of defense response to virus by host / fever generation / regulation of establishment of endothelial barrier / CLEC7A/inflammasome pathway / Interleukin-1 processing / positive regulation of macrophage derived foam cell differentiation / positive regulation of monocyte chemotactic protein-1 production / interleukin-1 receptor binding / positive regulation of p38MAPK cascade / negative regulation of synaptic transmission / response to carbohydrate / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of granulocyte macrophage colony-stimulating factor production / positive regulation of heterotypic cell-cell adhesion / positive regulation of membrane protein ectodomain proteolysis / regulation of canonical NF-kappaB signal transduction / interleukin-1-mediated signaling pathway / positive regulation of neuroinflammatory response / Interleukin-10 signaling / response to ATP / regulation of insulin secretion / positive regulation of cell division / positive regulation of vascular endothelial growth factor production / positive regulation of glial cell proliferation / Pyroptosis / regulation of neurogenesis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ectopic germ cell programmed cell death / positive regulation of epithelial to mesenchymal transition / negative regulation of lipid catabolic process / regulation of ERK1 and ERK2 cascade / positive regulation of interleukin-2 production / Purinergic signaling in leishmaniasis infection / JNK cascade / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of MAPK cascade / neutrophil chemotaxis / positive regulation of mitotic nuclear division / negative regulation of insulin receptor signaling pathway / embryo implantation / positive regulation of T cell proliferation / secretory granule / astrocyte activation / response to interleukin-1 / positive regulation of protein export from nucleus / cytokine activity / positive regulation of interleukin-8 production / cellular response to mechanical stimulus / positive regulation of non-canonical NF-kappaB signal transduction / negative regulation of neurogenesis / positive regulation of interleukin-6 production / positive regulation of JNK cascade / integrin binding / cellular response to xenobiotic stimulus / positive regulation of type II interferon production / cytokine-mediated signaling pathway / positive regulation of angiogenesis / Interleukin-1 signaling / positive regulation of nitric oxide biosynthetic process / positive regulation of inflammatory response / cell-cell signaling / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / response to lipopolysaccharide / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / lysosome / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / defense response to Gram-positive bacterium / immune response / positive regulation of cell migration / inflammatory response / negative regulation of cell population proliferation / protein domain specific binding / apoptotic process / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.49 Å
AuthorsHou, J. / Townson, S.A. / Kovalchin, J.T. / Masci, A. / Kiner, O. / Shu, Y. / King, B. / Thomas, C. / Garcia, K.C. / Furfine, E.S. / Barnes, T.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Design of a superior cytokine antagonist for topical ophthalmic use.
Authors: Hou, J. / Townson, S.A. / Kovalchin, J.T. / Masci, A. / Kiner, O. / Shu, Y. / King, B.M. / Schirmer, E. / Golden, K. / Thomas, C. / Garcia, K.C. / Zarbis-Papastoitsis, G. / Furfine, E.S. / Barnes, T.M.
History
DepositionJul 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: EBI-005
B: EBI-005


Theoretical massNumber of molelcules
Total (without water)35,4392
Polymers35,4392
Non-polymers00
Water6,377354
1
A: EBI-005


Theoretical massNumber of molelcules
Total (without water)17,7191
Polymers17,7191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: EBI-005


Theoretical massNumber of molelcules
Total (without water)17,7191
Polymers17,7191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.392, 66.910, 216.266
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein EBI-005


Mass: 17719.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01584*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O

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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: 2.21 Å3/Da / Density % sol: 44.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG 3350, 200 mM MgCl2, 100 mM HEPES, pH 7.5, 0.5% w/v n-Dodecy- -D-maltoside (DDM), VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 28, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. all: 294637 / Num. obs: 51907 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Rmerge(I) obs: 0.06 / Χ2: 1.024 / Net I/σ(I): 12
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.49-1.545.20.58250891.008199.4
1.54-1.615.70.45651581.021100
1.61-1.685.70.32551021.0211100
1.68-1.775.70.22651391.0231100
1.77-1.885.70.15751701.051100
1.88-2.025.70.10951751.0431100
2.02-2.235.80.07852041.0131100
2.23-2.555.70.07752011.0141100
2.55-3.215.80.06152601.0181100
3.21-505.80.04154091.033198.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.49 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2194 2638 5.1 %RANDOM
Rwork0.1872 49176 --
obs0.1888 51814 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 66.55 Å2 / Biso mean: 28.475 Å2 / Biso min: 4.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2--1.6 Å20 Å2
3----1.22 Å2
Refinement stepCycle: LAST / Resolution: 1.49→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2385 0 0 354 2739
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222557
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.9753478
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.815325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.94725.968124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02915496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.209158
X-RAY DIFFRACTIONr_chiral_restr0.2580.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211936
X-RAY DIFFRACTIONr_mcbond_it1.2111.51529
X-RAY DIFFRACTIONr_mcangle_it1.9922510
X-RAY DIFFRACTIONr_scbond_it3.05531028
X-RAY DIFFRACTIONr_scangle_it4.9284.5951
LS refinement shellResolution: 1.49→1.529 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 202 -
Rwork0.274 3512 -
all-3714 -
obs--97.69 %
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)
12.1284-0.40050.17431.72730.17042.66450.0318-0.0032-0.0071-0.0856-0.02030.02620.0239-0.0597-0.01160.02120.00970.00830.00790.01020.02644.14-16.734-11.559
22.5142-0.61780.72781.79360.05423.70670.04510.28290.0327-0.201-0.06670.0136-0.01150.15850.02170.10980.02370.02040.07860.00920.040710.799-16.396-39.615
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 152
2X-RAY DIFFRACTION1A201 - 412
3X-RAY DIFFRACTION2B1 - 151
4X-RAY DIFFRACTION2B201 - 342

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