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- PDB-4ni7: Crystal structure of human interleukin 6 in complex with a modifi... -

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Basic information

Entry
Database: PDB / ID: 4ni7
TitleCrystal structure of human interleukin 6 in complex with a modified nucleotide aptamer (SOMAMER SL1025)
Components
  • Interleukin-6
  • SOMAmer SL1025
KeywordsCYTOKINE/DNA / Interleukin-6 / CYTOKINE-DNA complex
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 primary miRNA processing / regulation of vascular endothelial growth factor production / negative regulation of interleukin-1-mediated signaling pathway / regulation of microglial cell activation / 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 primary miRNA processing / regulation of vascular endothelial growth factor production / negative regulation of interleukin-1-mediated signaling pathway / regulation of microglial cell activation / interleukin-6 receptor complex / positive regulation of apoptotic DNA fragmentation / positive regulation of type B pancreatic cell apoptotic process / hepatocyte proliferation / response to peptidoglycan / neutrophil apoptotic process / germinal center B cell differentiation / positive regulation of extracellular matrix disassembly / 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 / endocrine pancreas development / negative regulation of collagen biosynthetic process / regulation of neuroinflammatory response / positive regulation of acute inflammatory response / vascular endothelial growth factor production / negative regulation of chemokine production / T follicular helper cell differentiation / 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 / cell surface receptor signaling pathway via STAT / positive regulation of leukocyte adhesion to vascular endothelial cell / negative regulation of bone resorption / CD163 mediating an anti-inflammatory response / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of immunoglobulin production / Interleukin-6 signaling / interleukin-6-mediated signaling pathway / negative regulation of fat cell differentiation / MAPK3 (ERK1) activation / maintenance of blood-brain barrier / MAPK1 (ERK2) activation / Interleukin-10 signaling / monocyte chemotaxis / positive regulation of interleukin-17 production / humoral immune response / positive regulation of vascular endothelial growth factor production / Transcriptional Regulation by VENTX / positive regulation of interleukin-10 production / negative regulation of lipid storage / positive regulation of glial cell proliferation / positive regulation of peptidyl-serine phosphorylation / regulation of angiogenesis / cell surface receptor signaling pathway via JAK-STAT / positive regulation of osteoblast differentiation / positive regulation of epithelial to mesenchymal transition / positive regulation of DNA-binding transcription factor activity / positive regulation of chemokine production / positive regulation of T cell proliferation / liver regeneration / positive regulation of smooth muscle cell proliferation / regulation of insulin secretion / response to glucocorticoid / positive regulation of translation / positive regulation of interleukin-1 beta production / cytokine activity / response to activity / acute-phase response / positive regulation of interleukin-8 production / positive regulation of receptor signaling pathway via JAK-STAT / Post-translational protein phosphorylation / growth factor activity / neuron cellular homeostasis / cellular response to virus / platelet activation / negative regulation of neurogenesis / positive regulation of interleukin-6 production / positive regulation of miRNA transcription / cellular response to hydrogen peroxide / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cytokine-mediated signaling pathway / 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) / 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 / positive regulation of apoptotic process / endoplasmic reticulum lumen / inflammatory response
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; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Interleukin-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD WITH molecular replacement / Resolution: 2.4 Å
AuthorsDavies, D. / Edwards, T. / Gelinas, A. / Jarvis, T. / Clifton, M.C.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Crystal structure of interleukin-6 in complex with a modified nucleic Acid ligand.
Authors: Gelinas, A.D. / Davies, D.R. / Edwards, T.E. / Rohloff, J.C. / Carter, J.D. / Zhang, C. / Gupta, S. / Ishikawa, Y. / Hirota, M. / Nakaishi, Y. / Jarvis, T.C. / Janjic, N.
History
DepositionNov 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Apr 9, 2014Group: Database references
Revision 1.3Jun 1, 2016Group: Structure summary
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 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
A: Interleukin-6
B: SOMAmer SL1025
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5864
Polymers32,5402
Non-polymers462
Water52229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.230, 50.230, 103.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
DetailsBIOMOLECULE: NULL SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. REMARK: MONOMER

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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
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: DNA chain SOMAmer SL1025


Mass: 11402.860 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
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: 2.31 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 31% PEG 3350, 180 mM LiNO3, 100 mM Sodium Acetate (pH 5.5), 2.5% Hexamine Cobalt Chloride, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.03318 / Wavelength: 1.03318 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionHighest resolution: 2.4 Å / Num. obs: 11411 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 65.61 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 26.89
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD WITH molecular replacement
Starting model: PDB ENTRY 1IL6

1il6


Resolution: 2.4→43.5 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.916 / SU B: 14.87 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.26 570 5 %RANDOM
Rwork0.222 ---
obs0.224 11384 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.79 Å2
Baniso -1Baniso -2Baniso -3
1-11.15 Å20 Å20 Å2
2--11.15 Å20 Å2
3----22.3 Å2
Refinement stepCycle: LAST / Resolution: 2.4→43.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1130 729 2 29 1890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211959
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9222.4312779
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9155148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.30824.18643
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.02115195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.769157
X-RAY DIFFRACTIONr_chiral_restr0.1280.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021278
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6991.5753
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.28621193
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6131206
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4984.51586
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 35 -
Rwork0.28 777 -
obs--99.15 %
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)
12.6899-0.5615-2.16811.33432.00444.59290.07030.2612-0.05750.1967-0.18130.15280.0076-0.18670.1110.06780.01850.07720.1090.0070.2194-6.686412.17358.9461
21.89521.5758-1.61582.5957-1.77063.1618-0.11210.0587-0.15520.10990.0755-0.00570.1480.35980.03650.04220.03290.02170.13380.01640.17779.92794.52326.6574
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 218
2X-RAY DIFFRACTION2B1 - 211

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