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- PDB-1uc6: Solution Structure of the Carboxyl Terminal Domain of the Ciliary... -

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Basic information

Entry
Database: PDB / ID: 1uc6
TitleSolution Structure of the Carboxyl Terminal Domain of the Ciliary Neurotrophic Factor Receptor
ComponentsCiliary Neurotrophic Factor Receptor alpha
KeywordsPROTEIN BINDING / cytokine / ciliary neurotrophic factor / leukemia inhibitory factor / cytokine receptor / fibronectin type III domain-like topology / seven beta-strands / two anti-parallel beta-sheets
Function / homology
Function and homology information


CNTFR-CLCF1 complex / skeletal muscle organ development / ciliary neurotrophic factor receptor activity / ciliary neurotrophic factor-mediated signaling pathway / interleukin-11 receptor activity / interleukin-11 binding / ciliary neurotrophic factor receptor complex / brainstem development / sex differentiation / IL-6-type cytokine receptor ligand interactions ...CNTFR-CLCF1 complex / skeletal muscle organ development / ciliary neurotrophic factor receptor activity / ciliary neurotrophic factor-mediated signaling pathway / interleukin-11 receptor activity / interleukin-11 binding / ciliary neurotrophic factor receptor complex / brainstem development / sex differentiation / IL-6-type cytokine receptor ligand interactions / negative regulation of motor neuron apoptotic process / motor neuron apoptotic process / extrinsic component of membrane / suckling behavior / cytokine binding / nervous system development / negative regulation of neuron apoptotic process / apical plasma membrane / external side of plasma membrane / signaling receptor binding / positive regulation of cell population proliferation / signal transduction / plasma membrane
Similarity search - Function
: / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. / 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 ...: / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ciliary neurotrophic factor receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsMan, D. / He, W. / Sze, K.H. / Ke, G. / Smith, D.K. / Ip, N.Y. / Zhu, G.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Solution structure of the C-terminal domain of the ciliary neurotrophic factor (CNTF) receptor and ligand free associations among components of the CNTF receptor complex
Authors: Man, D. / He, W. / Sze, K.H. / Gong, K. / Smith, D.K. / Zhu, G. / Ip, N.Y.
History
DepositionApr 8, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: 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: Ciliary Neurotrophic Factor Receptor alpha


Theoretical massNumber of molelcules
Total (without water)12,3341
Polymers12,3341
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)21 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Ciliary Neurotrophic Factor Receptor alpha / CNTF receptor


Mass: 12333.676 Da / Num. of mol.: 1 / Fragment: Carboxyl Terminal Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-6p1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P26992

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
132HNHA
141nJ-HMQC
NMR detailsText: For determination of hydrogen bonds, amide protons exchanging slowly with deuterons were identified by time course 1H-15N HSQC experiments on a freeze-dried 15N-labelled sample of BC dissolved in D2O buffer.

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM CNTFR-BC U-15N; 100mM NaCl, 10mM sodium phosphate, 0.1mM EDTA90% H2O, 10% D2O, pH 6.5
21.3mM CNTFR-BC U-15N,13C; 100mM NaCl, 10mM sodium phosphate, 0.1mM EDTA90% H2O, 10% D2O, pH 6.5
Sample conditionsIonic strength: 100mM NaCl, 10mM sodium phosphate, 0.1mM EDTA
pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe2F. Delaglioprocessing
PIPP1Garrett Ddata analysis
Sparky1.06Goddard, T. Ddata analysis
ARIA1.1Nilges, M.structure solution
CNS1.1Brunger, A.T.structure solution
CNS1.1refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Following identification of the global fold from manual inspection of the nuclear Overhauser effect spectroscopy data, ambiguous NOE restraints were resolved using the iterative ARIA method ...Details: Following identification of the global fold from manual inspection of the nuclear Overhauser effect spectroscopy data, ambiguous NOE restraints were resolved using the iterative ARIA method (Nilges et al., 1997) and the structure was determined by simulated annealing using the CNS package.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 21

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