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- PDB-8ywr: Crystal structure of the Fab fragment of the anti-IL-6 antibody 6... -

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Basic information

Entry
Database: PDB / ID: 8ywr
TitleCrystal structure of the Fab fragment of the anti-IL-6 antibody 68F2 in complex with a domain-swapped IL-6 dimer
Components
  • Heavy chain of the Fab fragment of anti-IL-6 antibody 68F2
  • Interleukin-6
  • Light chain of the Fab fragment of anti-IL-6 antibody 68F2
KeywordsIMMUNE SYSTEM / interleukin / dimer / swap
Function / homology
Function and homology information


regulation of astrocyte activation / glucagon secretion / positive regulation of interleukin-21 production / regulation of glucagon secretion / hepatic immune response / negative regulation of interleukin-1-mediated signaling pathway / regulation of vascular endothelial growth factor production / negative regulation of primary miRNA processing / germinal center B cell differentiation / interleukin-6 receptor complex ...regulation of astrocyte activation / glucagon secretion / positive regulation of interleukin-21 production / regulation of glucagon secretion / hepatic immune response / negative regulation of interleukin-1-mediated signaling pathway / regulation of vascular endothelial growth factor production / negative regulation of primary miRNA processing / germinal center B cell differentiation / interleukin-6 receptor complex / positive regulation of type B pancreatic cell apoptotic process / positive regulation of apoptotic DNA fragmentation / hepatocyte proliferation / positive regulation of extracellular matrix disassembly / regulation of microglial cell activation / response to peptidoglycan / neutrophil apoptotic process / interleukin-6 receptor binding / positive regulation of B cell activation / positive regulation of receptor signaling pathway via STAT / T-helper 17 cell lineage commitment / inflammatory response to wounding / positive regulation of T-helper 2 cell cytokine production / negative regulation of collagen biosynthetic process / endocrine pancreas development / positive regulation of acute inflammatory response / regulation of neuroinflammatory response / vascular endothelial growth factor production / positive regulation of neuroinflammatory response / T follicular helper cell differentiation / negative regulation of chemokine production / positive regulation of leukocyte chemotaxis / neutrophil mediated immunity / positive regulation of platelet aggregation / cell surface receptor signaling pathway via STAT / positive regulation of cytokine production involved in inflammatory response / negative regulation of bone resorption / positive regulation of leukocyte adhesion to vascular endothelial cell / CD163 mediating an anti-inflammatory response / Interleukin-6 signaling / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of immunoglobulin production / MAPK3 (ERK1) activation / interleukin-6-mediated signaling pathway / negative regulation of fat cell differentiation / maintenance of blood-brain barrier / MAPK1 (ERK2) activation / Interleukin-10 signaling / positive regulation of interleukin-17 production / monocyte chemotaxis / humoral immune response / positive regulation of interleukin-10 production / Transcriptional Regulation by VENTX / negative regulation of lipid storage / positive regulation of vascular endothelial growth factor production / cell surface receptor signaling pathway via JAK-STAT / regulation of angiogenesis / positive regulation of osteoblast differentiation / positive regulation of epithelial to mesenchymal transition / response to glucocorticoid / positive regulation of T cell proliferation / positive regulation of chemokine production / positive regulation of peptidyl-serine phosphorylation / positive regulation of glial cell proliferation / regulation of insulin secretion / positive regulation of DNA-binding transcription factor activity / liver regeneration / positive regulation of interleukin-1 beta production / positive regulation of translation / cytokine activity / acute-phase response / response to activity / positive regulation of interleukin-8 production / positive regulation of receptor signaling pathway via JAK-STAT / Post-translational protein phosphorylation / positive regulation of smooth muscle cell proliferation / growth factor activity / cytokine-mediated signaling pathway / cellular response to virus / positive regulation of miRNA transcription / platelet activation / negative regulation of neurogenesis / positive regulation of interleukin-6 production / cellular response to hydrogen peroxide / neuron cellular homeostasis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / neuron projection development / positive regulation of tumor necrosis factor production / ADORA2B mediated anti-inflammatory cytokines production / glucose homeostasis / cellular response to lipopolysaccharide / Senescence-Associated Secretory Phenotype (SASP) / defense response to Gram-negative bacterium / Interleukin-4 and Interleukin-13 signaling / defense response to virus / positive regulation of MAPK cascade / defense response to Gram-positive bacterium / positive regulation of apoptotic process / inflammatory response / endoplasmic reticulum lumen
Similarity search - Function
Interleukin-6 / Interleukin-6/G-CSF/MGF family / Interleukin-6/GCSF/MGF, conserved site / Interleukin-6 / G-CSF / MGF signature. / Interleukin-6/GCSF/MGF / Interleukin-6 homologues / Four-helical cytokine-like, core
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å
AuthorsBukhdruker, S. / Yudenko, A. / Borshchevskiy, V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Ministry of Education and Science of the Russian Federation075-15-2021-1354 Russian Federation
CitationJournal: Structure / Year: 2025
Title: Structural basis of signaling complex inhibition by IL-6 domain-swapped dimers.
Authors: Yudenko, A. / Bukhdruker, S. / Shishkin, P. / Rodin, S. / Burtseva, A. / Petrov, A. / Pigareva, N. / Sokolov, A. / Zinovev, E. / Eliseev, I. / Remeeva, A. / Marin, E. / Mishin, A. / ...Authors: Yudenko, A. / Bukhdruker, S. / Shishkin, P. / Rodin, S. / Burtseva, A. / Petrov, A. / Pigareva, N. / Sokolov, A. / Zinovev, E. / Eliseev, I. / Remeeva, A. / Marin, E. / Mishin, A. / Gordeliy, V. / Gushchin, I. / Ischenko, A. / Borshchevskiy, V.
History
DepositionMar 31, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 15, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-6
H: Heavy chain of the Fab fragment of anti-IL-6 antibody 68F2
L: Light chain of the Fab fragment of anti-IL-6 antibody 68F2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6355
Polymers66,4423
Non-polymers1922
Water905
1
A: Interleukin-6
H: Heavy chain of the Fab fragment of anti-IL-6 antibody 68F2
L: Light chain of the Fab fragment of anti-IL-6 antibody 68F2
hetero molecules

A: Interleukin-6
H: Heavy chain of the Fab fragment of anti-IL-6 antibody 68F2
L: Light chain of the Fab fragment of anti-IL-6 antibody 68F2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,26910
Polymers132,8856
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)46.550, 92.860, 84.630
Angle α, β, γ (deg.)90.000, 103.930, 90.000
Int Tables number3
Space group name H-MP121
Space group name HallP2y
Symmetry operation#1: x,y,z
#2: -x,y,-z

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Components

#1: Protein Interleukin-6 / IL-6 / B-cell stimulatory factor 2 / BSF-2 / CTL differentiation factor / CDF / Hybridoma growth ...IL-6 / B-cell stimulatory factor 2 / BSF-2 / CTL differentiation factor / CDF / Hybridoma growth factor / Interferon beta-2 / IFN-beta-2


Mass: 19670.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL6, IFNB2 / Production host: Escherichia coli (E. coli) / References: UniProt: P05231
#2: Antibody Heavy chain of the Fab fragment of anti-IL-6 antibody 68F2


Mass: 23822.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Lama glama (llama)
#3: Antibody Light chain of the Fab fragment of anti-IL-6 antibody 68F2


Mass: 22949.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Lama glama (llama)
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.88 Å3/Da / Density % sol: 57.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25% PEG 4K, 0.15 M (NH4)2SO4, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.971 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.971 Å / Relative weight: 1
ReflectionResolution: 2.93→45 Å / Num. obs: 14778 / % possible obs: 97.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 29.73 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 7.5
Reflection shellResolution: 2.93→3 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 969 / % possible all: 88.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
BUSTERrefinement
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZS7

4zs7


Resolution: 2.93→41.07 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 24.0983
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2556 1490 10.09 %
Rwork0.2142 13284 -
obs0.2183 14774 97.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.51 Å2
Refinement stepCycle: LAST / Resolution: 2.93→41.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4268 0 10 5 4283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00194371
X-RAY DIFFRACTIONf_angle_d0.5115961
X-RAY DIFFRACTIONf_chiral_restr0.0389689
X-RAY DIFFRACTIONf_plane_restr0.0042757
X-RAY DIFFRACTIONf_dihedral_angle_d10.80481546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.93-3.030.34231050.30041098X-RAY DIFFRACTION90.04
3.03-3.140.31921490.27421225X-RAY DIFFRACTION98.42
3.14-3.260.28641360.26041185X-RAY DIFFRACTION98.44
3.26-3.410.31721490.25031187X-RAY DIFFRACTION98.31
3.41-3.590.26081390.24471235X-RAY DIFFRACTION98.28
3.59-3.810.25531560.21921185X-RAY DIFFRACTION99.11
3.81-4.110.26421260.20161227X-RAY DIFFRACTION98.69
4.11-4.520.23281310.17011221X-RAY DIFFRACTION98.76
4.52-5.170.19881290.1671232X-RAY DIFFRACTION98.69
5.17-6.510.24881330.18941233X-RAY DIFFRACTION99.27
6.52-41.070.19161370.1861256X-RAY DIFFRACTION98.58
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)
10.00897864348444-0.00967732495044-0.009890218632820.0367222523298-0.009150291256730.01851303702270.01727212791120.02317376929110.0278505751043-0.0140627680080.01934341519860.0365807065984-0.0444795340949-0.02883448387780.05996270306490.1402695325010.00266866153110.02495125293530.04997375686840.03655719727110.20640683524128.308140409560.903227905211.885165451
20.03918395399470.0107941156795-0.06965853562350.0760354428359-0.04761841014540.1288045244640.0205278788360.05631260589340.0017208147577-0.03398677060240.001814772746490.05500449428010.0228505736165-0.108996237560.03286242720770.07319333208010.0312063122828-0.005239484198540.08615839189750.001813530741710.03970777208269.7008653316325.63003566118.7188981965
30.0831225890391-0.0545137741802-0.02970876317070.0801345992519-0.0375825655430.06327235882990.04420726230510.0429103147169-0.0453710571712-0.0671346334278-0.03579280073820.02249595328460.00759109353215-0.04991129432410.02608781346950.0608202359529-0.0329978522572-0.01975396538830.0752928834738-0.01527155826480.049869944637420.009844737512.967825411426.1818809313
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 23 through 184)AA23 - 1841 - 136
22(chain 'H' and resid 1 through 222)HB1 - 2221 - 218
33(chain 'L' and resid 3 through 212)LD3 - 2121 - 210

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