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- PDB-4o9h: Structure of Interleukin-6 in complex with a Camelid Fab fragment -

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Basic information

Entry
Database: PDB / ID: 4o9h
TitleStructure of Interleukin-6 in complex with a Camelid Fab fragment
Components
  • Heavy Chain of the Camelid Fab fragment 61H7
  • Interleukin-6
  • Light Chain of the Camelid Fab fragment 61H7
KeywordsIMMUNE SYSTEM / IL6: all alpha protein / Fab: all beta protein
Function / homology
Function and homology information


positive regulation of interleukin-21 production / regulation of astrocyte activation / glucagon secretion / regulation of glucagon secretion / negative regulation of interleukin-1-mediated signaling pathway / hepatic immune response / regulation of vascular endothelial growth factor production / negative regulation of primary miRNA processing / T follicular helper cell differentiation / germinal center B cell differentiation ...positive regulation of interleukin-21 production / regulation of astrocyte activation / glucagon secretion / regulation of glucagon secretion / negative regulation of interleukin-1-mediated signaling pathway / hepatic immune response / regulation of vascular endothelial growth factor production / negative regulation of primary miRNA processing / T follicular helper cell differentiation / germinal center B cell differentiation / regulation of microglial cell activation / interleukin-6 receptor complex / positive regulation of extracellular matrix disassembly / positive regulation of receptor signaling pathway via STAT / positive regulation of type B pancreatic cell apoptotic process / positive regulation of apoptotic DNA fragmentation / response to peptidoglycan / hepatocyte proliferation / neutrophil apoptotic process / interleukin-6 receptor binding / negative regulation of collagen biosynthetic process / inflammatory response to wounding / T-helper 17 cell lineage commitment / positive regulation of T-helper 2 cell cytokine production / positive regulation of B cell activation / endocrine pancreas development / positive regulation of acute inflammatory response / regulation of neuroinflammatory response / vascular endothelial growth factor production / negative regulation of chemokine production / positive regulation of neuroinflammatory response / positive regulation of platelet aggregation / neutrophil mediated immunity / positive regulation of cytokine production involved in inflammatory response / negative regulation of bone resorption / positive regulation of leukocyte chemotaxis / positive regulation of leukocyte adhesion to vascular endothelial cell / CD163 mediating an anti-inflammatory response / positive regulation of immunoglobulin production / maintenance of blood-brain barrier / interleukin-6-mediated signaling pathway / Interleukin-6 signaling / negative regulation of fat cell differentiation / MAPK3 (ERK1) activation / positive regulation of interleukin-17 production / Interleukin-10 signaling / MAPK1 (ERK2) activation / monocyte chemotaxis / regulation of insulin secretion / positive regulation of interleukin-10 production / humoral immune response / negative regulation of lipid storage / Transcriptional Regulation by VENTX / positive regulation of vascular endothelial growth factor production / regulation of angiogenesis / positive regulation of osteoblast differentiation / positive regulation of epithelial to mesenchymal transition / positive regulation of chemokine production / positive regulation of T cell proliferation / response to glucocorticoid / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of glial cell proliferation / positive regulation of interleukin-1 beta production / response to activity / cytokine activity / acute-phase response / positive regulation of interleukin-8 production / positive regulation of translation / liver regeneration / Post-translational protein phosphorylation / positive regulation of smooth muscle cell proliferation / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / platelet activation / cellular response to virus / cytokine-mediated signaling pathway / positive regulation of DNA-binding transcription factor activity / negative regulation of neurogenesis / cellular response to hydrogen peroxide / neuron cellular homeostasis / ADORA2B mediated anti-inflammatory cytokines production / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of interleukin-6 production / neuron projection development / positive regulation of tumor necrosis factor production / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of peptidyl-serine phosphorylation / glucose homeostasis / Senescence-Associated Secretory Phenotype (SASP) / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / defense response to Gram-negative bacterium / defense response to virus / positive regulation of MAPK cascade / defense response to Gram-positive bacterium / inflammatory response / positive regulation of apoptotic process / negative regulation of cell population proliferation / endoplasmic reticulum lumen / positive regulation of cell population proliferation
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 / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulins ...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 / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Llama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsKlarenbeek, A. / Blanchetot, C. / Schragel, G. / Sadi, A.S. / Ongenae, N. / Hemrika, W. / Wijdenes, J. / Spinelli, S. / Desmyter, A. / Cambillau, C. ...Klarenbeek, A. / Blanchetot, C. / Schragel, G. / Sadi, A.S. / Ongenae, N. / Hemrika, W. / Wijdenes, J. / Spinelli, S. / Desmyter, A. / Cambillau, C. / Hultberg, A. / Kretz-rommel, A. / Dreier, T. / De haard, H.J.W. / Roovers, R.C.
CitationJournal: To be Published
Title: Combining residues of naturally-occurring Camelid somatic affinity variants yields ultra-potent human therapeutic IL-6 antibodies
Authors: Klarenbeek, A. / Blanchetot, C. / Schragel, G. / Sadi, A.S. / Ongenae, N. / Hemrika, W. / Wijdenes, J. / Spinelli, S. / Desmyter, A. / Cambillau, C. / Hultberg, A. / Kretz-Rommel, A. / ...Authors: Klarenbeek, A. / Blanchetot, C. / Schragel, G. / Sadi, A.S. / Ongenae, N. / Hemrika, W. / Wijdenes, J. / Spinelli, S. / Desmyter, A. / Cambillau, C. / Hultberg, A. / Kretz-Rommel, A. / Dreier, T. / De haard, H.J.W. / Roovers, R.C.
History
DepositionJan 2, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interleukin-6
H: Heavy Chain of the Camelid Fab fragment 61H7
L: Light Chain of the Camelid Fab fragment 61H7


Theoretical massNumber of molelcules
Total (without water)67,1713
Polymers67,1713
Non-polymers00
Water5,008278
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.210, 47.470, 148.320
Angle α, β, γ (deg.)90.00, 97.00, 90.00
Int Tables number5
Space group name H-MC121

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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: 21137.156 Da / Num. of mol.: 1 / Fragment: UNP residues 28-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL6, IFNB2 / Production host: mammalia (mammals) / References: UniProt: P05231
#2: Antibody Heavy Chain of the Camelid Fab fragment 61H7


Mass: 23504.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Llama glama (llama) / Production host: mammalia (mammals)
#3: Antibody Light Chain of the Camelid Fab fragment 61H7


Mass: 22529.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Llama glama (llama) / Production host: mammalia (mammals)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsIN THIS STRUCTURE, THE SEQUENCES OF THE H AND L CHAINS WERE NOT AVAILABLE AT THE UNIPROT ...IN THIS STRUCTURE, THE SEQUENCES OF THE H AND L CHAINS WERE NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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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: 2.81 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 277 K / pH: 5.5
Details: 2M Ammonium sulfate, 0.15M Na citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 10, 2010
Details: KIRKPATRICK-BAEZ PAIR OF BI- MORPH MIRRORS PLUS CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL
RadiationMonochromator: KIRKPATRICK-BAEZ PAIR OF BI- MORPH MIRRORS PLUS CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.42→45 Å / Num. obs: 28984 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 54.17 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.2
Reflection shellResolution: 2.42→2.48 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
BUSTER2.11.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→38.65 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.862 / SU R Cruickshank DPI: 0.334 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1446 5 %RANDOM
Rwork0.216 ---
obs0.217 28918 99.7 %-
all-28918 --
Displacement parametersBiso mean: 65.51 Å2
Baniso -1Baniso -2Baniso -3
1-12.9085 Å20 Å2-4.5705 Å2
2---30.2894 Å20 Å2
3---17.3809 Å2
Refine analyzeLuzzati coordinate error obs: 0.396 Å
Refinement stepCycle: LAST / Resolution: 2.42→38.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4207 0 0 278 4485
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094301HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.315853HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1412SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes91HARMONIC2
X-RAY DIFFRACTIONt_gen_planes625HARMONIC5
X-RAY DIFFRACTIONt_it4301HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.28
X-RAY DIFFRACTIONt_other_torsion21.19
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion0582SEMIHARMONIC5
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_contact04822SEMIHARMONIC4
LS refinement shellResolution: 2.42→2.5 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.278 140 5 %
Rwork0.2595 2662 -
all0.2604 2802 -
obs--99.7 %
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)
10.2592-2.03090.61820.0859-1.10310.7313-0.0086-0.01270.0097-0.02090.025-0.003-0.0031-0.0311-0.01640.00360.0817-0.0189-0.00030.03810.0008-30.86623.451115.8987
20.3964-0.57860.08680.5120.21330.3308-0.0102-0.01240.0118-0.01690.01980.01510.0098-0.0209-0.00960.00170.0517-0.0888-0.03770.06020.017-36.436424.37888.792
30.6221-0.5961-0.21310.1626-0.8281.26010.0013-0.0467-0.00120.0123-0.0131-0.00220.0009-0.02430.0118-0.00310.1193-0.01160.05240.0781-0.0716-24.638610.985442.5663
40.29030.2283-0.69560-0.74111.1365-0.00050.0040.01710.00230.0141-0.0139-0.0073-0.0091-0.0136-0.04210.0170.03490.05330.0409-0.0254-4.55541.706364.4494
50.7425-0.9301-0.35560.376-1.24380.3969-0.0017-0.0181-0.0036-0.0147-0.0152-0.00970.03620.01380.01690.00230.14260.0232-0.03730.08570.0303-8.23488.203728.568
61.4278-1.6233-0.44380-0.51010.0001-0.00090.0042-0.01510.00150.0041-0.00380.01110.0023-0.0033-0.03240.05080.05190.04640.0346-0.02086.9903-9.46659.0396
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|19 - A|92 }
2X-RAY DIFFRACTION2{ A|93 - A|184 }
3X-RAY DIFFRACTION3{ H|1 - H|111 }
4X-RAY DIFFRACTION4{ H|112 - H|220 }
5X-RAY DIFFRACTION5{ L|1 - L|110 }
6X-RAY DIFFRACTION6{ L|111 - L|211 }

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