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- PDB-2irt: INITIAL CRYSTALLOGRAPHIC ANALYSES OF A RECOMBINANT INTERLEUKIN-1 ... -

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Entry
Database: PDB / ID: 2irt
TitleINITIAL CRYSTALLOGRAPHIC ANALYSES OF A RECOMBINANT INTERLEUKIN-1 RECEPTOR ANTAGONIST PROTEIN
ComponentsINTERLEUKIN-1 RECEPTOR ANTAGONIST
KeywordsSIGNAL PROTEIN
Function / homology
Function and homology information


interleukin-1 type I receptor antagonist activity / interleukin-1 type II receptor antagonist activity / interleukin-1, type I receptor binding / interleukin-1 receptor antagonist activity / interleukin-1, type II receptor binding / negative regulation of interleukin-1-mediated signaling pathway / negative regulation of heterotypic cell-cell adhesion / interleukin-1 receptor binding / insulin secretion / Interleukin-10 signaling ...interleukin-1 type I receptor antagonist activity / interleukin-1 type II receptor antagonist activity / interleukin-1, type I receptor binding / interleukin-1 receptor antagonist activity / interleukin-1, type II receptor binding / negative regulation of interleukin-1-mediated signaling pathway / negative regulation of heterotypic cell-cell adhesion / interleukin-1 receptor binding / insulin secretion / Interleukin-10 signaling / response to glucocorticoid / cytokine activity / acute-phase response / lipid metabolic process / Interleukin-1 signaling / immune response / inflammatory response / centrosome / extracellular space / extracellular exosome / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
Interleukin-1 receptor antagonist/Interleukin-36 / Interleukin-1 conserved site / Interleukin-1 signature. / Interleukin-1 homologues / Interleukin-1 family / Interleukin-1 / 18 / Cytokine IL1/FGF
Similarity search - Domain/homology
Interleukin-1 receptor antagonist protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 3.2 Å
AuthorsFinzel, B.C. / Clancy, L.L. / Einspahr, H.M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Initial crystallographic analysis of a recombinant human interleukin-1 receptor antagonist protein.
Authors: Clancy, L.L. / Finzel, B.C. / Yem, A.W. / Deibel, M.R. / Strakalaitis, N.A. / Brunner, D.P. / Sweet, R.M. / Einspahr, H.M.
#1: Journal: Nature / Year: 1990
Title: Purification, Cloning, Expression and Biological Characterization of an Interleukin-1 Receptor Antagonist Protein
Authors: Carter, D.B. / Deibel Junior, M.R. / Dunn, C.J. / Tomich, C.-S. / Laborde, A.L. / Slightom, J.L. / Berger, A.E. / Bienkowski, M.J. / Sun, F.F. / Mcewan, R.N. / Harris, P.K.W. / Yem, A.W. / ...Authors: Carter, D.B. / Deibel Junior, M.R. / Dunn, C.J. / Tomich, C.-S. / Laborde, A.L. / Slightom, J.L. / Berger, A.E. / Bienkowski, M.J. / Sun, F.F. / Mcewan, R.N. / Harris, P.K.W. / Yem, A.W. / Waszak, G.A. / Chosay, J.G. / Sieu, L.C. / Hardee, M.M. / Zurcher-Neely, H.A. / Reardon, I.M. / Heinrikson, R.L. / Truesdell, S.E. / Shelly, J.A. / Eessalu, T.T. / Taylor, B.M. / Tracey, D.E.
History
DepositionJul 13, 1994Processing site: BNL
Revision 1.0Oct 15, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Remark 700SHEET THE SHEETS PRESENTED AS *BLA* AND *BLB* ON SHEET RECORDS BELOW ARE ACTUALLY SIX-STRANDED BETA- ...SHEET THE SHEETS PRESENTED AS *BLA* AND *BLB* ON SHEET RECORDS BELOW ARE ACTUALLY SIX-STRANDED BETA-BARRELS. THIS IS REPRESENTED BY A SEVEN-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INTERLEUKIN-1 RECEPTOR ANTAGONIST
B: INTERLEUKIN-1 RECEPTOR ANTAGONIST


Theoretical massNumber of molelcules
Total (without water)34,2912
Polymers34,2912
Non-polymers00
Water00
1
A: INTERLEUKIN-1 RECEPTOR ANTAGONIST


Theoretical massNumber of molelcules
Total (without water)17,1451
Polymers17,1451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: INTERLEUKIN-1 RECEPTOR ANTAGONIST


Theoretical massNumber of molelcules
Total (without water)17,1451
Polymers17,1451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.350, 72.350, 114.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein INTERLEUKIN-1 RECEPTOR ANTAGONIST / Coordinate model: Cα atoms only


Mass: 17145.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P18510

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.76 %
Crystal grow
*PLUS
Temperature: 277 K / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 mg/mlprotein1drop
218-24 %(w/v)PEG40001reservoir
330 mMsodium PIPES1reservoir
41 mMdithiothreitol1reservoir
50.6 mMsodium azide1reservoir
6200-400 mM1reservoirNaCl

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Data collection

Reflection
*PLUS
Highest resolution: 2.3 Å / Num. all: 14143 / Num. obs: 11831 / Num. measured all: 55341 / Rmerge(I) obs: 0.066

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Processing

RefinementResolution: 3.2→20 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.44 --
obs-5328 93.5 %
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms290 0 0 0 290
Refinement
*PLUS
Rfactor Rwork: 0.44
Solvent computation
*PLUS
Displacement parameters
*PLUS

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