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- PDB-1rrb: THE RAS-BINDING DOMAIN OF RAF-1 FROM RAT, NMR, 1 STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1rrb
TitleTHE RAS-BINDING DOMAIN OF RAF-1 FROM RAT, NMR, 1 STRUCTURE
ComponentsRAF PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE
KeywordsTRANSFERASE / RAF-1 / RAS-BINDING DOMAIN / SERINE/THREONINE-PROTEIN KINASE / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


GP1b-IX-V activation signalling / CD209 (DC-SIGN) signaling / Rap1 signalling / : / small GTPase binding => GO:0031267 / Stimuli-sensing channels / RAF activation / Negative feedback regulation of MAPK pathway / Negative regulation of MAPK pathway / death-inducing signaling complex assembly ...GP1b-IX-V activation signalling / CD209 (DC-SIGN) signaling / Rap1 signalling / : / small GTPase binding => GO:0031267 / Stimuli-sensing channels / RAF activation / Negative feedback regulation of MAPK pathway / Negative regulation of MAPK pathway / death-inducing signaling complex assembly / MAP2K and MAPK activation / intermediate filament cytoskeleton organization / insulin secretion involved in cellular response to glucose stimulus / mitogen-activated protein kinase kinase binding / face development / pseudopodium / intracellular glucose homeostasis / somatic stem cell population maintenance / thyroid gland development / neurotrophin TRK receptor signaling pathway / adenylate cyclase binding / MAP kinase kinase kinase activity / negative regulation of protein-containing complex assembly / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / activation of adenylate cyclase activity / response to muscle stretch / adenylate cyclase activator activity / thymus development / MAPK cascade / positive regulation of peptidyl-serine phosphorylation / heart development / cell differentiation / non-specific serine/threonine protein kinase / response to hypoxia / protein kinase activity / intracellular signal transduction / nuclear speck / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / protein phosphorylation / protein serine/threonine kinase activity / protein-containing complex binding / negative regulation of apoptotic process / Golgi apparatus / enzyme binding / positive regulation of transcription by RNA polymerase II / mitochondrion / ATP binding / identical protein binding / metal ion binding / 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) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain ...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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ubiquitin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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 speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing
AuthorsTerada, T. / Ito, Y. / Shirouzu, M. / Tateno, M. / Hashimoto, K. / Kigawa, T. / Ebisuzaki, T. / Takio, K. / Shibata, T. / Yokoyama, S. ...Terada, T. / Ito, Y. / Shirouzu, M. / Tateno, M. / Hashimoto, K. / Kigawa, T. / Ebisuzaki, T. / Takio, K. / Shibata, T. / Yokoyama, S. / Smith, B.O. / Laue, E.D. / Cooper, J.A. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Nuclear magnetic resonance and molecular dynamics studies on the interactions of the Ras-binding domain of Raf-1 with wild-type and mutant Ras proteins.
Authors: Terada, T. / Ito, Y. / Shirouzu, M. / Tateno, M. / Hashimoto, K. / Kigawa, T. / Ebisuzaki, T. / Takio, K. / Shibata, T. / Yokoyama, S. / Smith, B.O. / Laue, E.D. / Cooper, J.A.
History
DepositionMar 26, 1998Processing site: BNL
Revision 1.0Mar 30, 1999Provider: 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: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name
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: RAF PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE


Theoretical massNumber of molelcules
Total (without water)11,9611
Polymers11,9611
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 80CLOSEST TO THE AVERAGE OF 20 LEAST ENERGY STRUCTURES
Representative

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Components

#1: Protein RAF PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE / RAF-1 RBD


Mass: 11960.821 Da / Num. of mol.: 1 / Fragment: RAS-BINDING DOMAIN, RESIDUES 56-131
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line: BL21 / Plasmid: PET-RID / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P11345, 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
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111H-1H NOESY
1211H-15N HSQC
1313D 15N-EDITED NOESY
1413D 15N-EDITED TOCSY
151HMQC-J
1613D HNCA
1713D (H)CCH-TOCSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C/15N-LABELED RAF-1 RBD

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Sample preparation

DetailsContents: 20 MM SODIUM PHOSPHATE BUFFER (PH 6.5)
Sample conditionsIonic strength: 5 mM MGCL2 / pH: 6.5 / Pressure: 1 atm / 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
Felix2.3structure solution
Azara1structure solution
X-PLOR3.1structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: SIMULATED ANNEALING REFINEMENT FOR NMR STRUCTURE DETERMINATION
NMR ensembleConformer selection criteria: CLOSEST TO THE AVERAGE OF 20 LEAST ENERGY STRUCTURES
Conformers calculated total number: 80 / Conformers submitted total number: 1

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