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- PDB-2kh2: Solution structure of a scFv-IL-1B complex -

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Basic information

Entry
Database: PDB / ID: 2kh2
TitleSolution structure of a scFv-IL-1B complex
Components
  • Interleukin-1 betaInterleukin 1 beta
  • scFvSingle-chain variable fragment
KeywordsCytokine/IMMUNE SYSTEM / scFv / single chain Fv / IL-1B / antibody / Cytokine / Inflammatory response / Mitogen / Pyrogen / Secreted / Cytokine-IMMUNE SYSTEM COMPLEX
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 / hyaluronan biosynthetic process / negative regulation of glucose transmembrane transport / 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 / hyaluronan biosynthetic process / negative regulation of glucose transmembrane transport / 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 / regulation of defense response to virus by host / fever generation / positive regulation of fever generation / neutrophil activation / CLEC7A/inflammasome pathway / regulation of establishment of endothelial barrier / 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 granulocyte macrophage colony-stimulating factor production / regulation of canonical NF-kappaB signal transduction / positive regulation of membrane protein ectodomain proteolysis / interleukin-1-mediated signaling pathway / positive regulation of p38MAPK cascade / : / regulation of nitric-oxide synthase activity / 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 / JNK cascade / positive regulation of glial cell proliferation / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of interleukin-2 production / embryo implantation / negative regulation of insulin receptor signaling pathway / 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 / astrocyte activation / positive regulation of interleukin-8 production / positive regulation of JNK cascade / positive regulation of MAP kinase activity / positive regulation of DNA-binding transcription factor activity / cytokine-mediated signaling pathway / negative regulation of neurogenesis / positive regulation of inflammatory response / Interleukin-1 signaling / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to mechanical stimulus / 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 / Interleukin-4 and Interleukin-13 signaling / positive regulation of canonical NF-kappaB signal transduction / cellular response to lipopolysaccharide / response to lipopolysaccharide / lysosome / positive regulation of cell migration / defense response to Gram-positive bacterium / inflammatory response / immune response / positive regulation of protein phosphorylation / negative regulation of cell population proliferation
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailsclosest to the average, model 1
AuthorsWilkinson, I.C. / Hall, C.J. / Veverka, V. / Muskett, F.W. / Stephens, P.E. / Taylor, R.J. / Henry, A.J. / Carr, M.D.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: High resolution NMR-based model for the structure of a scFv-IL-1beta complex: potential for NMR as a key tool in therapeutic antibody design and development.
Authors: Wilkinson, I.C. / Hall, C.J. / Veverka, V. / Shi, J.Y. / Muskett, F.W. / Stephens, P.E. / Taylor, R.J. / Henry, A.J. / Carr, M.D.
History
DepositionMar 23, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-1 beta
B: scFv


Theoretical massNumber of molelcules
Total (without water)44,7892
Polymers44,7892
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)77 / 77all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

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


Mass: 17395.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL1B, IL1F2 / Plasmid: pet-21 / Production host: Escherichia coli (E. coli) / References: UniProt: P01584
#2: Antibody scFv / Single-chain variable fragment


Mass: 27393.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pTTod / Production host: Escherichia coli (E. coli)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-15N HSQC
1242D 1H-15N HSQC
1352D 1H-15N HSQC
1462D 1H-15N HSQC
1513D CBCA(CO)NH
1623D CBCA(CO)NH
1713D HNCO
1823D HNCO
1913D HNCA
11023D HNCA
11113D HN(CA)CB
11223D HN(CA)CB
11313D CBCA(CO)NH
11423D CBCA(CO)NH
11533D 1H-15N NOESY
11643D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1400-700 uM [U-13C; U-15N; U-2H] IL1B, 400-700 uM scFv, 90% H2O/10% D2O90% H2O/10% D2O
2400-700 uM [U-13C; U-15N; U-2H] scFv, 400-700 uM IL1B, 90% H2O/10% D2O90% H2O/10% D2O
3200-500 uM [U-15N] IL1B, 200-500 uM scFv, 90% H2O/10% D2O90% H2O/10% D2O
4600 uM [U-15N] scFv, 600 uM IL1B, 90% H2O/10% D2O90% H2O/10% D2O
5250 uM [U-15N] IL1B, 250 uM scFv, 4 mg/mL Pf1 phage, 90% H2O/10% D2O90% H2O/10% D2O
6250 uM [U-15N] scFv, 250 uM IL1B, 4 mg/mL Pf1 phage, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
uMIL1B[U-13C; U-15N; U-2H]400-7001
uMscFv400-7001
uMscFv[U-13C; U-15N; U-2H]400-7002
uMIL1B400-7002
uMIL1B[U-15N]200-5003
uMscFv200-5003
600 uMscFv[U-15N]4
600 uMIL1B4
250 uMIL1B[U-15N]5
250 uMscFv5
4 mg/mLPf1 phage5
250 uMscFv[U-15N]6
250 uMIL1B6
4 mg/mLPf1 phage6
Sample conditionsIonic strength: 150 / pH: 6.5 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2Bruker Biospincollection
TopSpin2Bruker Biospinprocessing
Sparky3.11Goddardchemical shift assignment
Sparky3.11Goddardpeak picking
HADDOCK2Utrecht Universitystructure solution
HADDOCK2Utrecht Universityrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1 / Details: Refined as part of the HADDOCK docking protocol
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 77 / Conformers submitted total number: 77

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