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- PDB-1gcf: NMR STRUCTURE OF THE C-TERMINAL DOMAIN OF THE LIGAND-BINDING REGI... -

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Basic information

Entry
Database: PDB / ID: 1gcf
TitleNMR STRUCTURE OF THE C-TERMINAL DOMAIN OF THE LIGAND-BINDING REGION OF MURINE GRANULOCYTE COLONY-STIMULATING FACTOR RECEPTOR, 12 STRUCTURES
ComponentsGRANULOCYTE COLONY-STIMULATING FACTOR RECEPTOR
KeywordsBINDING PROTEIN / CYTOKINE RECEPTOR
Function / homology
Function and homology information


granulocyte colony-stimulating factor binding / regulation of myeloid cell differentiation / amelogenesis / cytokine receptor activity / neutrophil chemotaxis / endocytic vesicle membrane / cell adhesion / plasma membrane
Similarity search - Function
: / 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 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like domain superfamily ...: / 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 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Granulocyte colony-stimulating factor receptor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / RANDOM.INP, DGSA.INP, REFINE.INP
AuthorsYamasaki, K. / Naito, S. / Anaguchi, H. / Ohkubo, T. / Ota, Y.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: Solution structure of an extracellular domain containing the WSxWS motif of the granulocyte colony-stimulating factor receptor and its interaction with ligand.
Authors: Yamasaki, K. / Naito, S. / Anaguchi, H. / Ohkubo, T. / Ota, Y.
#1: Journal: J.Biol.Chem. / Year: 1995
Title: Ligand Binding Characteristics of the Carboxyl-Terminal Domain of the Cytokine Receptor Homologous Region of the Granulocyte Colony-Stimulating Factor Receptor
Authors: Anaguchi, H. / Hiraoka, O. / Yamasaki, K. / Naito, S. / Ota, Y.
History
DepositionApr 10, 1997Processing site: BNL
Revision 1.0Oct 22, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_database_status.process_site / _pdbx_nmr_software.authors ..._pdbx_database_status.process_site / _pdbx_nmr_software.authors / _pdbx_nmr_software.name / _pdbx_nmr_software.version / _pdbx_nmr_spectrometer.field_strength
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Assembly

Deposited unit
A: GRANULOCYTE COLONY-STIMULATING FACTOR RECEPTOR


Theoretical massNumber of molelcules
Total (without water)12,5361
Polymers12,5361
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7750 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)12 / 100TOTAL OF NOE, DIHEDRAL, AND VAN DER WAALS ENERGIES
Representative

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Components

#1: Protein GRANULOCYTE COLONY-STIMULATING FACTOR RECEPTOR


Mass: 12536.452 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN OF THE LIGAND-BINDING REGION / Mutation: INS(G1,S2,S3)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Description: EXPRESSED AS A FUSION PROTEIN WITH MALTOSE BINDING PROTEIN
Plasmid: PMAL-P / Production host: Escherichia coli (E. coli) / References: UniProt: P40223
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TRIPLE RESONANCE 2D
1213D NMR

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Sample preparation

Sample conditionspH: 5.5 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX600 / Manufacturer: Bruker / Model: AMX600 / Field strength: 600 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR3.1BRUNGERstructure solution
RefinementMethod: RANDOM.INP, DGSA.INP, REFINE.INP / Software ordinal: 1
NMR ensembleConformer selection criteria: TOTAL OF NOE, DIHEDRAL, AND VAN DER WAALS ENERGIES
Conformers calculated total number: 100 / Conformers submitted total number: 12

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