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- PDB-13du: BRAF/CRAF/14-3-3 complex -

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Basic information

Entry
Database: PDB / ID: 13du
TitleBRAF/CRAF/14-3-3 complex
Components
  • 14-3-3 protein epsilon
  • 14-3-3 protein zeta
  • RAF proto-oncogene serine/threonine-protein kinase
  • Serine/threonine-protein kinase B-raf
KeywordsSIGNALING PROTEIN / Ser/Thr kinase / map kinase signal / protein kinase
Function / homology
Function and homology information


Signalling to p38 via RIT and RIN / ARMS-mediated activation / regulation of Rho protein signal transduction / establishment of protein localization to membrane / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / positive regulation of D-glucose transmembrane transport / Negative feedback regulation of MAPK pathway / IFNG signaling activates MAPKs ...Signalling to p38 via RIT and RIN / ARMS-mediated activation / regulation of Rho protein signal transduction / establishment of protein localization to membrane / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / positive regulation of D-glucose transmembrane transport / Negative feedback regulation of MAPK pathway / IFNG signaling activates MAPKs / GP1b-IX-V activation signalling / Frs2-mediated activation / ERBB2-ERBB3 signaling pathway / MAP kinase kinase activity / regulation of cell differentiation / pseudopodium / neuromuscular junction development / positive regulation of peptidyl-serine phosphorylation / MAP kinase kinase kinase activity / type II interferon-mediated signaling pathway / Schwann cell development / serine/threonine protein kinase complex / postsynaptic modulation of chemical synaptic transmission / negative regulation of protein-containing complex assembly / myelination / insulin-like growth factor receptor signaling pathway / animal organ morphogenesis / cellular response to calcium ion / CD209 (DC-SIGN) signaling / adenylate cyclase activator activity / wound healing / RAF activation / Signaling by high-kinase activity BRAF mutants / Spry regulation of FGF signaling / MAP2K and MAPK activation / insulin receptor signaling pathway / epidermal growth factor receptor signaling pathway / Stimuli-sensing channels / 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 / MAPK cascade / Negative regulation of MAPK pathway / Signaling by BRAF and RAF1 fusions / cell body / scaffold protein binding / regulation of apoptotic process / positive regulation of ERK1 and ERK2 cascade / protein kinase activity / protein phosphorylation / positive regulation of MAPK cascade / non-specific serine/threonine protein kinase / neuron projection / mitochondrial outer membrane / postsynapse / apoptotic process / negative regulation of cell population proliferation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of gene expression / calcium ion binding / negative regulation of apoptotic process / glutamatergic synapse / Golgi apparatus / signal transduction / enzyme binding / 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 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / 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 / 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
Chem-29L / 14-3-3 protein epsilon / 14-3-3 protein zeta / RAF proto-oncogene serine/threonine-protein kinase / Serine/threonine-protein kinase B-raf
Similarity search - Component
Biological speciesHomo sapiens (human)
Spodoptera frugiperda (fall armyworm)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsHa, B.H. / Jeon, H. / Eck, M.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R35CA242461 United States
CitationJournal: To Be Published
Title: Complex structure of BRAF/CRAF/14-3-3
Authors: Ha, B.H. / Eck, M.J.
History
DepositionMay 1, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase B-raf
B: RAF proto-oncogene serine/threonine-protein kinase
X: 14-3-3 protein epsilon
Y: 14-3-3 protein zeta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,4536
Polymers139,7844
Non-polymers6692
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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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: 40261.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRAF, BRAF1, RAFB1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P15056, non-specific serine/threonine protein kinase
#2: Protein RAF proto-oncogene serine/threonine-protein kinase / Proto-oncogene c-RAF / cRaf / Raf-1


Mass: 41662.324 Da / Num. of mol.: 1 / Mutation: Y340D, Y341D, F559E, R563A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAF1, RAF / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P04049, non-specific serine/threonine protein kinase
#3: Protein 14-3-3 protein epsilon


Mass: 29752.178 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spodoptera frugiperda (fall armyworm) / Gene: LOC118274546, SFRICE_002878 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A2H1VA22
#4: Protein 14-3-3 protein zeta


Mass: 28108.514 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spodoptera frugiperda (fall armyworm) / Gene: LOC118271767 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A9R0D7T1
#5: Chemical ChemComp-29L / 2-{4-[(1E)-1-(hydroxyimino)-2,3-dihydro-1H-inden-5-yl]-3-(pyridin-4-yl)-1H-pyrazol-1-yl}ethanol


Mass: 334.372 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H18N4O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: BRAF/CRAF/14-3-3 complex / Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
Details: 25mM Tris-HCl pH 8.0, 0.15M NaCl, 5mM MgCl2, 1mM TCEP, 1uM ATP-gamma-S
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: UltrAuFoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 62.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 139194 / Symmetry type: POINT

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