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- PDB-7z4t: AAL160 FAB IN COMPLEX WITH HUMAN INTERLEUKIN-1 BETA -

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Basic information

Entry
Database: PDB / ID: 7z4t
TitleAAL160 FAB IN COMPLEX WITH HUMAN INTERLEUKIN-1 BETA
Components
  • AAL160 Fab heavy-chain
  • AAL160 light-chain
  • Interleukin-1 beta
KeywordsIMMUNE SYSTEM / OTHER / MONOCLONAL ANTIBODY / IL-1B / IMMUNOGLOBULIN
Function / homology
Function and homology information


positive regulation of T cell mediated immunity / positive regulation of cell adhesion molecule production / negative regulation of adiponectin secretion / monocyte aggregation / negative regulation of lipid metabolic process / smooth muscle adaptation / positive regulation of lipid catabolic process / negative regulation of D-glucose transmembrane transport / regulation of nitric-oxide synthase activity / hyaluronan biosynthetic process ...positive regulation of T cell mediated immunity / positive regulation of cell adhesion molecule production / negative regulation of adiponectin secretion / monocyte aggregation / negative regulation of lipid metabolic process / smooth muscle adaptation / positive regulation of lipid catabolic process / negative regulation of D-glucose transmembrane transport / regulation of nitric-oxide synthase activity / hyaluronan biosynthetic process / positive regulation of T-helper 1 cell cytokine production / positive regulation of complement activation / : / cellular response to interleukin-17 / positive regulation of RNA biosynthetic process / positive regulation of tight junction disassembly / positive regulation of prostaglandin biosynthetic process / negative regulation of gap junction assembly / positive regulation of immature T cell proliferation in thymus / vascular endothelial growth factor production / positive regulation of prostaglandin secretion / positive regulation of neuroinflammatory response / positive regulation of platelet-derived growth factor receptor signaling pathway / regulation of defense response to virus by host / fever generation / positive regulation of fever generation / regulation of establishment of endothelial barrier / CLEC7A/inflammasome pathway / Interleukin-1 processing / negative regulation of synaptic transmission / response to carbohydrate / positive regulation of monocyte chemotactic protein-1 production / interleukin-1 receptor binding / positive regulation of heterotypic cell-cell adhesion / positive regulation of macrophage derived foam cell differentiation / positive regulation of p38MAPK cascade / positive regulation of membrane protein ectodomain proteolysis / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of granulocyte macrophage colony-stimulating factor production / regulation of canonical NF-kappaB signal transduction / interleukin-1-mediated signaling pathway / response to ATP / Interleukin-10 signaling / positive regulation of cell division / regulation of neurogenesis / positive regulation of vascular endothelial growth factor production / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of MAP kinase activity / Pyroptosis / ectopic germ cell programmed cell death / negative regulation of lipid catabolic process / regulation of ERK1 and ERK2 cascade / Purinergic signaling in leishmaniasis infection / positive regulation of epithelial to mesenchymal transition / positive regulation of T cell proliferation / extrinsic apoptotic signaling pathway in absence of ligand / JNK cascade / positive regulation of glial cell proliferation / neutrophil chemotaxis / embryo implantation / negative regulation of insulin receptor signaling pathway / positive regulation of interleukin-2 production / response to interleukin-1 / positive regulation of mitotic nuclear division / regulation of insulin secretion / secretory granule / positive regulation of protein export from nucleus / cytokine activity / positive regulation of interleukin-8 production / astrocyte activation / positive regulation of JNK cascade / positive regulation of non-canonical NF-kappaB signal transduction / cytokine-mediated signaling pathway / negative regulation of neurogenesis / positive regulation of interleukin-6 production / positive regulation of type II interferon production / Interleukin-1 signaling / cellular response to mechanical stimulus / positive regulation of inflammatory response / positive regulation of angiogenesis / positive regulation of NF-kappaB transcription factor activity / positive regulation of nitric oxide biosynthetic process / integrin binding / cellular response to xenobiotic stimulus / cell-cell signaling / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / response to lipopolysaccharide / positive regulation of canonical NF-kappaB signal transduction / lysosome / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / defense response to Gram-positive bacterium / immune response / positive regulation of cell migration / inflammatory response / protein domain specific binding / negative regulation of cell population proliferation / apoptotic process
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 / Immunoglobulins / Immunoglobulin-like ...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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å
AuthorsRondeau, J.M. / Lehmann, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Biol / Year: 2023
Title: "Redirecting an anti-IL-1 beta antibody to bind a new, unrelated and computationally predicted epitope on hIL-17A".
Authors: Fischman, S. / Levin, I. / Rondeau, J.M. / Strajbl, M. / Lehmann, S. / Huber, T. / Nimrod, G. / Cebe, R. / Omer, D. / Kovarik, J. / Bernstein, S. / Sasson, Y. / Demishtein, A. / Shlamkovich, ...Authors: Fischman, S. / Levin, I. / Rondeau, J.M. / Strajbl, M. / Lehmann, S. / Huber, T. / Nimrod, G. / Cebe, R. / Omer, D. / Kovarik, J. / Bernstein, S. / Sasson, Y. / Demishtein, A. / Shlamkovich, T. / Bluvshtein, O. / Grossman, N. / Barak-Fuchs, R. / Zhenin, M. / Fastman, Y. / Twito, S. / Vana, T. / Zur, N. / Ofran, Y.
History
DepositionMar 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: AAL160 Fab heavy-chain
I: Interleukin-1 beta
L: AAL160 light-chain


Theoretical massNumber of molelcules
Total (without water)65,1243
Polymers65,1243
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-30 kcal/mol
Surface area26080 Å2
Unit cell
Length a, b, c (Å)185.795, 37.167, 97.069
Angle α, β, γ (deg.)90.000, 114.920, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein AAL160 Fab heavy-chain


Mass: 24228.166 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Homo sapiens x Mus musculus hybrid cell line (mammal)
#2: Protein Interleukin-1 beta / IL-1 beta / Catabolin


Mass: 17395.832 Da / Num. of mol.: 1 / Fragment: Fab light-chain
Source method: isolated from a genetically manipulated source
Details: Mature form / Source: (gene. exp.) Homo sapiens (human) / Gene: IL1B, IL1F2 / Plasmid: pET derived / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): T1 / References: UniProt: P01584
#3: Antibody AAL160 light-chain


Mass: 23500.119 Da / Num. of mol.: 1 / Fragment: Interleukin-1beta
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Homo sapiens x Mus musculus hybrid cell line (mammal)
Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 47.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M TRIS pH 8.5, 2.0M ammonium sulfate

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54178 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 27, 1999 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 3.3→48 Å / Num. obs: 9427 / % possible obs: 97.7 % / Redundancy: 4.1 % / Biso Wilson estimate: 67.08 Å2 / Rmerge(I) obs: 0.159 / Χ2: 0.933 / Net I/σ(I): 5.28 / Num. measured all: 38916
Reflection shellResolution: 3.3→3.42 Å / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1032 / Χ2: 1.02 / % possible all: 86.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-20001.9.1data reduction
SCALEPACK1.6.1data scaling
AMoRE3.4phasing
BUSTER2.11.8 (20-OCT-2021)refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I1B

2i1b


Resolution: 3.3→29.34 Å / Cor.coef. Fo:Fc: 0.868 / Cor.coef. Fo:Fc free: 0.822 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.605
Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2689 969 10.47 %RANDOM
Rwork0.2376 ---
obs0.2409 9257 98.2 %-
Displacement parametersBiso max: 109.58 Å2 / Biso mean: 62.82 Å2 / Biso min: 31.81 Å2
Baniso -1Baniso -2Baniso -3
1-9.6814 Å20 Å25.7981 Å2
2--1.5167 Å20 Å2
3----11.1981 Å2
Refine analyzeLuzzati coordinate error obs: 0.47 Å
Refinement stepCycle: final / Resolution: 3.3→29.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4456 0 0 0 4456
Num. residues----576
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2647SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1387HARMONIC5
X-RAY DIFFRACTIONt_it4563HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion595SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5831SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8926HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg16104HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion4.05
X-RAY DIFFRACTIONt_other_torsion14.57
LS refinement shellResolution: 3.3→3.33 Å / Rfactor Rfree error: 0 / Total num. of bins used: 49
RfactorNum. reflection% reflection
Rfree0.283 23 11.92 %
Rwork0.3096 170 -
all0.3056 193 -
obs--89.86 %
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)
14.12990.3335-0.00470.40710.21240.4285-0.06670.20340.2899-0.0805-0.09070.09210.03820.00910.15740.07150.0331-0.0627-0.22920.06720.07-42.4449-1.736176.3475
26.2589-0.0127-0.2245.2803-0.33735.0348-0.39520.38440.45-0.1690.2982-0.1467-0.25330.67860.0971-0.2614-0.2524-0.08610.12870.12-0.2528-1.70256.644159.5986
35.99670.284-0.44880.3883-0.010.8887-0.54951.01850.3142-0.27460.06420.2260.0443-0.04960.48520.0161-0.1471-0.1199-0.12160.0641-0.0792-50.5663-4.922160.2395
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ H|* }H1 - 218
2X-RAY DIFFRACTION2{ I|* }I3 - 153
3X-RAY DIFFRACTION3{ L|* }L1 - 212

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