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

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Basic information

Entry
Database: PDB / ID: 4gaf
TitleCrystal structure of EBI-005, a chimera of human IL-1beta and IL-1Ra, bound to human Interleukin-1 receptor type 1
Components
  • EBI-005
  • Interleukin-1 receptor type 1
KeywordsSIGNALING PROTEIN / IL-1beta / IL-1Ra / IL-1R1 / IL-1 signaling / Beta-trefoil
Function / homology
Function and homology information


positive regulation of interleukin-1-mediated signaling pathway / interleukin-1, type I, activating receptor activity / positive regulation of neutrophil extravasation / interleukin-1 receptor activity / interleukin-1 binding / 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 ...positive regulation of interleukin-1-mediated signaling pathway / interleukin-1, type I, activating receptor activity / positive regulation of neutrophil extravasation / interleukin-1 receptor activity / interleukin-1 binding / 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 glucose transmembrane transport / regulation of nitric-oxide synthase activity / hyaluronan biosynthetic process / positive regulation of cell adhesion molecule production / positive regulation of T-helper 1 cell cytokine production / positive regulation of complement activation / positive regulation of calcidiol 1-monooxygenase activity / cellular response to interleukin-17 / sequestering of triglyceride / positive regulation of RNA biosynthetic process / negative regulation of gap junction assembly / positive regulation of prostaglandin secretion / positive regulation of prostaglandin biosynthetic process / positive regulation of immature T cell proliferation in thymus / vascular endothelial growth factor production / positive regulation of neuroinflammatory response / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / regulation of defense response to virus by host / fever generation / NAD+ nucleosidase activity / positive regulation of fever generation / CLEC7A/inflammasome pathway / regulation of establishment of endothelial barrier / neutrophil activation / NAD+ nucleotidase, cyclic ADP-ribose generating / platelet-derived growth factor receptor binding / Interleukin-1 processing / response to carbohydrate / interleukin-1 receptor binding / positive regulation of monocyte chemotactic protein-1 production / 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 / : / macrophage chemotaxis / Interleukin-10 signaling / regulation of insulin secretion / 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 / positive regulation of T cell proliferation / positive regulation of glial cell proliferation / JNK cascade / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of interleukin-2 production / negative regulation of insulin receptor signaling pathway / embryo implantation / response to interleukin-1 / positive regulation of mitotic nuclear division / neutrophil chemotaxis / regulation of ERK1 and ERK2 cascade / positive regulation of protein export from nucleus / negative regulation of MAP kinase activity / secretory granule / cytokine activity / positive regulation of interleukin-8 production / astrocyte activation / positive regulation of JNK cascade / positive regulation of MAP kinase activity / cytokine-mediated signaling pathway / positive regulation of DNA-binding transcription factor activity / negative regulation of neurogenesis / Interleukin-1 signaling / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to mechanical stimulus / transmembrane signaling receptor activity / positive regulation of angiogenesis / positive regulation of interleukin-6 production / positive regulation of nitric oxide biosynthetic process / positive regulation of type II interferon production / cellular response to xenobiotic stimulus / integrin binding / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / regulation of inflammatory response
Similarity search - Function
Interleukin-1 receptor type 1 / Interleukin-1 receptor type I/II / IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Interleukin-1 receptor family / Interleukin-1 propeptide / Interleukin-1 propeptide / Interleukin-1 conserved site / Interleukin-1 signature. / Interleukin-1 homologues ...Interleukin-1 receptor type 1 / Interleukin-1 receptor type I/II / IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Interleukin-1 receptor family / Interleukin-1 propeptide / Interleukin-1 propeptide / Interleukin-1 conserved site / Interleukin-1 signature. / Interleukin-1 homologues / Interleukin-1 family / Interleukin-1 / 18 / TIR domain / Cytokine IL1/FGF / Toll - interleukin 1 - resistance / Immunoglobulin domain / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interleukin-1 beta / Interleukin-1 receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 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 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EBI-005
B: Interleukin-1 receptor type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3697
Polymers54,4612
Non-polymers9085
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-3 kcal/mol
Surface area22710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.350, 149.270, 126.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein EBI-005


Mass: 17719.332 Da / Num. of mol.: 1
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: Protein Interleukin-1 receptor type 1 / IL-1R-1 / IL-1RT-1 / IL-1RT1 / CD121 antigen-like family member A / Interleukin-1 receptor alpha / ...IL-1R-1 / IL-1RT-1 / IL-1RT1 / CD121 antigen-like family member A / Interleukin-1 receptor alpha / IL-1R-alpha / Interleukin-1 receptor type I / p80 / Interleukin-1 receptor type 1 / membrane form / mIL-1R1 / mIL-1RI / Interleukin-1 receptor type 1 / soluble form / sIL-1R1 / sIL-1RI


Mass: 36741.734 Da / Num. of mol.: 1 / Fragment: UNP residues 18-336
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL1R1, IL1R, IL1RA, IL1RT1 / Production host: Escherichia coli (E. coli) / References: UniProt: P14778
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.61 Å3/Da / Density % sol: 52.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 3350, 100 mM Tris, 200 mM lithium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9755 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 14, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9755 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 175866 / Num. obs: 31476 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Rmerge(I) obs: 0.061 / Χ2: 1.056 / Net I/σ(I): 12.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.15-2.235.60.5631021.0641100
2.23-2.325.60.42731091.0931100
2.32-2.425.60.31231111.0631100
2.42-2.555.60.2231141.0081100
2.55-2.715.60.14931091.0211100
2.71-2.925.60.11131371.0821100
2.92-3.215.60.0831461.0591100
3.21-3.685.60.04931701.0181100
3.68-4.635.50.06131751.081199.9
4.63-505.40.03533031.073198.9

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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: 2.15→41.86 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 14.35 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.255 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2712 1585 5.1 %RANDOM
Rwork0.2155 29798 --
obs0.2183 31383 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 78.2 Å2 / Biso mean: 53.367 Å2 / Biso min: 11.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2---0.59 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 2.15→41.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3716 0 57 209 3982
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0223904
X-RAY DIFFRACTIONr_angle_refined_deg1.9831.9765304
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4795465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.35825.161186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.99315688
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5571516
X-RAY DIFFRACTIONr_chiral_restr0.1450.2583
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212960
X-RAY DIFFRACTIONr_mcbond_it1.2321.52314
X-RAY DIFFRACTIONr_mcangle_it2.20923779
X-RAY DIFFRACTIONr_scbond_it3.32431590
X-RAY DIFFRACTIONr_scangle_it5.3564.51521
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 126 -
Rwork0.303 2148 -
all-2274 -
obs--100 %
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)
12.58231.2555-0.48964.1355-1.04043.49760.2051-0.1420.13520.1936-0.1081-0.0933-0.16460.1422-0.09710.1166-0.10070.01930.1142-0.0070.04740.502-33.23111.507
20.3040.95410.03553.67450.00080.0348-0.06850.08390.0208-0.27490.0696-0.0530.00460.0567-0.00110.1543-0.0812-0.00340.22380.0380.0691-5.851-39.8716.753
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 21
2X-RAY DIFFRACTION1A22 - 53
3X-RAY DIFFRACTION1A54 - 116
4X-RAY DIFFRACTION1A117 - 152
5X-RAY DIFFRACTION2B4 - 69
6X-RAY DIFFRACTION2B70 - 166
7X-RAY DIFFRACTION2B167 - 204
8X-RAY DIFFRACTION2B205 - 313

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