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- PDB-5j17: Solution structure of Ras Binding Domain (RBD) of B-Raf -

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Basic information

Entry
Database: PDB / ID: 5j17
TitleSolution structure of Ras Binding Domain (RBD) of B-Raf
ComponentsSerine/threonine-protein kinase B-raf
KeywordsPROTEIN BINDING / MAPK / PI3K
Function / homology
Function and homology information


CD4-positive, alpha-beta T cell differentiation / positive regulation of axon regeneration / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative regulation of synaptic vesicle exocytosis / Signalling to p38 via RIT and RIN / head morphogenesis / ARMS-mediated activation / myeloid progenitor cell differentiation / endothelial cell apoptotic process / SHOC2 M1731 mutant abolishes MRAS complex function ...CD4-positive, alpha-beta T cell differentiation / positive regulation of axon regeneration / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative regulation of synaptic vesicle exocytosis / Signalling to p38 via RIT and RIN / head morphogenesis / ARMS-mediated activation / myeloid progenitor cell differentiation / endothelial cell apoptotic process / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / positive regulation of D-glucose transmembrane transport / negative regulation of fibroblast migration / establishment of protein localization to membrane / positive regulation of axonogenesis / regulation of T cell differentiation / Negative feedback regulation of MAPK pathway / mitogen-activated protein kinase kinase binding / Frs2-mediated activation / stress fiber assembly / face development / MAP kinase kinase activity / synaptic vesicle exocytosis / thyroid gland development / somatic stem cell population maintenance / positive regulation of peptidyl-serine phosphorylation / MAP kinase kinase kinase activity / postsynaptic modulation of chemical synaptic transmission / negative regulation of endothelial cell apoptotic process / response to cAMP / positive regulation of stress fiber assembly / ERK1 and ERK2 cascade / positive regulation of substrate adhesion-dependent cell spreading / substrate adhesion-dependent cell spreading / cellular response to calcium ion / thymus development / animal organ morphogenesis / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H2AS121 kinase activity / histone H3S57 kinase activity / histone H3S28 kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / ribosomal protein S6 kinase activity / histone H2AT120 kinase activity / eukaryotic translation initiation factor 2alpha kinase activity / histone H2BS36 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H3S10 kinase activity / AMP-activated protein kinase activity / histone H3T11 kinase activity / histone H3T3 kinase activity / 3-phosphoinositide-dependent protein kinase activity / histone H3T45 kinase activity / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / RAF activation / cellular response to nerve growth factor stimulus / Spry regulation of FGF signaling / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / visual learning / response to peptide hormone / centriolar satellite / long-term synaptic potentiation / epidermal growth factor receptor signaling pathway / 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 / cellular response to xenobiotic stimulus / MAPK cascade / T cell differentiation in thymus / T cell receptor signaling pathway / presynapse / regulation of cell population proliferation / cell body / scaffold protein binding / negative regulation of neuron apoptotic process / positive regulation of ERK1 and ERK2 cascade / postsynapse / non-specific serine/threonine protein kinase / protein kinase activity / neuron projection / protein phosphorylation / ciliary basal body / cilium / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / calcium ion binding / positive regulation of gene expression / negative regulation of apoptotic process / protein-containing complex binding / glutamatergic synapse / mitochondrion / zinc ion binding
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) / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
Serine/threonine-protein kinase B-raf
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsDutta, K. / Vasquez-Del Carpio, R. / Aggarwal, A.K. / Reddy, E.P.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA158209 United States
Onconova Therapeutics Inc (OCI) United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)CO6RR015495 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM066354 United States
CitationJournal: Cell / Year: 2016
Title: A Small Molecule RAS-Mimetic Disrupts RAS Association with Effector Proteins to Block Signaling.
Authors: Athuluri-Divakar, S.K. / Vasquez-Del Carpio, R. / Dutta, K. / Baker, S.J. / Cosenza, S.C. / Basu, I. / Gupta, Y.K. / Reddy, M.V. / Ueno, L. / Hart, J.R. / Vogt, P.K. / Mulholland, D. / Guha, ...Authors: Athuluri-Divakar, S.K. / Vasquez-Del Carpio, R. / Dutta, K. / Baker, S.J. / Cosenza, S.C. / Basu, I. / Gupta, Y.K. / Reddy, M.V. / Ueno, L. / Hart, J.R. / Vogt, P.K. / Mulholland, D. / Guha, C. / Aggarwal, A.K. / Reddy, E.P.
History
DepositionMar 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support
Item: _entity.pdbx_number_of_molecules / _pdbx_audit_support.funding_organization
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 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 1.4May 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

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Assembly

Deposited unit
A: Serine/threonine-protein kinase B-raf


Theoretical massNumber of molelcules
Total (without water)10,3111
Polymers10,3111
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5300 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 1024structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Serine/threonine-protein kinase B-raf / Proto-oncogene B-Raf / p94 / v-Raf murine sarcoma viral oncogene homolog B1


Mass: 10311.078 Da / Num. of mol.: 1 / Fragment: residues 151-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRAF, BRAF1, RAFB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS
References: UniProt: P15056, non-specific serine/threonine protein kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic42D 1H-15N HSQC
122isotropic42D 1H-13C HSQC
132isotropic33D HNCO
142isotropic33D Hn(CA)CO
152isotropic33D HNCA
1132isotropic33D HN(CO)CA
1122isotropic33D CBCA(CO)NH
1112isotropic33D HN(CA)CB
1102isotropic43D 1H-15N NOESY
192isotropic43D 1H-13C NOESY aliphatic
182isotropic43D 1H-13C NOESY aromatic
172isotropic13D H(CCO)NH
162isotropic13D (H)CCH-TOCSY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1200 uM [U-99% 15N] B-RAF RBD, 90% H2O/10% D2ONMR buffer (20 mM KH2PO4, 200 mM NaCl, pH 7.4)N15 Sample90% H2O/10% D2O
solution2200 uM [U-99% 13C; U-99% 15N] B-RAF RBD, 90% H2O/10% D2ONMR buffer (20 mM KH2PO4, 200 mM NaCl, pH 7.4)C13-N15 Sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
200 uMB-RAF RBD[U-99% 15N]1
200 uMB-RAF RBD[U-99% 13C; U-99% 15N]2
Sample conditionsDetails: NMR buffer (20 mM KH2PO4, 200 mM NaCl, pH 7.4) / Ionic strength: 0.2 M / Label: 1 / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE7002
Bruker AVANCEBrukerAVANCE8003
Bruker AVANCEBrukerAVANCE9004

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Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue and Nilgesrefinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1024 / Conformers submitted total number: 10

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