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- PDB-1bqu: CYTOKYNE-BINDING REGION OF GP130 -

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Basic information

Entry
Database: PDB / ID: 1bqu
TitleCYTOKYNE-BINDING REGION OF GP130
ComponentsPROTEIN (GP130)
KeywordsSIGNALING PROTEIN / CYTOKINE RECEPTOR / GLYCOPROTEIN 130 / GP130 / INTERLEUKINE 6 RECEPTOR BETA SUBUNIT
Function / homology
Function and homology information


interleukin-27 receptor activity / oncostatin-M receptor complex / ciliary neurotrophic factor receptor activity / leukemia inhibitory factor signaling pathway / interleukin-11 binding / interleukin-11 receptor activity / ciliary neurotrophic factor receptor complex / ciliary neurotrophic factor-mediated signaling pathway / interleukin-6 receptor complex / ciliary neurotrophic factor receptor binding ...interleukin-27 receptor activity / oncostatin-M receptor complex / ciliary neurotrophic factor receptor activity / leukemia inhibitory factor signaling pathway / interleukin-11 binding / interleukin-11 receptor activity / ciliary neurotrophic factor receptor complex / ciliary neurotrophic factor-mediated signaling pathway / interleukin-6 receptor complex / ciliary neurotrophic factor receptor binding / oncostatin-M-mediated signaling pathway / negative regulation of interleukin-6-mediated signaling pathway / positive regulation of adaptive immune response / positive regulation of astrocyte differentiation / positive regulation of acute inflammatory response / intestinal epithelial cell development / interleukin-35-mediated signaling pathway / Interleukin-27 signaling / IL-6-type cytokine receptor ligand interactions / Interleukin-35 Signalling / interleukin-27-mediated signaling pathway / cytokine receptor activity / growth factor binding / positive regulation of cardiac muscle hypertrophy / Interleukin-6 signaling / cytokine binding / MAPK3 (ERK1) activation / positive regulation of vascular endothelial growth factor production / MAPK1 (ERK2) activation / interleukin-6-mediated signaling pathway / glycogen metabolic process / positive regulation of Notch signaling pathway / positive regulation of osteoblast differentiation / positive regulation of T cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / response to cytokine / receptor complex / external side of plasma membrane / neuronal cell body / cytokine-mediated signaling pathway / dendrite / positive regulation of cell population proliferation / viral process / negative regulation of apoptotic process / extracellular space / extracellular exosome / membrane / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Ig-like C2-type domain / Immunoglobulin C2-set-like, ligand-binding / Long hematopoietin receptor, gp130 family signature. / Long hematopoietin receptor, Gp130 family 2, conserved site / Type I cytokine receptor, cytokine-binding domain / Interleukin-6 receptor alpha chain, binding / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III ...Ig-like C2-type domain / Immunoglobulin C2-set-like, ligand-binding / Long hematopoietin receptor, gp130 family signature. / Long hematopoietin receptor, Gp130 family 2, conserved site / Type I cytokine receptor, cytokine-binding domain / Interleukin-6 receptor alpha chain, binding / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Immunoglobulins / 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 / MAD / Resolution: 2 Å
AuthorsBravo, J. / Staunton, D. / Heath, J.K. / Jones, E.Y.
CitationJournal: EMBO J. / Year: 1998
Title: Crystal structure of a cytokine-binding region of gp130.
Authors: Bravo, J. / Staunton, D. / Heath, J.K. / Jones, E.Y.
History
DepositionAug 18, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 26, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Non-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (GP130)
B: PROTEIN (GP130)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,29813
Polymers49,2612
Non-polymers1,03711
Water4,990277
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)84.480, 132.295, 121.933
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PROTEIN (GP130)


Mass: 24630.586 Da / Num. of mol.: 2 / Fragment: CYTOKINE-BINDING REGION DOMAINS
Source method: isolated from a genetically manipulated source
Details: INTERLEUKIN-6 RECEPTOR BETA FRAGMENT INTERLEUKIN 6 SIGNAL TRANSDUCER MEMBRANE GLYCOPROTEIN 130 GP130 ONCOSTATIN M RECEPTOR
Source: (gene. exp.) Homo sapiens (human) / Gene: IL6ST / Plasmid: PMALP2 / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): HW1110 / References: UniProt: P40189
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTER ALA: RESIDUES 207 - 214 CORRESPOND TO A 3 ALA LINKER AND A C-MYC TAG ALA: RESIDUES 207 - 215 ...TER ALA: RESIDUES 207 - 214 CORRESPOND TO A 3 ALA LINKER AND A C-MYC TAG ALA: RESIDUES 207 - 215 CORRESPOND TO A 3 ALA LINKER AND A C-MYC TAG

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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: 3.2 Å3/Da / Density % sol: 62 %
Crystal growpH: 8 / Details: 1.8-2.1M AMMONIUM SULFATE, 0.1M TRIS PH 8.0
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein1drop
220 mMTris-HCl1drop
31.8-2.1 Mammonium sulfate1reservoir
40.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.03
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 48189 / % possible obs: 98.8 % / Redundancy: 6 % / Biso Wilson estimate: 8.6 Å2 / Rsym value: 0.058 / Net I/σ(I): 19.4
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 5 / Rsym value: 0.206 / % possible all: 96.6
Reflection
*PLUS
Rmerge(I) obs: 0.058
Reflection shell
*PLUS
% possible obs: 96.6 % / Rmerge(I) obs: 0.206

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851refinement
RefinementMethod to determine structure: MAD / Resolution: 2→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.255 3380 7.6 %RANDOM
Rwork0.221 ---
obs0.221 44627 96.2 %-
Displacement parametersBiso mean: 20.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3358 0 60 277 3695
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.1
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.561.5
X-RAY DIFFRACTIONx_mcangle_it2.422
X-RAY DIFFRACTIONx_scbond_it2.952
X-RAY DIFFRACTIONx_scangle_it4.312.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.303 554 7.9 %
Rwork0.259 6499 -
obs--92.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3GOL.PARGOL.TOP
X-RAY DIFFRACTION4SO4.PARSO4.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.1

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