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- PDB-2l7w: Solution structure of the human Raf-1 kinase inhibitor protein -

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Basic information

Entry
Database: PDB / ID: 2l7w
TitleSolution structure of the human Raf-1 kinase inhibitor protein
ComponentsPhosphatidylethanolamine-binding protein 1
KeywordsSignaling Protein Inhibitor / Raf-1 kinase inhibitor protein
Function / homology
Function and homology information


phosphatidylethanolamine binding / negative regulation of MAPK cascade / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / serine-type endopeptidase inhibitor activity / Negative regulation of MAPK pathway / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions ...phosphatidylethanolamine binding / negative regulation of MAPK cascade / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / serine-type endopeptidase inhibitor activity / Negative regulation of MAPK pathway / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / protein kinase binding / enzyme binding / RNA binding / extracellular exosome / ATP binding / nucleus / cytosol
Similarity search - Function
Phosphatidylethanolamine-binding, conserved site / Phosphatidylethanolamine-binding protein family signature. / Phosphatidylethanolamine-binding Protein / PEBP-like / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein, eukaryotic / PEBP-like superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Phosphatidylethanolamine-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsYi, C.Y.
CitationJournal: To be Published
Title: Solution structure of the human Raf-1 kinase inhibitor protein
Authors: Yi, C.Y. / Lin, D.
History
DepositionDec 24, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphatidylethanolamine-binding protein 1


Theoretical massNumber of molelcules
Total (without water)21,0871
Polymers21,0871
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)20 / 200all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

#1: Protein Phosphatidylethanolamine-binding protein 1 / Raf-1 kinase inhibitor protein / PEBP-1 / HCNPpp / Neuropolypeptide h3 / Prostatic-binding protein ...Raf-1 kinase inhibitor protein / PEBP-1 / HCNPpp / Neuropolypeptide h3 / Prostatic-binding protein / Raf kinase inhibitor protein / RKIP / Hippocampal cholinergic neurostimulating peptide / HCNP


Mass: 21086.787 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RKIP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P30086

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY

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Sample preparation

DetailsContents: 3mM [U-100% 13C; U-100% 15N] Raf-1 kinase inhibitor protein; 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 3 mM / Component: Raf-1 kinase inhibitor protein-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 200 / pH: 4 / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA6002

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Processing

NMR softwareName: CNS / Developer: Brunger, Adams, Clore, Gros, Nilges and Read / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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