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- EMDB-70053: Autoinhibited BRAF:(14-3-3)2:MEK complex from Insect cells -

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Basic information

Entry
Database: EMDB / ID: EMD-70053
TitleAutoinhibited BRAF:(14-3-3)2:MEK complex from Insect cells
Map data
Sample
  • Complex: Autoinhibited B-Raf:(14-3-3)2:MEK complex
    • Protein or peptide: Serine/threonine-protein kinase B-raf
    • Protein or peptide: Dual specificity mitogen-activated protein kinase kinase 1
    • Protein or peptide: 14-3-3 protein zeta/delta
  • Ligand: ZINC ION
  • Ligand: N-(3-fluoro-4-{[4-methyl-2-oxo-7-(pyrimidin-2-yloxy)-2H-chromen-3-yl]methyl}pyridin-2-yl)-N'-methylsulfuric diamide
KeywordsB-Raf / MEK / 14-3-3 / B-Raf complex / B-Raf monomer / Inactive B-Raf / Serine/threonine-protein kinase B-raf / RBD / signaling protein / SIGNALING PROTEIN-TRANSFERASE complex
Function / homology
Function and homology information


epithelial cell proliferation involved in lung morphogenesis / synaptic target recognition / negative regulation of homotypic cell-cell adhesion / Golgi reassembly / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / positive regulation of endodermal cell differentiation / regulation of vascular associated smooth muscle contraction / CD4-positive, alpha-beta T cell differentiation / positive regulation of axon regeneration / NOTCH4 Activation and Transmission of Signal to the Nucleus ...epithelial cell proliferation involved in lung morphogenesis / synaptic target recognition / negative regulation of homotypic cell-cell adhesion / Golgi reassembly / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / positive regulation of endodermal cell differentiation / regulation of vascular associated smooth muscle contraction / CD4-positive, alpha-beta T cell differentiation / positive regulation of axon regeneration / NOTCH4 Activation and Transmission of Signal to the Nucleus / mitogen-activated protein kinase kinase / Golgi inheritance / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / placenta blood vessel development / MAP-kinase scaffold activity / negative regulation of synaptic vesicle exocytosis / positive regulation of muscle contraction / establishment of Golgi localization / labyrinthine layer development / regulation of axon regeneration / cerebellar cortex formation / Signalling to p38 via RIT and RIN / melanosome transport / respiratory system process / head morphogenesis / ARMS-mediated activation / type B pancreatic cell proliferation / tube formation / endothelial cell apoptotic process / regulation of synapse maturation / myeloid progenitor cell differentiation / Signaling by MAP2K mutants / 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 / Rap1 signalling / vesicle transport along microtubule / establishment of protein localization to membrane / positive regulation of axonogenesis / positive regulation of Ras protein signal transduction / negative regulation of protein localization to nucleus / regulation of Golgi inheritance / mitogen-activated protein kinase kinase kinase binding / central nervous system neuron differentiation / regulation of T cell differentiation / triglyceride homeostasis / trachea formation / KSRP (KHSRP) binds and destabilizes mRNA / Negative feedback regulation of MAPK pathway / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / GP1b-IX-V activation signalling / Frs2-mediated activation / stress fiber assembly / MAPK3 (ERK1) activation / ERBB2-ERBB3 signaling pathway / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / endodermal cell differentiation / face development / MAP kinase kinase activity / Bergmann glial cell differentiation / positive regulation of ATP biosynthetic process / thyroid gland development / Uptake and function of anthrax toxins / neuron projection morphogenesis / synaptic vesicle exocytosis / Interleukin-3, Interleukin-5 and GM-CSF signaling / Regulation of localization of FOXO transcription factors / protein kinase activator activity / positive regulation of protein serine/threonine kinase activity / positive regulation of peptidyl-serine phosphorylation / somatic stem cell population maintenance / MAP kinase kinase kinase activity / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of endothelial cell apoptotic process / protein targeting / postsynaptic modulation of chemical synaptic transmission / response to axon injury / regulation of ERK1 and ERK2 cascade / Schwann cell development / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / cellular response to glucose starvation / keratinocyte differentiation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / MAP3K8 (TPL2)-dependent MAPK1/3 activation / positive regulation of stress fiber assembly / negative regulation of TORC1 signaling / ERK1 and ERK2 cascade / myelination / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of autophagy / protein serine/threonine/tyrosine kinase activity / Transcriptional and post-translational regulation of MITF-M expression and activity / substrate adhesion-dependent cell spreading / dendrite cytoplasm / insulin-like 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. ...: / 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. / 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
Serine/threonine-protein kinase B-raf / 14-3-3 protein zeta/delta / Dual specificity mitogen-activated protein kinase kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.83 Å
AuthorsMartinez Fiesco JA / Zhang P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: Autoinhibited BRAF:(14-3-3)2:MEK complex from Insect cells
Authors: Martinez Fiesco JA / Zhang P
History
DepositionApr 4, 2025-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70053.png

Downloads & links

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Map

FileDownload / File: emd_70053.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 340 pix.
= 275.4 Å		0.81 Å/pix.
x 340 pix.
= 275.4 Å		0.81 Å/pix.
x 340 pix.
= 275.4 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.079
Minimum - Maximum-0.38099712 - 0.534253
Average (Standard dev.)0.00018087454 (±0.01229643)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 275.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_70053_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_70053_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Autoinhibited B-Raf:(14-3-3)2:MEK complex

EntireName: Autoinhibited B-Raf:(14-3-3)2:MEK complex
Components
  • Complex: Autoinhibited B-Raf:(14-3-3)2:MEK complex
    • Protein or peptide: Serine/threonine-protein kinase B-raf
    • Protein or peptide: Dual specificity mitogen-activated protein kinase kinase 1
    • Protein or peptide: 14-3-3 protein zeta/delta
  • Ligand: ZINC ION
  • Ligand: N-(3-fluoro-4-{[4-methyl-2-oxo-7-(pyrimidin-2-yloxy)-2H-chromen-3-yl]methyl}pyridin-2-yl)-N'-methylsulfuric diamide

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Supramolecule #1: Autoinhibited B-Raf:(14-3-3)2:MEK complex

SupramoleculeName: Autoinhibited B-Raf:(14-3-3)2:MEK complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
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: 84.697695 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAALSGGGGG GAEPGQALFN GDMEPEAGAG AGAAASSAAD PAIPEEVWNI KQMIKLTQEH IEALLDKFGG EHNPPSIYLE AYEEYTSKL DALQQREQQL LESLGNGTDF SVSSSASMDT VTSSSSSSLS VLPSSLSVFQ NPTDVARSNP KSPQKPIVRV F LPNKQRTV ...String:
MAALSGGGGG GAEPGQALFN GDMEPEAGAG AGAAASSAAD PAIPEEVWNI KQMIKLTQEH IEALLDKFGG EHNPPSIYLE AYEEYTSKL DALQQREQQL LESLGNGTDF SVSSSASMDT VTSSSSSSLS VLPSSLSVFQ NPTDVARSNP KSPQKPIVRV F LPNKQRTV VPARCGVTVR DSLKKALMMR GLIPECCAVY RIQDGEKKPI GWDTDISWLT GEELHVEVLE NVPLTTHNFV RK TFFTLAF CDFCRKLLFQ GFRCQTCGYK FHQRCSTEVP LMCVNYDQLD LLFVSKFFEH HPIPQEEASL AETALTSGSS PSA PASDSI GPQILTSPSP SKSIPIPQPF RPADEDHRNQ FGQRDRSS(SEP)A PNVHINTIEP VNIDDLIRDQ GFRGDGGSTT GLSATPPAS LPGSLTNVKA LQKSPGPQRE RKSSSSSEDR NRMKTLGRRD SSDDWEIPDG QITVGQRIGS GSFGTVYKGK W HGDVAVKM LNVTAPTPQQ LQAFKNEVGV LRKTRHVNIL LFMGYSTKPQ LAIVTQWCEG SSLYHHLHII ETKFEMIKLI DI ARQTAQG MDYLHAKSII HRDLKSNNIF LHEDLTVKIG DFGLATVKSR WSGSHQFEQL SGSILWMAPE VIRMQDKNPY SFQ SDVYAF GIVLYELMTG QLPYSNINNR DQIIFMVGRG YLSPDLSKVR SNCPKAMKRL MAECLKKKRD ERPLFPQILA SIEL LARSL PKIHRSA(SEP)EP SLNRAGFQTE DFSLYACASP KTPIQAGGYG AFPVH

UniProtKB: Serine/threonine-protein kinase B-raf

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Macromolecule #2: Dual specificity mitogen-activated protein kinase kinase 1

MacromoleculeName: Dual specificity mitogen-activated protein kinase kinase 1
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: mitogen-activated protein kinase kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.493938 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MPKKKPTPIQ LNPAPDGSAV NGTSSAETNL EALQKKLEEL ELDEQQRKRL EAFLTQKQKV GELKDDDFEK ISELGAGNGG VVFKVSHKP SGLVMARKLI HLEIKPAIRN QIIRELQVLH ECNSPYIVGF YGAFYSDGEI SICMEHMDGG SLDQVLKKAG R IPEQILGK ...String:
MPKKKPTPIQ LNPAPDGSAV NGTSSAETNL EALQKKLEEL ELDEQQRKRL EAFLTQKQKV GELKDDDFEK ISELGAGNGG VVFKVSHKP SGLVMARKLI HLEIKPAIRN QIIRELQVLH ECNSPYIVGF YGAFYSDGEI SICMEHMDGG SLDQVLKKAG R IPEQILGK VSIAVIKGLT YLREKHKIMH RDVKPSNILV NSRGEIKLCD FGVSGQLIDS MANSFVGTRS YMSPERLQGT HY SVQSDIW SMGLSLVEMA VGRYPIPPPD AKELELMFGC QVEGDAAETP PRPRTPGRPL SSYGMDSRPP MAIFELLDYI VNE PPPKLP SGVFSLEFQD FVNKCLIKNP AERADLKQLM VHAFIKRSDA EEVDFAGWLC STIGLNQPST PTHAAGV

UniProtKB: Dual specificity mitogen-activated protein kinase kinase 1

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

MacromoleculeName: 14-3-3 protein zeta/delta / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.777092 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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 #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: N-(3-fluoro-4-{[4-methyl-2-oxo-7-(pyrimidin-2-yloxy)-2H-chromen-3...

MacromoleculeName: N-(3-fluoro-4-{[4-methyl-2-oxo-7-(pyrimidin-2-yloxy)-2H-chromen-3-yl]methyl}pyridin-2-yl)-N'-methylsulfuric diamide
type: ligand / ID: 5 / Number of copies: 1 / Formula: CHU
Molecular weightTheoretical: 471.462 Da
Chemical component information

ChemComp-CHU:
N-(3-fluoro-4-{[4-methyl-2-oxo-7-(pyrimidin-2-yloxy)-2H-chromen-3-yl]methyl}pyridin-2-yl)-N'-methylsulfuric diamide

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm

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Image processing

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

7mfd

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 144979
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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