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- PDB-3l5j: Crystal structure of FnIII domains of human GP130 (Domains 4-6) -

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Basic information

Entry
Database: PDB / ID: 3l5j
TitleCrystal structure of FnIII domains of human GP130 (Domains 4-6)
ComponentsInterleukin-6 receptor subunit beta
KeywordsIMMUNE SYSTEM / Cytokine Receptor / Fibronectin Type III domain
Function / homology
Function and homology information


interleukin-27 receptor activity / oncostatin-M receptor complex / interleukin-11 receptor activity / interleukin-11 binding / oncostatin-M-mediated signaling pathway / ciliary neurotrophic factor receptor activity / ciliary neurotrophic factor receptor binding / negative regulation of interleukin-6-mediated signaling pathway / leukemia inhibitory factor signaling pathway / ciliary neurotrophic factor receptor complex ...interleukin-27 receptor activity / oncostatin-M receptor complex / interleukin-11 receptor activity / interleukin-11 binding / oncostatin-M-mediated signaling pathway / ciliary neurotrophic factor receptor activity / ciliary neurotrophic factor receptor binding / negative regulation of interleukin-6-mediated signaling pathway / leukemia inhibitory factor signaling pathway / ciliary neurotrophic factor receptor complex / interleukin-27-mediated signaling pathway / ciliary neurotrophic factor-mediated signaling pathway / interleukin-6 receptor complex / interleukin-11-mediated signaling pathway / T-helper 17 cell lineage commitment / positive regulation of adaptive immune response / positive regulation of acute inflammatory response / positive regulation of astrocyte differentiation / intestinal epithelial cell development / positive regulation of platelet aggregation / Interleukin-35 Signalling / Interleukin-27 signaling / IL-6-type cytokine receptor ligand interactions / cytokine receptor activity / glycogen metabolic process / Interleukin-6 signaling / interleukin-6-mediated signaling pathway / cytokine binding / positive regulation of Notch signaling pathway / protein tyrosine kinase activator activity / positive regulation of cardiac muscle hypertrophy / MAPK3 (ERK1) activation / growth factor binding / MAPK1 (ERK2) activation / positive regulation of vascular endothelial growth factor production / positive regulation of osteoblast differentiation / coreceptor activity / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of T cell proliferation / response to cytokine / cytokine-mediated signaling pathway / scaffold protein binding / negative regulation of neuron apoptotic process / receptor complex / membrane raft / external side of plasma membrane / dendrite / neuronal cell body / positive regulation of cell population proliferation / negative regulation of apoptotic process / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
Type I cytokine receptor, cytokine-binding domain / Interleukin-6 receptor alpha chain, binding / 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. / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III ...Type I cytokine receptor, cytokine-binding domain / Interleukin-6 receptor alpha chain, binding / 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. / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interleukin-6 receptor subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.042 Å
AuthorsKershaw, N.J. / Zhang, J.-G. / Garrett, T.P.J. / Czabotar, P.E.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal structure of the entire ectodomain of gp130: insights into the molecular assembly of the tall cytokine receptor complexes.
Authors: Xu, Y. / Kershaw, N.J. / Luo, C.S. / Soo, P. / Pocock, M.J. / Czabotar, P.E. / Hilton, D.J. / Nicola, N.A. / Garrett, T.P. / Zhang, J.G.
History
DepositionDec 22, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 5, 2017Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-6 receptor subunit beta
B: Interleukin-6 receptor subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5487
Polymers65,3442
Non-polymers2045
Water27015
1
A: Interleukin-6 receptor subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7693
Polymers32,6721
Non-polymers982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Interleukin-6 receptor subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7784
Polymers32,6721
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.936, 89.221, 106.877
Angle α, β, γ (deg.)90.000, 117.720, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Interleukin-6 receptor subunit beta / / IL-6R-beta / Interleukin-6 signal transducer / Membrane glycoprotein 130 / gp130 / CDw130 / ...IL-6R-beta / Interleukin-6 signal transducer / Membrane glycoprotein 130 / gp130 / CDw130 / Oncostatin-M receptor subunit alpha


Mass: 32671.889 Da / Num. of mol.: 2 / Fragment: UNP residues 323-610
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GP130 / Plasmid: pET-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40189
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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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: 3.32 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, NaCl, Tris-HCl, pH 8.5, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95443 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 12, 2009
RadiationMonochromator: dipole/benging magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95443 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. all: 16510 / Num. obs: 16494 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 36.45 Å2
Reflection shellResolution: 3.05→3.16 Å / Redundancy: 3.5 % / % possible all: 99.3

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Processing

Software
NameVersionClassificationNB
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.042→35.154 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 2.55 / σ(F): 0.07 / σ(I): 2.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.265 791 5.05 %RANDOM
Rwork0.213 ---
all0.213 16578 --
obs0.215 15678 94.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 1.362 Å2 / ksol: 0.286 e/Å3
Displacement parametersBiso max: 111.48 Å2 / Biso mean: 30.225 Å2 / Biso min: 5.98 Å2
Baniso -1Baniso -2Baniso -3
1-3.875 Å20 Å2-1.618 Å2
2---4.768 Å2-0 Å2
3---0.893 Å2
Refinement stepCycle: LAST / Resolution: 3.042→35.154 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4292 0 8 15 4315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024409
X-RAY DIFFRACTIONf_angle_d0.6216060
X-RAY DIFFRACTIONf_chiral_restr0.042710
X-RAY DIFFRACTIONf_plane_restr0.002775
X-RAY DIFFRACTIONf_dihedral_angle_d13.621469
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.042-3.2330.311050.2652232233785
3.233-3.4820.2881340.2382420255494
3.482-3.8320.2921440.2282534267897
3.832-4.3860.2741060.1922518262495
4.386-5.5220.2161530.1682545269898
5.522-35.1560.241490.2072638278799

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