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- PDB-4ni9: Crystal structure of human interleukin 6 in complex with a modifi... -

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Basic information

Entry
Database: PDB / ID: 4ni9
TitleCrystal structure of human interleukin 6 in complex with a modified nucleotide aptamer (SOMAMER SL1025), FORM 2
Components
  • Interleukin-6Interleukin 6
  • SOMAmer SL1025
KeywordsCYTOKINE/DNA / SELEX / SOMAMER / CYTOKINE-DNA complex
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 / 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 / molecular replacement / Resolution: 2.55 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 1.4Apr 3, 2024Group: 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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: SOMAmer SL1025
A: Interleukin-6
C: Interleukin-6
D: SOMAmer SL1025
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1266
Polymers65,0804
Non-polymers462
Water39622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.020, 69.020, 108.470
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A14 - 184
2116C14 - 184
1126B1 - 32
2126D1 - 32

NCS ensembles :
ID
1
2
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: DNA chain SOMAmer SL1025


Mass: 11402.860 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: 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: 21137.156 Da / Num. of mol.: 2
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
#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 / Water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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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, 90 mM Magnesium Sulfate, 90 mM Sodium Acetate (pH 5.5) 100 mM LiCl, 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
ReflectionResolution: 2.55→50 Å / Num. obs: 18817 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 67.12 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 22.61
Reflection shellResolution: 2.55→2.62 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: molecular replacement
Starting model: first crystal form

Resolution: 2.55→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / SU B: 24.026 / SU ML: 0.221 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.239 963 5.1 %RANDOM
Rwork0.186 ---
obs0.189 18789 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.29 Å2
Baniso -1Baniso -2Baniso -3
1-7.36 Å20 Å20 Å2
2--7.36 Å20 Å2
3----14.72 Å2
Refinement stepCycle: LAST / Resolution: 2.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2231 1538 2 22 3793
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213983
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8452.4465659
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7985286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.11824.1392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.89715394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5151515
X-RAY DIFFRACTIONr_chiral_restr0.1240.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022579
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_it0.3721.51456
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.69522310
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.94132527
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.4934.53349
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1073loose positional0.465
22C769loose positional0.415
11B1073loose thermal1.3910
22D769loose thermal2.7410
LS refinement shellResolution: 2.55→2.62 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 69 -
Rwork0.252 1291 -
obs--97.7 %
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)
13.0944-0.4514-1.27872.52980.48034.2602-0.04320.0969-0.109-0.1613-0.12150.13120.1168-0.38450.16470.1244-0.02680.01130.0426-0.0220.1489-2.891221.69398.0848
21.78561.914-0.09132.3282-0.65741.66280.0544-0.129-0.3909-0.184-0.2326-0.46720.32770.31220.17820.20060.05810.06420.06950.0320.293313.950917.3956.3367
32.4488-0.24940.70571.8553-0.63794.71160.0053-0.20530.17940.1709-0.1364-0.076-0.3869-0.11480.13120.1221-0.0551-0.07650.05480.02720.185413.374951.9414.2202
41.17591.2186-1.57783.5182-1.71651.8863-0.039-0.1656-0.1495-0.0809-0.1489-0.53940.03030.18930.1880.0543-0.0434-0.0330.14190.11630.275326.511139.00816.0717
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 208
2X-RAY DIFFRACTION2B1 - 205
3X-RAY DIFFRACTION3C16 - 205
4X-RAY DIFFRACTION4D1 - 104

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