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- EMDB-43678: Cryo-EM Structure of the BRAF WT monomer bound to PLX8394 -

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Basic information

Entry
Database: EMDB / ID: EMD-43678
TitleCryo-EM Structure of the BRAF WT monomer bound to PLX8394
Map data
Sample
  • Complex: BRAF WT - 14.3.3 complex bound to PLX8394
    • Protein or peptide: Serine/threonine-protein kinase B-raf
    • Protein or peptide: 14-3-3 protein zeta/delta
  • Ligand: (3S)-N-{3-[5-(2-cyclopropylpyrimidin-5-yl)-1H-pyrrolo[2,3-b]pyridine-3-carbonyl]-2,4-difluorophenyl}-3-fluoropyrrolidine-1-sulfonamide
KeywordsBRAF Kinase Monomer Inhibitor / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


synaptic target recognition / Golgi reassembly / CD4-positive, alpha-beta T cell differentiation / positive regulation of axon regeneration / NOTCH4 Activation and Transmission of Signal to the Nucleus / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative regulation of synaptic vesicle exocytosis / establishment of Golgi localization / Signalling to p38 via RIT and RIN / respiratory system process ...synaptic target recognition / Golgi reassembly / CD4-positive, alpha-beta T cell differentiation / positive regulation of axon regeneration / NOTCH4 Activation and Transmission of Signal to the Nucleus / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative regulation of synaptic vesicle exocytosis / establishment of Golgi localization / Signalling to p38 via RIT and RIN / respiratory system process / head morphogenesis / ARMS-mediated activation / tube formation / myeloid progenitor cell differentiation / endothelial cell apoptotic process / regulation of synapse maturation / 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 regulation of fibroblast migration / establishment of protein localization to membrane / positive regulation of axonogenesis / negative regulation of protein localization to nucleus / regulation of T cell differentiation / Negative feedback regulation of MAPK pathway / KSRP (KHSRP) binds and destabilizes mRNA / mitogen-activated protein kinase kinase binding / GP1b-IX-V activation signalling / Frs2-mediated activation / stress fiber assembly / face development / MAP kinase kinase activity / synaptic vesicle exocytosis / thyroid gland development / Regulation of localization of FOXO transcription factors / Interleukin-3, Interleukin-5 and GM-CSF signaling / somatic stem cell population maintenance / phosphoserine residue binding / positive regulation of peptidyl-serine phosphorylation / MAP kinase kinase kinase activity / Activation of BAD and translocation to mitochondria / postsynaptic modulation of chemical synaptic transmission / protein targeting / negative regulation of endothelial cell apoptotic process / regulation of ERK1 and ERK2 cascade / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / response to cAMP / cellular response to glucose starvation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / negative regulation of TORC1 signaling / ERK1 and ERK2 cascade / positive regulation of substrate adhesion-dependent cell spreading / Transcriptional and post-translational regulation of MITF-M expression and activity / substrate adhesion-dependent cell spreading / cellular response to calcium ion / protein sequestering activity / negative regulation of innate immune response / hippocampal mossy fiber to CA3 synapse / 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 / Translocation of SLC2A4 (GLUT4) to the plasma membrane / histone H3T45 kinase activity / TP53 Regulates Metabolic Genes / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / Deactivation of the beta-catenin transactivating complex / lung development / RAF activation / cellular response to nerve growth factor stimulus / Negative regulation of NOTCH4 signaling / Spry regulation of FGF signaling / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / visual learning / regulation of protein stability / response to peptide hormone / centriolar satellite / long-term synaptic potentiation / epidermal growth factor receptor signaling pathway
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 / 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 / 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
Serine/threonine-protein kinase B-raf / 14-3-3 protein zeta/delta
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.07 Å
AuthorsLavoie H / Lajoie D / Jin T / Decossas M / Maisonneuve P / Therrien M
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)FDN-388023 Canada
CitationJournal: Science / Year: 2025
Title: BRAF oncogenic mutants evade autoinhibition through a common mechanism.
Authors: Hugo Lavoie / Ting Jin / Driss Lajoie / Marion Decossas / Patrick Gendron / Bing Wang / Frantisek Filandr / Malha Sahmi / Chang Hwa Jo / Sandra Weber / Geneviève Arseneault / Sasmita ...Authors: Hugo Lavoie / Ting Jin / Driss Lajoie / Marion Decossas / Patrick Gendron / Bing Wang / Frantisek Filandr / Malha Sahmi / Chang Hwa Jo / Sandra Weber / Geneviève Arseneault / Sasmita Tripathy / Pierre Beaulieu / Doris A Schuetz / David C Schriemer / Anne Marinier / William J Rice / Pierre Maisonneuve / Marc Therrien /
Abstract: Uncontrolled activation of the rat sarcoma (RAS)-extracellular signal-regulated kinase (ERK) pathway drives tumor growth, often because of oncogenic BRAF mutations. BRAF regulation, involving ...Uncontrolled activation of the rat sarcoma (RAS)-extracellular signal-regulated kinase (ERK) pathway drives tumor growth, often because of oncogenic BRAF mutations. BRAF regulation, involving monomeric autoinhibition and activation by dimerization, has been intensely scrutinized, but mechanisms enabling oncogenic mutants to evade regulation remain unclear. By using cryo-electron microscopy, we solved the three-dimensional structures of the three oncogenic BRAF mutant classes, including the common V600E variant. These mutations disrupted wild-type BRAF's autoinhibited state, mediated by interactions between the cysteine-rich domain and kinase domain, thereby shifting the kinase domain into a preactivated conformation. This structural change likely results from helix αC displacement. PLX8394, a BRAF inhibitor that stabilizes helix αC in an inactive conformation, restored the autoinhibited conformation of oncogenic BRAF, explaining the properties of this class of compounds.
History
DepositionFeb 9, 2024-
Header (metadata) releaseMay 28, 2025-
Map releaseMay 28, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43678.png

Downloads & links

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Map

FileDownload / File: emd_43678.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 256 pix.
= 218.112 Å		0.85 Å/pix.
x 256 pix.
= 218.112 Å		0.85 Å/pix.
x 256 pix.
= 218.112 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.852 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.14670873 - 0.2596743
Average (Standard dev.)0.0002902862 (±0.008022727)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 218.112 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_43678_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_43678_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : BRAF WT - 14.3.3 complex bound to PLX8394

EntireName: BRAF WT - 14.3.3 complex bound to PLX8394
Components
  • Complex: BRAF WT - 14.3.3 complex bound to PLX8394
    • Protein or peptide: Serine/threonine-protein kinase B-raf
    • Protein or peptide: 14-3-3 protein zeta/delta
  • Ligand: (3S)-N-{3-[5-(2-cyclopropylpyrimidin-5-yl)-1H-pyrrolo[2,3-b]pyridine-3-carbonyl]-2,4-difluorophenyl}-3-fluoropyrrolidine-1-sulfonamide

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Supramolecule #1: BRAF WT - 14.3.3 complex bound to PLX8394

SupramoleculeName: BRAF WT - 14.3.3 complex bound to PLX8394 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: BRAF WT complex purified by Flag affinity purification followed by TEV elution from FreeStyle 293F cells
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 141 KDa

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Macromolecule #1: Serine/threonine-protein kinase B-raf

MacromoleculeName: Serine/threonine-protein kinase B-raf / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human) / Cell: FreeStyle 293-F cells
Molecular weightTheoretical: 84.770766 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GMAALSGGGG GGAEPGQALF NGDMEPEAGA GAGAAASSAA DPAIPEEVWN IKQMIKLTQE HIEALLDKFG GEHNPPSIYL EAYEEYTSK LDALQQREQQ LLESLGNGTD FSVSSSASMD TVTSSSSSSL SVLPSSLSVF QNPTDVARSN PKSPQKPIVR V FLPNKQRT ...String:
GMAALSGGGG GGAEPGQALF NGDMEPEAGA GAGAAASSAA DPAIPEEVWN IKQMIKLTQE HIEALLDKFG GEHNPPSIYL EAYEEYTSK LDALQQREQQ LLESLGNGTD FSVSSSASMD TVTSSSSSSL SVLPSSLSVF QNPTDVARSN PKSPQKPIVR V FLPNKQRT VVPARCGVTV RDSLKKALMM RGLIPECCAV YRIQDGEKKP IGWDTDISWL TGEELHVEVL ENVPLTTHNF VR KTFFTLA FCDFCRKLLF QGFRCQTCGY KFHQRCSTEV PLMCVNYDQL DLLFVSKFFE HHPIPQEEAS LAETALTSGS SPS APASDS IGPQILTSPS PSKSIPIPQP FRPADEDHRN QFGQRDRSS(SEP) APNVHINTIE PVNIDDLIRD QGFRGDGGST TGLSATPPA SLPGSLTNVK ALQKSPGPQR ERKSSSSSED RNRMKTLGRR DSSDDWEIPD GQITVGQRIG SGSFGTVYKG K WHGDVAVK MLNVTAPTPQ QLQAFKNEVG VLRKTRHVNI LLFMGYSTKP QLAIVTQWCE GSSLYHHLHI IETKFEMKKL ID IARQTAQ GMDYLHAKSI IHRDLKSNNI FLHEDLTVKI GDFGLATVKS RWSGSHQFEQ LSGSILWMAP EVIRMQDKNP YSF QSDVYA FGIVLYELMT GQLPYSNINN RDQIIFMVGR GYLSPDLSKV RSNCPKAMKR LMAECLKKKR DERPLFPQIL ASIE LLARS LPKIHRSA(SEP)E PSLNRAGFQT EDFSLYACAS PKTPIQAGGY GAFPVH

UniProtKB: Serine/threonine-protein kinase B-raf

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Macromolecule #2: 14-3-3 protein zeta/delta

MacromoleculeName: 14-3-3 protein zeta/delta / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.777092 KDa
SequenceString: MDKNELVQKA KLAEQAERYD DMAACMKSVT EQGAELSNEE RNLLSVAYKN VVGARRSSWR VVSSIEQKTE GAEKKQQMAR EYREKIETE LRDICNDVLS LLEKFLIPNA SQAESKVFYL KMKGDYYRYL AEVAAGDDKK GIVDQSQQAY QEAFEISKKE M QPTHPIRL ...String:
MDKNELVQKA KLAEQAERYD DMAACMKSVT EQGAELSNEE RNLLSVAYKN VVGARRSSWR VVSSIEQKTE GAEKKQQMAR EYREKIETE LRDICNDVLS LLEKFLIPNA SQAESKVFYL KMKGDYYRYL AEVAAGDDKK GIVDQSQQAY QEAFEISKKE M QPTHPIRL GLALNFSVFY YEILNSPEKA CSLAKTAFDE AIAELDTLSE ESYKDSTLIM QLLRDNLTLW TSDTQGDEAE AG EGGEN

UniProtKB: 14-3-3 protein zeta/delta

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Macromolecule #3: (3S)-N-{3-[5-(2-cyclopropylpyrimidin-5-yl)-1H-pyrrolo[2,3-b]pyrid...

MacromoleculeName: (3S)-N-{3-[5-(2-cyclopropylpyrimidin-5-yl)-1H-pyrrolo[2,3-b]pyridine-3-carbonyl]-2,4-difluorophenyl}-3-fluoropyrrolidine-1-sulfonamide
type: ligand / ID: 3 / Number of copies: 1 / Formula: A1AEN
Molecular weightTheoretical: 542.533 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H17N2NaO4SHEPES
137.0 mMNaClSodium Chloride
5.0 mMMgCl2Magnesium chloride
1.0 mMC9H15O6PTCEP
0.0005 mMC10H12Li4N5O12P3SATPgammaS
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Details: Chameleon system (SPT Labtech).

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 52.82 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.4 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7mfe

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.07 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Resolution corresponds to the FSC 0.143 cut-off of the masked map.
Number images used: 45558
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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