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- PDB-1rfa: NMR SOLUTION STRUCTURE OF THE RAS-BINDING DOMAIN OF C-RAF-1 -

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Entry
Database: PDB / ID: 1rfa
TitleNMR SOLUTION STRUCTURE OF THE RAS-BINDING DOMAIN OF C-RAF-1
ComponentsRAF1
KeywordsSERINE/THREONINE-PROTEIN KINASE / SIGNAL TRANSDUCTION PROTEIN / SERINE-THREONINE-PROTEIN KINASE complex
Function / homology
Function and homology information


death-inducing signaling complex assembly / intermediate filament cytoskeleton organization / type B pancreatic cell proliferation / regulation of Rho protein signal transduction / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / insulin secretion involved in cellular response to glucose stimulus / Negative feedback regulation of MAPK pathway / IFNG signaling activates MAPKs ...death-inducing signaling complex assembly / intermediate filament cytoskeleton organization / type B pancreatic cell proliferation / regulation of Rho protein signal transduction / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / insulin secretion involved in cellular response to glucose stimulus / Negative feedback regulation of MAPK pathway / IFNG signaling activates MAPKs / GP1b-IX-V activation signalling / ERBB2-ERBB3 signaling pathway / face development / pseudopodium / neurotrophin TRK receptor signaling pathway / regulation of cell differentiation / thyroid gland development / somatic stem cell population maintenance / extrinsic apoptotic signaling pathway via death domain receptors / MAP kinase kinase kinase activity / type II interferon-mediated signaling pathway / negative regulation of protein-containing complex assembly / Schwann cell development / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / activation of adenylate cyclase activity / positive regulation of peptidyl-serine phosphorylation / response to muscle stretch / myelination / CD209 (DC-SIGN) signaling / insulin-like growth factor receptor signaling pathway / thymus development / RAF activation / wound healing / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / Stimuli-sensing channels / Signaling by RAF1 mutants / 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 / MAPK cascade / insulin receptor signaling pathway / regulation of apoptotic process / mitochondrial outer membrane / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / positive regulation of MAPK cascade / protein phosphorylation / negative regulation of cell population proliferation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / negative regulation of apoptotic process / enzyme binding / Golgi apparatus / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / zinc ion binding / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / : / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) ...Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / : / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha Beta
Similarity search - Domain/homology
RAF proto-oncogene serine/threonine-protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsEmerson, S.D. / Madison, V.S. / Palermo, R.E. / Waugh, D.S. / Scheffler, J.E. / Tsao, K.-L. / Kiefer, S.E. / Liu, S.P. / Fry, D.C.
Citation
Journal: Biochemistry / Year: 1995
Title: Solution structure of the Ras-binding domain of c-Raf-1 and identification of its Ras interaction surface.
Authors: Emerson, S.D. / Madison, V.S. / Palermo, R.E. / Waugh, D.S. / Scheffler, J.E. / Tsao, K.L. / Kiefer, S.E. / Liu, S.P. / Fry, D.C.
#1: Journal: Biochemistry / Year: 1994
Title: Chemical Shift Assignments and Folding Topology of the Ras-Binding Domain of Human Raf-1 as Determined by Heteronuclear Three-Dimensional NMR Spectroscopy
Authors: Emerson, S.D. / Waugh, D.S. / Scheffler, J.E. / Tsao, K.L. / Prinzo, K.M. / Fry, D.C.
#2: Journal: J.Biol.Chem. / Year: 1994
Title: Characterization of a 78-Residue Fragment of C-Raf-1 that Comprises a Minimal Binding Domain for the Interaction with Ras-GTP
Authors: Scheffler, J.E. / Waugh, D.S. / Bekesi, E. / Kiefer, S.E. / Losardo, J.E. / Neri, A. / Prinzo, K.M. / Tsao, K.L. / Wegrzynski, B. / Emerson, S.D. / al., et
History
DepositionApr 26, 1995Processing site: BNL
Revision 1.0Jun 20, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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 viewerMolecule:
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Assembly

Deposited unit
A: RAF1


Theoretical massNumber of molelcules
Total (without water)8,9751
Polymers8,9751
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)30 / -
Representative

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Components

#1: Protein RAF1 / RAF-RBD / C-RAF-1


Mass: 8975.455 Da / Num. of mol.: 1
Fragment: RAS BINDING DOMAIN, RESIDUES 55 - 132 WITH AN ADDITIONAL ALA AT THE N-TERMINUS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: FETAL LIVER / Plasmid: PDW333 / Production host: Escherichia coli (E. coli)
References: UniProt: P04049, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other

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Processing

NMR softwareName: CHARMM / Version: 22 / Developer: BROOKS ET AL. / Classification: refinement
NMR ensembleConformers submitted total number: 30

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