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- PDB-5mvz: Fab 4AB007 bound to Interleukin-1-beta -

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Basic information

Entry
Database: PDB / ID: 5mvz
TitleFab 4AB007 bound to Interleukin-1-beta
Components
  • Fab 4AB007 H-chain
  • Fab 4AB007 L-chain
  • Interleukin-1 betaInterleukin 1 beta
KeywordsSIGNALING PROTEIN / Interleukin-1-beta / Fab 4AB007
Function / homology
Function and homology information


smooth muscle adaptation / positive regulation of T cell mediated immunity / hyaluronan biosynthetic process / positive regulation of myosin light chain kinase activity / negative regulation of adiponectin secretion / negative regulation of lipid metabolic process / positive regulation of lipid catabolic process / negative regulation of glucose transmembrane transport / positive regulation of cell adhesion molecule production / positive regulation of T-helper 1 cell cytokine production ...smooth muscle adaptation / positive regulation of T cell mediated immunity / hyaluronan biosynthetic process / positive regulation of myosin light chain kinase activity / negative regulation of adiponectin secretion / negative regulation of lipid metabolic process / positive regulation of lipid catabolic 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 / monocyte aggregation / 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 / fever generation / regulation of defense response to virus by host / positive regulation of fever generation / CLEC7A/inflammasome pathway / regulation of establishment of endothelial barrier / positive regulation of membrane protein ectodomain proteolysis / 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 granulocyte macrophage colony-stimulating factor production / negative regulation of synaptic transmission / regulation of canonical NF-kappaB signal transduction / positive regulation of heterotypic cell-cell adhesion / interleukin-1-mediated signaling pathway / positive regulation of p38MAPK cascade / regulation of nitric-oxide synthase activity / cellular response to organic substance / response to ATP / 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 / positive regulation of epithelial to mesenchymal transition / ectopic germ cell programmed cell death / Pyroptosis / Purinergic signaling in leishmaniasis infection / negative regulation of lipid catabolic process / positive regulation of glial cell proliferation / JNK cascade / embryo implantation / negative regulation of insulin receptor signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / response to interleukin-1 / regulation of ERK1 and ERK2 cascade / neutrophil chemotaxis / negative regulation of MAP kinase activity / positive regulation of mitotic nuclear division / positive regulation of protein export from nucleus / secretory granule / cytokine activity / positive regulation of interleukin-8 production / astrocyte activation / positive regulation of JNK cascade / positive regulation of MAP kinase activity / positive regulation of inflammatory response / negative regulation of neurogenesis / positive regulation of interleukin-6 production / Interleukin-1 signaling / cytokine-mediated signaling pathway / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to mechanical stimulus / positive regulation of angiogenesis / positive regulation of nitric oxide biosynthetic process / positive regulation of DNA-binding transcription factor activity / 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 / positive regulation of canonical NF-kappaB signal transduction / Interleukin-4 and Interleukin-13 signaling / cellular response to lipopolysaccharide / response to lipopolysaccharide / lysosome / positive regulation of cell migration / defense response to Gram-positive bacterium / immune response / inflammatory response / positive regulation of protein phosphorylation / protein domain specific binding / negative regulation of cell population proliferation / apoptotic process
Similarity search - Function
Interleukin-1 beta / 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 ...Interleukin-1 beta / 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
Multifunctional fusion protein / Interleukin-1 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsStark, W. / Seibert, V.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
KTI12972.1 Switzerland
CitationJournal: To Be Published
Title: Structure of a novel, fully Human Fab binding to Interleukin 1-beta.
Authors: Stark, W. / Seibert, V.
History
DepositionJan 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_symm_contact ...pdbx_data_processing_status / pdbx_validate_symm_contact / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab 4AB007 H-chain
L: Fab 4AB007 L-chain
U: Interleukin-1 beta
A: Fab 4AB007 H-chain
B: Fab 4AB007 L-chain
V: Interleukin-1 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,63614
Polymers146,8996
Non-polymers7378
Water11,422634
1
H: Fab 4AB007 H-chain
L: Fab 4AB007 L-chain
U: Interleukin-1 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8187
Polymers73,4503
Non-polymers3684
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Fab 4AB007 H-chain
B: Fab 4AB007 L-chain
V: Interleukin-1 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8187
Polymers73,4503
Non-polymers3684
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.041, 158.385, 153.437
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11L-426-

HOH

21U-227-

HOH

31B-519-

HOH

41V-224-

HOH

51V-227-

HOH

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Components

#1: Antibody Fab 4AB007 H-chain


Mass: 25437.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Fab 4AB007 L-chain


Mass: 27678.803 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Interleukin-1 beta / Interleukin 1 beta


Mass: 20333.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL1B / Production host: Homo sapiens (human) / References: UniProt: B5BUQ8, UniProt: P01584*PLUS
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 634 / 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 Å3/Da / Density % sol: 68.86 % / Description: plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Protein mix: 10mg/ml Protein 10mM Imidazole buffer, pH=8.0 50mM NaCl Reservoir: 18% PEG4000 (w/v), 0.1M Hepes pH=7.0, 10mM ATP, Drop Ratio 1:1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1.000, 2.066
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
22.0661
ReflectionResolution: 2.093→47.68 Å / Num. obs: 79698 / % possible obs: 95.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.085 / Net I/σ(I): 10.4
Reflection shellResolution: 2.093→2.21 Å / % possible all: 94.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→47.68 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.897 / SU B: 7.628 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.228 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28107 3665 5 %RANDOM
Rwork0.21945 ---
obs0.22253 69661 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 65.942 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å2-0 Å20 Å2
2---0.94 Å2-0 Å2
3---1.53 Å2
Refinement stepCycle: 1 / Resolution: 2.15→47.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8857 0 48 634 9539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.029105
X-RAY DIFFRACTIONr_bond_other_d0.0020.028455
X-RAY DIFFRACTIONr_angle_refined_deg1.6771.96112346
X-RAY DIFFRACTIONr_angle_other_deg0.862319587
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.64951140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72724.751362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.633151514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.681532
X-RAY DIFFRACTIONr_chiral_restr0.0960.21385
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110208
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022000
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.0166.494593
X-RAY DIFFRACTIONr_mcbond_other5.016.494592
X-RAY DIFFRACTIONr_mcangle_it6.6269.7165722
X-RAY DIFFRACTIONr_mcangle_other6.6279.7175723
X-RAY DIFFRACTIONr_scbond_it4.8686.7744510
X-RAY DIFFRACTIONr_scbond_other4.8686.7744510
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.55610.026625
X-RAY DIFFRACTIONr_long_range_B_refined9.2753.0510565
X-RAY DIFFRACTIONr_long_range_B_other9.2753.0510565
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 268 -
Rwork0.288 5086 -
obs--99.42 %

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