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- PDB-8jog: solution structure of Ras Binding Domein (RBD) in C-RAF with nega... -

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Basic information

Entry
Database: PDB / ID: 8jog
Titlesolution structure of Ras Binding Domein (RBD) in C-RAF with negative allosteric modulator.
ComponentsRAF proto-oncogene serine/threonine-protein kinase
KeywordsSIGNALING PROTEIN / MAPK
Function / homology
Function and homology information


death-inducing signaling complex assembly / intermediate filament cytoskeleton organization / regulation of Rho protein signal transduction / type B pancreatic cell proliferation / 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 / regulation of Rho protein signal transduction / type B pancreatic cell proliferation / 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 / neurotrophin TRK receptor signaling pathway / face development / pseudopodium / regulation of cell differentiation / thyroid gland development / extrinsic apoptotic signaling pathway via death domain receptors / somatic stem cell population maintenance / positive regulation of peptidyl-serine phosphorylation / MAP kinase kinase kinase activity / type II interferon-mediated signaling pathway / Schwann cell development / negative regulation of protein-containing complex assembly / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / response to muscle stretch / myelination / CD209 (DC-SIGN) signaling / insulin-like growth factor receptor signaling pathway / thymus development / adenylate cyclase activator activity / wound healing / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / Stimuli-sensing channels / Negative regulation of MAPK pathway / Signaling by RAF1 mutants / 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 / insulin receptor signaling pathway / MAPK cascade / regulation of apoptotic process / mitochondrial outer membrane / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / positive regulation of MAPK cascade / 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 / cytoplasm / cytosol
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 / 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 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
RAF proto-oncogene serine/threonine-protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMakino, Y. / Matsumoto, S. / Yoshikawa, Y. / Kawamura, T. / Kumasaka, T. / Shima, F.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)17nk0101309h0003 Japan
Japan Science and Technology22-20103170 Japan
CitationJournal: To Be Published
Title: Small-molecule RAS/RAF-binding Inhibitors Allosterically Disrupt RAF Conformation and Exert Efficacy Against Broad-spectrum RAS-driven Cancers
Authors: Yoshikawa, Y. / Makino, Y. / Kubota, H. / Kawamura, T. / Matsumoto, S. / Yuki, H. / Shibaike, A. / Okamura, M. / Okada, T. / Kataoka, T. / Honma, T. / Kumasaka, T. / Koyama, H. / Shima, F.
History
DepositionJun 7, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: RAF proto-oncogene serine/threonine-protein kinase


Theoretical massNumber of molelcules
Total (without water)9,6151
Polymers9,6151
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 2020
RepresentativeModel #1target function

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Components

#1: Protein RAF proto-oncogene serine/threonine-protein kinase / Proto-oncogene c-RAF / cRaf / Raf-1


Mass: 9615.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAF1, RAF / Plasmid: pGEx6p-1 / Production host: Escherichia coli (E. coli)
References: UniProt: P04049, 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
111isotropic12D 1H-15N HSQC
1111isotropic12D 1H-13C HSQC aliphatic
1141isotropic12D 1H-13C HSQC aromatic
121isotropic13D CBCA(CO)NH
161isotropic13D HN(CA)CB
141isotropic13D HNCA
171isotropic13D HN(CO)CA
151isotropic13D HNCO
1131isotropic13D HN(CA)CO
1121isotropic13D 1H-15N NOESY
181isotropic13D 1H-13C NOESY aliphatic
191isotropic13D 1H-13C NOESY aromatic
1101isotropic13D (H)CCH-TOCSY

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Sample preparation

DetailsType: solution
Contents: 0.3 mM [U-100% 13C; U-100% 15N] Serin/threonine protein kinase C-RAF, 25 mM sodium phosphate, 50 mM sodium chloride, 10 mM magnesium dichloride, 90% H2O/10% D2O
Label: 13C/15N_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMSerin/threonine protein kinase C-RAF[U-100% 13C; U-100% 15N]1
25 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
10 mMmagnesium dichloridenatural abundance1
Sample conditionsIonic strength: 85 mM / Label: condition_1 / pH: 6.8 / Pressure: ambient atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz / Details: cryo-probe

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Processing

NMR software
NameDeveloperClassification
MagRO-NMRViewKobayashi et al.chemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
MagRO-NMRViewKobayashi et al.peak picking
nmrpprocessing
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: 20 / Conformers calculated total number: 20 / Conformers submitted total number: 20

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