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- PDB-7nxz: Synthetic glycoform of Human Interleukin 6 -

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Basic information

Entry
Database: PDB / ID: 7nxz
TitleSynthetic glycoform of Human Interleukin 6
ComponentsInterleukin-6Interleukin 6
KeywordsCYTOKINE / glycosylated interleukin-6
Function / homology
Function and homology information


positive regulation of interleukin-21 production / regulation of astrocyte activation / glucagon secretion / negative regulation of interleukin-1-mediated signaling pathway / hepatic immune response / regulation of glucagon secretion / 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 / negative regulation of interleukin-1-mediated signaling pathway / hepatic immune response / regulation of glucagon secretion / 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 leukocyte chemotaxis / positive regulation of platelet aggregation / neutrophil mediated immunity / positive regulation of cytokine production involved in inflammatory response / negative regulation of bone resorption / CD163 mediating an anti-inflammatory response / positive regulation of leukocyte adhesion to vascular endothelial cell / negative regulation of fat cell differentiation / maintenance of blood-brain barrier / Interleukin-6 signaling / interleukin-6-mediated signaling pathway / positive regulation of interleukin-17 production / MAPK3 (ERK1) activation / Interleukin-10 signaling / monocyte chemotaxis / MAPK1 (ERK2) activation / positive regulation of interleukin-10 production / regulation of insulin secretion / humoral immune response / negative regulation of lipid storage / positive regulation of immunoglobulin production / Transcriptional Regulation by VENTX / positive regulation of vascular endothelial growth factor production / positive regulation of epithelial to mesenchymal transition / positive regulation of osteoblast differentiation / regulation of angiogenesis / positive regulation of chemokine production / positive regulation of glial cell proliferation / response to glucocorticoid / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of T cell proliferation / positive regulation of translation / response to activity / positive regulation of interleukin-1 beta production / cytokine activity / liver regeneration / positive regulation of interleukin-8 production / Post-translational protein phosphorylation / acute-phase response / positive regulation of smooth muscle cell proliferation / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / cellular response to hydrogen peroxide / platelet activation / cellular response to virus / ADORA2B mediated anti-inflammatory cytokines production / negative regulation of neurogenesis / positive regulation of interleukin-6 production / neuron cellular homeostasis / cytokine-mediated signaling pathway / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / neuron projection development / positive regulation of DNA-binding transcription factor activity / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of tumor necrosis factor production / glucose homeostasis / positive regulation of peptidyl-serine phosphorylation / Senescence-Associated Secretory Phenotype (SASP) / defense response to virus / Interleukin-4 and Interleukin-13 signaling / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / positive regulation of MAPK cascade / defense response to Gram-positive bacterium / inflammatory response / positive regulation of apoptotic process / endoplasmic reticulum lumen / negative regulation of cell population proliferation / 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 / Four-helical cytokine-like, core
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.998 Å
AuthorsWeyand, M. / Unverzagt, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)DFG UN63/5-1 + SPPP1368 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Natural Glycoforms of Human Interleukin 6 Show Atypical Plasma Clearance.
Authors: Reif, A. / Lam, K. / Weidler, S. / Lott, M. / Boos, I. / Lokau, J. / Bretscher, C. / Monnich, M. / Perkams, L. / Schmalzlein, M. / Graf, C. / Fischer, J.P. / Lechner, C. / Hallstein, K. / ...Authors: Reif, A. / Lam, K. / Weidler, S. / Lott, M. / Boos, I. / Lokau, J. / Bretscher, C. / Monnich, M. / Perkams, L. / Schmalzlein, M. / Graf, C. / Fischer, J.P. / Lechner, C. / Hallstein, K. / Becker, S. / Weyand, M. / Steegborn, C. / Schultheiss, G. / Rose-John, S. / Garbers, C. / Unverzagt, C.
History
DepositionMar 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Interleukin-6


Theoretical massNumber of molelcules
Total (without water)20,8201
Polymers20,8201
Non-polymers00
Water1,49583
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9140 Å2
Unit cell
Length a, b, c (Å)72.100, 129.020, 50.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11AAA-282-

HOH

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Components

#1: Protein Interleukin-6 / 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: 20819.730 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P05231
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsThe conflict is caused by the synthesis of the protein.

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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: 2.93 Å3/Da / Density % sol: 58.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2-0.25 M sodium malonate, pH 7.0 and 18-22% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918007 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918007 Å / Relative weight: 1
ReflectionResolution: 1.998→50 Å / Num. obs: 16028 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.22 % / Biso Wilson estimate: 46.024 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.084 / Net I/σ(I): 10.62
Reflection shellResolution: 1.998→2.12 Å / Redundancy: 3.38 % / Rmerge(I) obs: 1.412 / Mean I/σ(I) obs: 0.72 / Num. unique obs: 2465 / CC1/2: 0.434 / Rrim(I) all: 1.67 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
pointlessdata scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1alu

1alu


Resolution: 1.998→39.569 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 11.959 / SU ML: 0.152 / Cross valid method: FREE R-VALUE / ESU R: 0.154 / ESU R Free: 0.152
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2526 802 5.004 %
Rwork0.2063 15226 -
all0.209 --
obs-16028 98.622 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 52.097 Å2
Baniso -1Baniso -2Baniso -3
1-2.71 Å20 Å2-0 Å2
2---1.547 Å20 Å2
3----1.163 Å2
Refinement stepCycle: LAST / Resolution: 1.998→39.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1233 0 0 83 1316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131263
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171215
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.651711
X-RAY DIFFRACTIONr_angle_other_deg1.3511.5732787
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3785161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.38624.09861
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.33715228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.345156
X-RAY DIFFRACTIONr_chiral_restr0.0770.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021435
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02281
X-RAY DIFFRACTIONr_nbd_refined0.2070.2258
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1730.21081
X-RAY DIFFRACTIONr_nbtor_refined0.1620.2629
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2647
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.263
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2020.212
X-RAY DIFFRACTIONr_nbd_other0.230.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1330.210
X-RAY DIFFRACTIONr_mcbond_it2.1133.528638
X-RAY DIFFRACTIONr_mcbond_other2.0713.524637
X-RAY DIFFRACTIONr_mcangle_it3.2475.264795
X-RAY DIFFRACTIONr_mcangle_other3.2645.267796
X-RAY DIFFRACTIONr_scbond_it2.7493.693625
X-RAY DIFFRACTIONr_scbond_other2.7453.69625
X-RAY DIFFRACTIONr_scangle_it4.2145.452914
X-RAY DIFFRACTIONr_scangle_other4.2145.449914
X-RAY DIFFRACTIONr_lrange_it6.8941.9591408
X-RAY DIFFRACTIONr_lrange_other6.70341.641395
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.998-2.0490.469530.5410070.53711460.0570.07792.49560.532
2.049-2.1050.446580.45810910.45711670.5230.46698.45760.46
2.105-2.1660.381550.32810500.33111100.6540.70599.54960.326
2.166-2.2330.339550.29810470.311070.7630.81399.54830.284
2.233-2.3060.334520.2489930.25210510.8130.86899.42910.227
2.306-2.3860.273510.2519660.25210300.8750.8798.73790.228
2.386-2.4760.212490.2159310.2159860.9040.90799.39150.19
2.476-2.5770.234470.218880.2129420.9290.92399.25690.179
2.577-2.6910.259450.1988640.2019200.9170.93598.80440.168
2.691-2.8210.256440.1848280.1888770.9350.94399.42990.159
2.821-2.9730.256410.1937900.1968390.9170.94399.04650.17
2.973-3.1520.18400.1957540.1948010.9440.94599.12610.175
3.152-3.3680.279370.1927030.1967450.9130.94299.32890.175
3.368-3.6360.273350.1986680.2017080.9270.94699.29380.18
3.636-3.980.278320.1866080.1916440.920.95199.37890.175
3.98-4.4440.18300.1575570.1585920.9520.96899.15540.15
4.444-5.1210.157260.1414980.1425280.9720.97599.24240.138
5.121-6.2460.313230.2474390.254630.9160.94899.7840.239
6.246-8.7240.261180.2153360.2173610.930.94998.06090.218
8.724-39.5690.232110.1762080.1792330.9510.9793.99140.208
Refinement TLS params.Method: refined / Origin x: -17.0712 Å / Origin y: -19.2571 Å / Origin z: 5.6967 Å
111213212223313233
T0.0422 Å2-0.0184 Å20.0567 Å2-0.0643 Å2-0.0261 Å2--0.0998 Å2
L3.8927 °21.9672 °21.7233 °2-4.9849 °21.1639 °2--4.2226 °2
S0.0925 Å °-0.2117 Å °0.0997 Å °0.0032 Å °-0.2849 Å °0.274 Å °0.1959 Å °-0.4986 Å °0.1924 Å °
Refinement TLS groupSelection: ALL

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