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- PDB-1p9m: Crystal structure of the hexameric human IL-6/IL-6 alpha receptor... -

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Basic information

Entry
Database: PDB / ID: 1p9m
TitleCrystal structure of the hexameric human IL-6/IL-6 alpha receptor/gp130 complex
Components
  • Interleukin-6
  • Interleukin-6 receptor alpha chain
  • Interleukin-6 receptor beta chain
Keywordssignaling protein/cytokine / Ig domain / four helix bundle / cytokine / interleukin-6 / gp130 / signaling protein-cytokine COMPLEX
Function / homology
Function and homology information


ciliary neurotrophic factor binding / regulation of astrocyte activation / glucagon secretion / positive regulation of interleukin-21 production / interleukin-6 receptor activity / interleukin-6 binding / regulation of glucagon secretion / hepatic immune response / oncostatin-M-mediated signaling pathway / negative regulation of interleukin-1-mediated signaling pathway ...ciliary neurotrophic factor binding / regulation of astrocyte activation / glucagon secretion / positive regulation of interleukin-21 production / interleukin-6 receptor activity / interleukin-6 binding / regulation of glucagon secretion / hepatic immune response / oncostatin-M-mediated signaling pathway / negative regulation of interleukin-1-mediated signaling pathway / interleukin-27 receptor activity / ciliary neurotrophic factor receptor activity / leukemia inhibitory factor signaling pathway / regulation of vascular endothelial growth factor production / negative regulation of primary miRNA processing / negative regulation of interleukin-6-mediated signaling pathway / oncostatin-M receptor complex / : / ciliary neurotrophic factor receptor binding / T follicular helper cell differentiation / interleukin-11 receptor activity / interleukin-11 binding / ciliary neurotrophic factor-mediated signaling pathway / germinal center B cell differentiation / ciliary neurotrophic factor receptor complex / interleukin-27-mediated signaling pathway / interleukin-6 receptor complex / positive regulation of extracellular matrix disassembly / positive regulation of receptor signaling pathway via STAT / positive regulation of apoptotic DNA fragmentation / positive regulation of type B pancreatic cell apoptotic process / response to peptidoglycan / regulation of microglial cell activation / hepatocyte proliferation / neutrophil apoptotic process / cell surface receptor signaling pathway via STAT / interleukin-6 receptor binding / negative regulation of collagen biosynthetic process / endocrine pancreas development / interleukin-11-mediated signaling pathway / positive regulation of B cell activation / inflammatory response to wounding / T-helper 17 cell lineage commitment / positive regulation of T-helper 2 cell cytokine production / positive regulation of adaptive immune response / negative regulation of interleukin-8 production / positive regulation of acute inflammatory response / regulation of neuroinflammatory response / positive regulation of glomerular mesangial cell proliferation / vascular endothelial growth factor production / negative regulation of chemokine production / positive regulation of astrocyte differentiation / positive regulation of neuroinflammatory response / positive regulation of leukocyte chemotaxis / intestinal epithelial cell development / neutrophil mediated immunity / positive regulation of platelet aggregation / positive regulation of cytokine production involved in inflammatory response / Interleukin-27 signaling / IL-6-type cytokine receptor ligand interactions / Interleukin-35 Signalling / cytokine receptor activity / negative regulation of bone resorption / positive regulation of leukocyte adhesion to vascular endothelial cell / CD163 mediating an anti-inflammatory response / positive regulation of immunoglobulin production / glycogen metabolic process / Interleukin-6 signaling / maintenance of blood-brain barrier / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / protein tyrosine kinase activator activity / negative regulation of fat cell differentiation / positive regulation of cardiac muscle hypertrophy / MAPK3 (ERK1) activation / monocyte chemotaxis / cytokine binding / growth factor binding / positive regulation of interleukin-17 production / Interleukin-10 signaling / MAPK1 (ERK2) activation / 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 / coreceptor activity / positive regulation of epithelial to mesenchymal transition / positive regulation of T cell proliferation / response to glucocorticoid / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of chemokine production / positive regulation of glial cell proliferation / extrinsic apoptotic signaling pathway / regulation of insulin secretion / response to cytokine / positive regulation of interleukin-1 beta production / positive regulation of translation
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 / Type I cytokine receptor, cytokine-binding domain / Interleukin-6 receptor alpha chain, binding / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. ...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 / Type I cytokine receptor, cytokine-binding domain / Interleukin-6 receptor alpha chain, binding / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. / Immunoglobulin C2-set-like, ligand-binding / Ig-like C2-type domain / Long hematopoietin receptor, Gp130 family 2, conserved site / Long hematopoietin receptor, gp130 family signature. / : / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulin / Immunoglobulin domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Interleukin-6 / Interleukin-6 receptor subunit alpha / Interleukin-6 receptor subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.65 Å
AuthorsBoulanger, M.J. / Chow, D.C. / Brevnova, E.E. / Garcia, K.C.
CitationJournal: Science / Year: 2003
Title: Hexameric Structure and Assembly of the Interleukin-6/IL-6 alpha-Receptor/gp130 Complex
Authors: Boulanger, M.J. / Chow, D.C. / Brevnova, E.E. / Garcia, K.C.
History
DepositionMay 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-6 receptor beta chain
B: Interleukin-6
C: Interleukin-6 receptor alpha chain


Theoretical massNumber of molelcules
Total (without water)78,2533
Polymers78,2533
Non-polymers00
Water00
1
A: Interleukin-6 receptor beta chain
B: Interleukin-6
C: Interleukin-6 receptor alpha chain

A: Interleukin-6 receptor beta chain
B: Interleukin-6
C: Interleukin-6 receptor alpha chain


Theoretical massNumber of molelcules
Total (without water)156,5076
Polymers156,5076
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_455y-2/3,x+2/3,-z+2/31
Buried area13030 Å2
ΔGint-67 kcal/mol
Surface area65930 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)279.800, 279.800, 96.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Interleukin-6 receptor beta chain / IL-6R-beta / Interleukin 6 signal transducer / Membrane glycoprotein 130 / GP130 / Oncostatin M ...IL-6R-beta / Interleukin 6 signal transducer / Membrane glycoprotein 130 / GP130 / Oncostatin M receptor / CDw130 / CD130 antigen


Mass: 34099.535 Da / Num. of mol.: 1 / Fragment: extracellular domains D1 - D3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL6ST / Plasmid: pACGP67A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P40189
#2: Protein Interleukin-6 / IL-6 / B-cell stimulatory factor 2 / BSF-2 / Interferon beta-2 / Hybridoma growth factor


Mass: 21103.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL6 OR IFNB2 / Plasmid: pACGP67A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P05231
#3: Protein Interleukin-6 receptor alpha chain / IL-6R-alpha / IL-6R 1 / CD126 antigen


Mass: 23050.865 Da / Num. of mol.: 1 / Fragment: extracellular domains D2 - D3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL6R / Plasmid: pACGP67A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08887

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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: 4.65 Å3/Da / Density % sol: 73.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Sodium formate, Sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
22.0 Msodium formate1reservoirpH4.5
30.1 Msodium acetate1reservoirpH4.5

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 5, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.65→50 Å / Num. all: 16144 / Num. obs: 15861 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.065 / Net I/σ(I): 13
Reflection shellResolution: 3.65→3.84 Å / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 1.85 / % possible all: 98.1
Reflection
*PLUS
Num. obs: 16144 / Num. measured all: 120957
Reflection shell
*PLUS
% possible obs: 98.1 % / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ALU

1alu


Resolution: 3.65→19.99 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.334 1237 7.8 %RANDOM
Rwork0.282 ---
obs0.282 15767 98.2 %-
all-16061 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.115109 e/Å3
Displacement parametersBiso mean: 117.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.77 Å230.66 Å20 Å2
2--2.77 Å20 Å2
3----5.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.65 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a1.29 Å0.94 Å
Refinement stepCycle: LAST / Resolution: 3.65→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5322 0 0 0 5322
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d1.03
LS refinement shellResolution: 3.65→3.88 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.487 185 7.2 %
Rwork0.403 2396 -
obs--97.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5&_1_TOPOLOGY_INFILE_5
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.03
LS refinement shell
*PLUS
Rfactor Rfree: 0.494 / Rfactor Rwork: 0.406

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