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- PDB-1bj8: THIRD N-TERMINAL DOMAIN OF GP130, NMR, MINIMIZED AVERAGE STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1bj8
TitleTHIRD N-TERMINAL DOMAIN OF GP130, NMR, MINIMIZED AVERAGE STRUCTURE
ComponentsGP130
KeywordsRECEPTOR / SIGNAL TRANSDUCER OF IL-6 TYPE CYTOKINES / THIRD N-TERMINAL DOMAIN / TRANSMEMBRANE / GLYCOPROTEIN
Function / homology
Function and homology information


negative regulation of cytokine activity / type I oncostatin-M receptor complex / interleukin-27 receptor activity / ciliary neurotrophic factor receptor activity / leukemia inhibitory factor signaling pathway / ciliary neurotrophic factor receptor binding / oncostatin-M-mediated signaling pathway / interleukin-11 receptor activity / interleukin-11 binding / negative regulation of interleukin-6-mediated signaling pathway ...negative regulation of cytokine activity / type I oncostatin-M receptor complex / interleukin-27 receptor activity / ciliary neurotrophic factor receptor activity / leukemia inhibitory factor signaling pathway / ciliary neurotrophic factor receptor binding / oncostatin-M-mediated signaling pathway / interleukin-11 receptor activity / interleukin-11 binding / negative regulation of interleukin-6-mediated signaling pathway / ciliary neurotrophic factor receptor complex / interleukin-6 receptor complex / positive regulation of acute inflammatory response / ciliary neurotrophic factor-mediated signaling pathway / negative regulation of fat cell proliferation / negative regulation of cytokine-mediated signaling pathway / interleukin-27-mediated signaling pathway / megakaryocyte differentiation / negative regulation of T-helper 1 type immune response / autocrine signaling / interleukin-11-mediated signaling pathway / T-helper 17 cell lineage commitment / positive regulation of adaptive immune response / intestinal epithelial cell development / paracrine signaling / positive regulation of platelet aggregation / Interleukin-27 signaling / IL-6-type cytokine receptor ligand interactions / Interleukin-35 Signalling / cell surface receptor signaling pathway via STAT / cytokine receptor activity / Interleukin-6 signaling / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / positive regulation of cardiac muscle hypertrophy / growth factor binding / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / cytokine binding / regulation of insulin secretion / positive regulation of osteoblast differentiation / positive regulation of interleukin-10 production / positive regulation of vascular endothelial growth factor production / protein tyrosine kinase activator activity / cell surface receptor signaling pathway via JAK-STAT / coreceptor activity / B cell differentiation / response to cytokine / positive regulation of T cell proliferation / cytokine-mediated signaling pathway / negative regulation of neuron apoptotic process / scaffold protein binding / positive regulation of MAPK cascade / signaling receptor complex / inflammatory response / membrane raft / external side of plasma membrane / neuronal cell body / positive regulation of cell population proliferation / negative regulation of apoptotic process / dendrite / : / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
Leukemia inhibitory factor receptor D4 domain / : / 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 ...Leukemia inhibitory factor receptor D4 domain / : / 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 / 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)
MethodSOLUTION NMR / DISTANCE GEOMETRY, RESTRAINED MOLECULAR DYNAMICS, SIMULATED ANNEALING
AuthorsKernebeck, T. / Pflanz, S. / Muller-Newen, G. / Kurapkat, G. / Scheek, R.M. / Dijkstra, K. / Heinrich, P.C. / Wollmer, A. / Grzesiek, S. / Grotzinger, J.
Citation
Journal: Protein Sci. / Year: 1999
Title: The signal transducer gp130: solution structure of the carboxy-terminal domain of the cytokine receptor homology region.
Authors: Kernebeck, T. / Pflanz, S. / Muller-Newen, G. / Kurapkat, G. / Scheek, R.M. / Dijkstra, K. / Heinrich, P.C. / Wollmer, A. / Grzesiek, S. / Grotzinger, J.
#1: Journal: Eur.J.Biochem. / Year: 1997
Title: The Signal Transducer Gp130--Bacterial Expression, Refolding and Properties of the Carboxy-Terminal Domain of the Cytokine-Binding Module
Authors: Muller-Newen, G. / Pflanz, S. / Hassiepen, U. / Stahl, J. / Wollmer, A. / Heinrich, P.C. / Grotzinger, J.
History
DepositionJul 2, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GP130


Theoretical massNumber of molelcules
Total (without water)12,6521
Polymers12,6521
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 22LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein GP130


Mass: 12652.174 Da / Num. of mol.: 1 / Fragment: THIRD N-TERMINAL DOMAIN / Mutation: V1M, Y2D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P40189

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111CBCA(CO)NH
121CBCANH
131C(CO)NH
141HNCA
151HBHA(CO)NH
16115N-EDITED HOHAHA
17113C-EDITED TOCSY
18115N-EDITED NOESY
19113C-EDITED NOESY
1101HNHA
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED PROTEIN

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Sample preparation

DetailsContents: WATER
Sample conditionsIonic strength: 200 mM NACL / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITY500VarianUNITY5005001
Varian INOVA600VarianINOVA6006002
Bruker DMX600BrukerDMX6006003

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Processing

NMR software
NameDeveloperClassification
DDDSCHEEKrefinement
DDDstructure solution
RefinementMethod: DISTANCE GEOMETRY, RESTRAINED MOLECULAR DYNAMICS, SIMULATED ANNEALING
Software ordinal: 1
Details: THE FINAL 22 STRUCTURES WERE CALCULATED USING A TOTAL OF 1575 RESTRAINTS. DISTANCE BOUND DRIVEN DYNAMICS WAS DONE FOR 1000 STEPS AT 1000 KELVIN, FOLLOWED BY 1000 STEPS OF SIMULATED ANNEALING ...Details: THE FINAL 22 STRUCTURES WERE CALCULATED USING A TOTAL OF 1575 RESTRAINTS. DISTANCE BOUND DRIVEN DYNAMICS WAS DONE FOR 1000 STEPS AT 1000 KELVIN, FOLLOWED BY 1000 STEPS OF SIMULATED ANNEALING TO 10 KELVIN. THE MEAN STRUCTURE WAS ENERGY MINIMIZED USING THE GROMOS PROGRAMM PACKAGE.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 22 / Conformers submitted total number: 1

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