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- EMDB-77012: BRAF/CRAF/MEK1/14-3-3 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-77012
TitleBRAF/CRAF/MEK1/14-3-3 complex
Map data
Sample
  • Complex: BRAF/CRAF/MEK1/14-3-3 complex
    • Protein or peptide: 14-3-3 protein epsilon
    • Protein or peptide: 14-3-3 protein zeta
  • Protein or peptide: Serine/threonine-protein kinase B-raf
  • Protein or peptide: RAF proto-oncogene serine/threonine-protein kinase
  • Protein or peptide: Dual specificity mitogen-activated protein kinase kinase 1
  • Ligand: 2-{4-[(1E)-1-(hydroxyimino)-2,3-dihydro-1H-inden-5-yl]-3-(pyridin-4-yl)-1H-pyrazol-1-yl}ethanol
  • Ligand: 5-[(2-fluoro-4-iodophenyl)amino]-N-(2-hydroxyethoxy)imidazo[1,5-a]pyridine-6-carboxamide
KeywordsSer/Thr kinase / map kinase signal / protein kinase / SIGNALING PROTEIN
Function / homology
Function and homology information


negative regulation of homotypic cell-cell adhesion / regulation of vascular associated smooth muscle contraction / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / mitogen-activated protein kinase kinase / melanosome transport / Golgi inheritance / MAP kinase scaffold activity / Signalling to p38 via RIT and RIN / positive regulation of muscle contraction / ARMS-mediated activation ...negative regulation of homotypic cell-cell adhesion / regulation of vascular associated smooth muscle contraction / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / mitogen-activated protein kinase kinase / melanosome transport / Golgi inheritance / MAP kinase scaffold activity / Signalling to p38 via RIT and RIN / positive regulation of muscle contraction / ARMS-mediated activation / regulation of Rho protein signal transduction / establishment of protein localization to membrane / Signaling by MAP2K mutants / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / positive regulation of D-glucose transmembrane transport / vesicle transport along microtubule / regulation of Golgi inheritance / mitogen-activated protein kinase kinase kinase binding / positive regulation of protein serine/threonine kinase activity / regulation of early endosome to late endosome transport / triglyceride homeostasis / regulation of stress-activated MAPK cascade / Negative feedback regulation of MAPK pathway / IFNG signaling activates MAPKs / GP1b-IX-V activation signalling / Frs2-mediated activation / MAPK3 (ERK1) activation / ERBB2-ERBB3 signaling pathway / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / MAP kinase kinase activity / regulation of cell differentiation / pseudopodium / response to axon injury / positive regulation of ATP biosynthetic process / ERK1 and ERK2 cascade / neuromuscular junction development / Uptake and function of anthrax toxins / positive regulation of peptidyl-serine phosphorylation / MAP kinase kinase kinase activity / type II interferon-mediated signaling pathway / protein kinase activator activity / 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 / protein serine/threonine/tyrosine kinase activity / cellular response to calcium ion / positive regulation of autophagy / neuron projection morphogenesis / CD209 (DC-SIGN) signaling / response to glucocorticoid / protein serine/threonine kinase activator activity / dendrite cytoplasm / adenylate cyclase activator activity / wound healing / Signal transduction by L1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / positive regulation of transcription elongation by RNA polymerase II / RAF activation / Signaling by high-kinase activity BRAF mutants / Spry regulation of FGF signaling / MAP2K and MAPK activation / chemotaxis / cellular senescence / insulin receptor signaling pathway / small GTPase binding / 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 / neuron differentiation / late endosome / microtubule / ciliary basal body / response to oxidative stress / protein tyrosine kinase activity / cell body / scaffold protein binding / cell cortex / early endosome / regulation of apoptotic process / perikaryon / 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
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. ...: / 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. / 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
14-3-3 protein epsilon / 14-3-3 protein zeta / RAF proto-oncogene serine/threonine-protein kinase / Serine/threonine-protein kinase B-raf / Dual specificity mitogen-activated protein kinase kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human) / Spodoptera frugiperda (fall armyworm)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsHa BH / Jeon H / Eck MJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R35CA242461 United States
CitationJournal: To Be Published
Title: Complex structure of BRAF/CRAF/MEK1/14-3-3
Authors: Ha BH / Eck MJ
History
DepositionMay 1, 2026-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77012.png

Downloads & links

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Map

FileDownload / File: emd_77012.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.99 Å/pix.
x 300 pix.
= 296.957 Å		0.99 Å/pix.
x 300 pix.
= 296.957 Å		0.99 Å/pix.
x 300 pix.
= 296.957 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.98986 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005588
Minimum - Maximum-0.03363202 - 0.05356775
Average (Standard dev.)0.000016198517 (±0.0011301574)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 296.9568 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_77012_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_77012_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_77012_half_map_2.map
Projections & Slices
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Sample components

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Entire : BRAF/CRAF/MEK1/14-3-3 complex

EntireName: BRAF/CRAF/MEK1/14-3-3 complex
Components
  • Complex: BRAF/CRAF/MEK1/14-3-3 complex
    • Protein or peptide: 14-3-3 protein epsilon
    • Protein or peptide: 14-3-3 protein zeta
  • Protein or peptide: Serine/threonine-protein kinase B-raf
  • Protein or peptide: RAF proto-oncogene serine/threonine-protein kinase
  • Protein or peptide: Dual specificity mitogen-activated protein kinase kinase 1
  • Ligand: 2-{4-[(1E)-1-(hydroxyimino)-2,3-dihydro-1H-inden-5-yl]-3-(pyridin-4-yl)-1H-pyrazol-1-yl}ethanol
  • Ligand: 5-[(2-fluoro-4-iodophenyl)amino]-N-(2-hydroxyethoxy)imidazo[1,5-a]pyridine-6-carboxamide

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Supramolecule #1: BRAF/CRAF/MEK1/14-3-3 complex

SupramoleculeName: BRAF/CRAF/MEK1/14-3-3 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #4-#5
Source (natural)Organism: Homo sapiens (human)

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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)
Molecular weightTheoretical: 40.26107 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDWSHPQFEK SAVDENLYFQ GGRNRMKTLG RRDSSDDWEI PDGQITVGQR IGSGSFGTVY KGKWHGDVAV KMLNVTAPTP QQLQAFKNE VGVLRKTRHV NILLFMGYST KPQLAIVTQW CEGSSLYHHL HIIETKFEMI KLIDIARQTA QGMDYLHAKS I IHRDLKSN ...String:
MDWSHPQFEK SAVDENLYFQ GGRNRMKTLG RRDSSDDWEI PDGQITVGQR IGSGSFGTVY KGKWHGDVAV KMLNVTAPTP QQLQAFKNE VGVLRKTRHV NILLFMGYST KPQLAIVTQW CEGSSLYHHL HIIETKFEMI KLIDIARQTA QGMDYLHAKS I IHRDLKSN NIFLHEDLTV KIGDFGLATV KSRWSGSHQF EQLSGSILWM APEVIRMQDK NPYSFQSDVY AFGIVLYELM TG QLPYSNI NNRDQIIFMV GRGYLSPDLS KVRSNCPKAM KRLMAECLKK KRDERPLFPQ ILASIELLAR SLPKIHRSA (SEP)EPSLNRAGF QTEDFSLYAC ASPKTPIQAG GYGAFPVH

UniProtKB: Serine/threonine-protein kinase B-raf

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Macromolecule #2: RAF proto-oncogene serine/threonine-protein kinase

MacromoleculeName: RAF proto-oncogene serine/threonine-protein kinase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.662324 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGSSHHHHHH SAVDENLYFQ GGGRSQPKTP VPAQRERAPV SGTQEKNKIR PRGQRDSSDD WEIEASEVML STRIGSGSFG TVYKGKWHG DVAVKILKVV DPTPEQFQAF RNEVAVLRKT RHVNILLFMG YMTKDNLAIV TQWCEGSSLY KHLHVQETKF Q MFQLIDIA ...String:
MGSSHHHHHH SAVDENLYFQ GGGRSQPKTP VPAQRERAPV SGTQEKNKIR PRGQRDSSDD WEIEASEVML STRIGSGSFG TVYKGKWHG DVAVKILKVV DPTPEQFQAF RNEVAVLRKT RHVNILLFMG YMTKDNLAIV TQWCEGSSLY KHLHVQETKF Q MFQLIDIA RQTAQGMDYL HAKNIIHRDM KSNNIFLHEG LTVKIGDFGL ATVKSRWSGS QQVEQPTGSV LWMAPEVIRM QD NNPFSFQ SDVYSYGIVL YELMTGELPY SHINNRDQII EMVGAGYASP DLSKLYKNCP KAMKRLVADC VKKVKEERPL FPQ ILSSIE LLQHSLPKIN RSA(SEP)EPSLHR AAHTEDINAC TLTTSPRLPV F

UniProtKB: RAF proto-oncogene serine/threonine-protein kinase

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Macromolecule #3: Dual specificity mitogen-activated protein kinase kinase 1

MacromoleculeName: Dual specificity mitogen-activated protein kinase kinase 1
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: mitogen-activated protein kinase kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.477148 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGSSHHHHHH SAVDENLYFQ GGGRSQLMPK KKPTPIQLNP APDGSAVNGT SSAETNLEAL QKKLEELELD EQQRKRLEAF LTQKQKVGE LKDDDFEKIS ELGAGNGGVV FKVSHKPSGL VMARKLIHLE IKPAIRNQII RELQVLHECN SPYIVGFYGA F YSDGEISI ...String:
MGSSHHHHHH SAVDENLYFQ GGGRSQLMPK KKPTPIQLNP APDGSAVNGT SSAETNLEAL QKKLEELELD EQQRKRLEAF LTQKQKVGE LKDDDFEKIS ELGAGNGGVV FKVSHKPSGL VMARKLIHLE IKPAIRNQII RELQVLHECN SPYIVGFYGA F YSDGEISI CMEHMDGGSL DQVLKKAGRI PEQILGKVSI AVIKGLTYLR EKHKIMHRDV KPSNILVNSR GEIKLCDFGV SG QLIDAMA NAFVGTRSYM SPERLQGTHY SVQSDIWSMG LSLVEMAVGR YPIPPPDAKE LELMFGCQVE GDAAETPPRP RTP GRPLSS YGMDSRPPMA IFELLDYIVN EPPPKLPSGV FSLEFQDFVN KCLIKNPAER ADLKQLMVHA FIKRSDAEEV DFAG WLCST IGLNQPSTPT HAAGV

UniProtKB: Dual specificity mitogen-activated protein kinase kinase 1

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Macromolecule #4: 14-3-3 protein epsilon

MacromoleculeName: 14-3-3 protein epsilon / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spodoptera frugiperda (fall armyworm)
Molecular weightTheoretical: 29.752178 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSEREDNVYK AKLAEQAERY DEMVEAMKNV ASRNVSDNEL TVEERNLLSV AYKNVIGARR ASWRIISSIE QKEETKGAEG KLNMIRAYR SQVEKELRDI CSDILGVLDK HLIPSSQTGE SKVFYYKMKG DYHRYLAEFA TGNDRKEAAE NSLVAYKAAS D IAMTELPP ...String:
MSEREDNVYK AKLAEQAERY DEMVEAMKNV ASRNVSDNEL TVEERNLLSV AYKNVIGARR ASWRIISSIE QKEETKGAEG KLNMIRAYR SQVEKELRDI CSDILGVLDK HLIPSSQTGE SKVFYYKMKG DYHRYLAEFA TGNDRKEAAE NSLVAYKAAS D IAMTELPP THPIRLGLAL NFSVFYYEIL NSPDRACRLA KAAFDDAIAE LDTLSEESYK DSTLIMQLLR DNLTLWTSDM QG DGESGET EQKEQPQDVE DQDVS

UniProtKB: 14-3-3 protein epsilon

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Macromolecule #5: 14-3-3 protein zeta

MacromoleculeName: 14-3-3 protein zeta / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spodoptera frugiperda (fall armyworm)
Molecular weightTheoretical: 28.108514 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSVDKEELVQ RAKLAEQAER YDDMAAAMKE VTETGVELSN EERNLLSVAY KNVVGARRSS WRVISSIEQK TEGSERKQQM AKEYRVKVE KELREICYDV LGLLDKHLIP KASNPESKVF YLKMKGDYYR YLAEVATGET RNSVVEDSQK AYQDAFEISK A KMQPTHPI ...String:
MSVDKEELVQ RAKLAEQAER YDDMAAAMKE VTETGVELSN EERNLLSVAY KNVVGARRSS WRVISSIEQK TEGSERKQQM AKEYRVKVE KELREICYDV LGLLDKHLIP KASNPESKVF YLKMKGDYYR YLAEVATGET RNSVVEDSQK AYQDAFEISK A KMQPTHPI RLGLALNFSV FYYEILNSPD KACQLAKQAF DDAIAELDTL NEDSYKDSTL IMQLLRDNLT LWTSDTQGDG DE PAEGGDN

UniProtKB: 14-3-3 protein zeta

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Macromolecule #6: 2-{4-[(1E)-1-(hydroxyimino)-2,3-dihydro-1H-inden-5-yl]-3-(pyridin...

MacromoleculeName: 2-{4-[(1E)-1-(hydroxyimino)-2,3-dihydro-1H-inden-5-yl]-3-(pyridin-4-yl)-1H-pyrazol-1-yl}ethanol
type: ligand / ID: 6 / Number of copies: 2 / Formula: 29L
Molecular weightTheoretical: 334.372 Da
Chemical component information

ChemComp-29L:
2-{4-[(1E)-1-(hydroxyimino)-2,3-dihydro-1H-inden-5-yl]-3-(pyridin-4-yl)-1H-pyrazol-1-yl}ethanol

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Macromolecule #7: 5-[(2-fluoro-4-iodophenyl)amino]-N-(2-hydroxyethoxy)imidazo[1,5-a...

MacromoleculeName: 5-[(2-fluoro-4-iodophenyl)amino]-N-(2-hydroxyethoxy)imidazo[1,5-a]pyridine-6-carboxamide
type: ligand / ID: 7 / Number of copies: 1 / Formula: LCJ
Molecular weightTheoretical: 456.21 Da
Chemical component information

ChemComp-LCJ:
5-[(2-fluoro-4-iodophenyl)amino]-N-(2-hydroxyethoxy)imidazo[1,5-a]pyridine-6-carboxamide

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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

BufferpH: 8
Details: 25mM Tris-HCl pH 8.0, 0.15M NaCl, 5mM MgCl2, 1mM TCEP, 1uM ATP-gamma-S
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 62.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6nyb

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 171208
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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