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- PDB-1g0y: IL-1 RECEPTOR TYPE 1 COMPLEXED WITH ANTAGONIST PEPTIDE AF10847 -

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Basic information

Entry
Database: PDB / ID: 1g0y
TitleIL-1 RECEPTOR TYPE 1 COMPLEXED WITH ANTAGONIST PEPTIDE AF10847
Components
  • ANTAGONIST PEPTIDE AF10847
  • INTERLEUKIN-1 RECEPTOR, TYPE I
KeywordsIMMUNE SYSTEM / Immunoglobulin
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 / positive regulation of T-helper 1 cell cytokine production / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD+ nucleotidase, cyclic ADP-ribose generating / platelet-derived growth factor receptor binding ...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 / positive regulation of T-helper 1 cell cytokine production / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD+ nucleotidase, cyclic ADP-ribose generating / platelet-derived growth factor receptor binding / interleukin-1-mediated signaling pathway / Interleukin-10 signaling / response to interleukin-1 / Interleukin-1 signaling / positive regulation of type II interferon production / transmembrane signaling receptor activity / regulation of inflammatory response / protease binding / Potential therapeutics for SARS / cell surface receptor signaling pathway / inflammatory response / immune response / external side of plasma membrane / extracellular region / membrane / plasma membrane
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 / TIR domain / Toll - interleukin 1 - resistance / Immunoglobulin domain / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain ...Interleukin-1 receptor type 1 / Interleukin-1 receptor type I/II / IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Interleukin-1 receptor family / TIR domain / Toll - interleukin 1 - resistance / Immunoglobulin domain / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / 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 receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsVigers, G.P.A. / Dripps, D.J. / Edwards, C.K. / Brandhuber, B.J.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: X-ray crystal structure of a small antagonist peptide bound to interleukin-1 receptor type 1.
Authors: Vigers, G.P. / Dripps, D.J. / Edwards III, C.K. / Brandhuber, B.J.
History
DepositionOct 9, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Jan 31, 2018Group: Database references / Experimental preparation / Category: citation_author / exptl_crystal_grow
Item: _citation_author.name / _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: INTERLEUKIN-1 RECEPTOR, TYPE I
I: ANTAGONIST PEPTIDE AF10847


Theoretical massNumber of molelcules
Total (without water)38,5162
Polymers38,5162
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-15 kcal/mol
Surface area17060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.898, 95.898, 208.017
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein INTERLEUKIN-1 RECEPTOR, TYPE I


Mass: 35909.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): SF9 CELLS / Production host: unidentified baculovirus / References: UniProt: P14778
#2: Protein/peptide ANTAGONIST PEPTIDE AF10847


Mass: 2605.804 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was synthesized by solid-phase synthesis.

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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: 3.58 Å3/Da / Density % sol: 65.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 25% polyethylene glycol 4000, 0.2 M ammonium sulfate, 100 mM sodium acetate pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13.3 mg/mlIL-1R11drop
325 %PEG40001reservoir
40.2 Mammonium sulfate1reservoir
5100 mMsodium acetate1reservoir
2AF108471drop1:2 molar ratio

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 3, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 13070 / Num. obs: 11894 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 21.9
Reflection shellResolution: 3→3.11 Å / Redundancy: 73.3 % / Rmerge(I) obs: 0.369 / Num. unique all: 1159 / % possible all: 82.3
Reflection
*PLUS
Num. measured all: 125320
Reflection shell
*PLUS
% possible obs: 82.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
X-PLOR3.851refinement
RefinementResolution: 3→30 Å / σ(F): 3 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.332 1106 -10% of observed
Rwork0.223 ---
all-11973 --
obs-11171 93.3 %-
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2694 0 0 0 2694
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.0121
X-RAY DIFFRACTIONx_angle_deg1.91

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