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- EMDB-48401: Cryo-EM structure of CRAF/MEK1/14-3-3 complex (open monomer confo... -

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Entry
Database: EMDB / ID: EMD-48401
TitleCryo-EM structure of CRAF/MEK1/14-3-3 complex (open monomer conformation, CRAF Y340D/Y341D mutant)
Map data
Sample
  • Complex: CRAF/MEK1/14-3-3 complex
    • Complex: CRAF
      • Protein or peptide: RAF proto-oncogene serine/threonine-protein kinase
    • Complex: MEK1
      • Protein or peptide: Dual specificity mitogen-activated protein kinase kinase 1
    • Complex: 14-3-3 dimer
      • Protein or peptide: 14-3-3 protein zeta
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: 5-[(2-fluoro-4-iodophenyl)amino]-N-(2-hydroxyethoxy)imidazo[1,5-a]pyridine-6-carboxamide
KeywordsCRAF-MEK1-14-3-3 complex / MAPK pathway / TRANSFERASE
Function / homology
Function and homology information


insulin secretion involved in cellular response to glucose stimulus / death-inducing signaling complex assembly / negative regulation of homotypic cell-cell adhesion / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / regulation of vascular associated smooth muscle contraction / intermediate filament cytoskeleton organization / mitogen-activated protein kinase kinase / Golgi inheritance / MAP kinase scaffold activity / type B pancreatic cell proliferation ...insulin secretion involved in cellular response to glucose stimulus / death-inducing signaling complex assembly / negative regulation of homotypic cell-cell adhesion / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / regulation of vascular associated smooth muscle contraction / intermediate filament cytoskeleton organization / mitogen-activated protein kinase kinase / Golgi inheritance / MAP kinase scaffold activity / type B pancreatic cell proliferation / positive regulation of muscle contraction / melanosome transport / regulation of Rho protein signal transduction / Signaling by MAP2K mutants / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / vesicle transport along microtubule / regulation of Golgi inheritance / mitogen-activated protein kinase kinase kinase binding / triglyceride homeostasis / regulation of early endosome to late endosome transport / Negative feedback regulation of MAPK pathway / neurotrophin TRK receptor signaling pathway / regulation of stress-activated MAPK cascade / IFNG signaling activates MAPKs / GP1b-IX-V activation signalling / Frs2-mediated activation / face development / MAPK3 (ERK1) activation / thyroid gland development / ERBB2-ERBB3 signaling pathway / MAP kinase kinase activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of protein serine/threonine kinase activity / extrinsic apoptotic signaling pathway via death domain receptors / pseudopodium / somatic stem cell population maintenance / regulation of cell differentiation / positive regulation of ATP biosynthetic process / neuromuscular junction development / Uptake and function of anthrax toxins / positive regulation of peptidyl-serine phosphorylation / MAP kinase kinase kinase activity / response to axon injury / type II interferon-mediated signaling pathway / protein kinase activator activity / ERK1 and ERK2 cascade / Schwann cell development / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of protein-containing complex assembly / response to muscle stretch / neuron projection morphogenesis / myelination / insulin-like growth factor receptor signaling pathway / protein serine/threonine/tyrosine kinase activity / thymus development / CD209 (DC-SIGN) signaling / positive regulation of autophagy / dendrite cytoplasm / response to glucocorticoid / adenylate cyclase activator activity / Signal transduction by L1 / protein serine/threonine kinase activator activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / wound healing / positive regulation of transcription elongation by RNA polymerase II / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / cellular senescence / small GTPase binding / Stimuli-sensing channels / chemotaxis / neuron differentiation / 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 / Negative regulation of MAPK pathway / insulin receptor signaling pathway / Signaling by BRAF and RAF1 fusions / late endosome / MAPK cascade / protein tyrosine kinase activity / response to oxidative stress / scaffold protein binding / regulation of apoptotic process / cell cortex / microtubule / perikaryon / protein phosphorylation / positive regulation of MAPK cascade / early endosome / positive regulation of ERK1 and ERK2 cascade / protein kinase activity / mitochondrial outer membrane / non-specific serine/threonine protein kinase / ciliary basal body / postsynaptic density
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
RAF proto-oncogene serine/threonine-protein kinase / Dual specificity mitogen-activated protein kinase kinase 1 / 14-3-3 protein zeta
Similarity search - Component
Biological speciesHomo sapiens (human) / Spodoptera exigua (beet armyworm)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsJang DM / Jeon H / Eck MJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R35CA242461-06 United States
CitationJournal: Nat Commun / Year: 2025
Title: Cryo-EM structures of CRAF/MEK1/14-3-3 complexes in autoinhibited and open-monomer states reveal features of RAF regulation.
Authors: Dong Man Jang / Kayla Boxer / Byung Hak Ha / Emre Tkacik / Talya Levitz / Shaun Rawson / Rebecca J Metivier / Anna Schmoker / Hyesung Jeon / Michael J Eck /
Abstract: CRAF (RAF1) is one of three RAF-family kinases that initiate MAP kinase signaling in response to activated RAS and is essential for oncogenic signaling from mutant KRAS. Like BRAF, CRAF is regulated ...CRAF (RAF1) is one of three RAF-family kinases that initiate MAP kinase signaling in response to activated RAS and is essential for oncogenic signaling from mutant KRAS. Like BRAF, CRAF is regulated by 14-3-3 engagement and by intramolecular autoinhibitory interactions of its N-terminal regulatory region. Unlike BRAF, it is thought to require tyrosine phosphorylation in its N-terminal acidic (NtA) motif for full catalytic activation. Here we describe cryo-EM reconstructions of full-length CRAF in complex with MEK1 and a 14-3-3 dimer. These structures reveal a fully autoinhibited conformation analogous to that observed for BRAF and two "open monomer" states in which the inhibitory interactions of the CRD and 14-3-3 dimer are released or rearranged, but the kinase domain remains inactive. Structure-function studies of the NtA motif indicate that phosphorylation or acidic mutations in this segment increase catalytic activity by destabilizing the inactive conformation of the kinase domain. Collectively, these studies provide a structural foundation for understanding the shared and unique regulatory features of CRAF and will inform efforts to selectively block CRAF signaling in cancer.
History
DepositionDec 20, 2024-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48401.png

Downloads & links

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Map

FileDownload / File: emd_48401.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 350 pix.
= 255.5 Å		0.73 Å/pix.
x 350 pix.
= 255.5 Å		0.73 Å/pix.
x 350 pix.
= 255.5 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.03701385 - 0.0860925
Average (Standard dev.)0.000016444255 (±0.002287388)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 255.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48401_msk_1.map
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Half map: #2

Fileemd_48401_half_map_1.map
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Half map: #1

Fileemd_48401_half_map_2.map
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Sample components

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

EntireName: CRAF/MEK1/14-3-3 complex
Components
  • Complex: CRAF/MEK1/14-3-3 complex
    • Complex: CRAF
      • Protein or peptide: RAF proto-oncogene serine/threonine-protein kinase
    • Complex: MEK1
      • Protein or peptide: Dual specificity mitogen-activated protein kinase kinase 1
    • Complex: 14-3-3 dimer
      • Protein or peptide: 14-3-3 protein zeta
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: 5-[(2-fluoro-4-iodophenyl)amino]-N-(2-hydroxyethoxy)imidazo[1,5-a]pyridine-6-carboxamide

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

SupramoleculeName: CRAF/MEK1/14-3-3 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55 KDa

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Supramolecule #2: CRAF

SupramoleculeName: CRAF / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: MEK1

SupramoleculeName: MEK1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: 14-3-3 dimer

SupramoleculeName: 14-3-3 dimer / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Spodoptera exigua (beet armyworm)

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Macromolecule #1: RAF proto-oncogene serine/threonine-protein kinase

MacromoleculeName: RAF proto-oncogene serine/threonine-protein kinase / 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: 76.961586 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGSSHHHHHH SAVDENLYFQ GGMEHIQGAW KTISNGFGFK DAVFDGSSCI SPTIVQQFGY QRRASDDGKL TDPSKTSNTI RVFLPNKQR TVVNVRNGMS LHDCLMKALK VRGLQPECCA VFRLLHEHKG KKARLDWNTD AASLIGEELQ VDFLDHVPLT T HNFARKTF ...String:
MGSSHHHHHH SAVDENLYFQ GGMEHIQGAW KTISNGFGFK DAVFDGSSCI SPTIVQQFGY QRRASDDGKL TDPSKTSNTI RVFLPNKQR TVVNVRNGMS LHDCLMKALK VRGLQPECCA VFRLLHEHKG KKARLDWNTD AASLIGEELQ VDFLDHVPLT T HNFARKTF LKLAFCDICR KFLLNGFRCQ TCGYKFHEHC STKVPTMCVD WSNIRQLLLF PNSTIGDSGV PALPSLTMRR MR ESVSRMP VSSQHRYSTP HAFTFNTSSP SSEGSLSQRQ RSTSTPNVHM VSTTLPVDSR MIEDAIRSHS ESASPSALSS SPN NLSPTG WSQPKTPVPA QRERAPVSGT QEKNKIRPRG QRDSSDDWEI EASEVMLSTR IGSGSFGTVY KGKWHGDVAV KILK VVDPT PEQFQAFRNE VAVLRKTRHV NILLFMGYMT KDNLAIVTQW CEGSSLYKHL HVQETKFQMF QLIDIARQTA QGMDY LHAK NIIHRDMKSN NIFLHEGLTV KIGDFGLATV KSRWSGSQQV EQPTGSVLWM APEVIRMQDN NPFSFQSDVY SYGIVL YEL MTGELPYSHI NNRDQIIFMV GRGYASPDLS KLYKNCPKAM KRLVAECVKK VKEERPLFPQ ILSSIELLQH SLPKINR SA (SEP)EPSLHRAAH TEDINACTLT TSPRLPVFVP AWSHPQFEK

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

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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: 45.934543 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGSSHHHHHH SAVDENLYFQ GGMPKKKPTP IQLNPAPDGS AVNGTSSAET NLEALQKKLE ELELDEQQRK RLEAFLTQKQ KVGELKDDD FEKISELGAG NGGVVFKVSH KPSGLVMARK LIHLEIKPAI RNQIIRELQV LHECNSPYIV GFYGAFYSDG E ISICMEHM ...String:
MGSSHHHHHH SAVDENLYFQ GGMPKKKPTP IQLNPAPDGS AVNGTSSAET NLEALQKKLE ELELDEQQRK RLEAFLTQKQ KVGELKDDD FEKISELGAG NGGVVFKVSH KPSGLVMARK LIHLEIKPAI RNQIIRELQV LHECNSPYIV GFYGAFYSDG E ISICMEHM DGGSLDQVLK KAGRIPEQIL GKVSIAVIKG LTYLREKHKI MHRDVKPSNI LVNSRGEIKL CDFGVSGQLI DA MANAFVG TRSYMSPERL QGTHYSVQSD IWSMGLSLVE MAVGRYPIPP PDAKELELMF GCQVEGDAAE TPPRPRTPGR PLS SYGMDS RPPMAIFELL DYIVNEPPPK LPSGVFSLEF QDFVNKCLIK NPAERADLKQ LMVHAFIKRS DAEEVDFAGW LCST IGLNQ PSTPTHAAGV

UniProtKB: Dual specificity mitogen-activated protein kinase kinase 1

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Macromolecule #3: 14-3-3 protein zeta

MacromoleculeName: 14-3-3 protein zeta / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Spodoptera exigua (beet armyworm)
Molecular weightTheoretical: 28.108514 KDa
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 #4: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 4 / Number of copies: 2 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: 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: 6 / 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

Concentration0.4 mg/mL
BufferpH: 7.5
Details: 50 mM Tris pH 7.5, 150 mM NaCl, 2 mM MgCl2, 0.5 mM TCEP, 2 uM ATPgS, 1 uM GDC0623
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON I (4k x 4k) / Number grids imaged: 1 / Number real images: 6060 / Average electron dose: 56.65 e/Å2 / Details: tilt by 30 degree
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Details: The final resolution was calculated without a mask / Number images used: 131061
Initial angle assignmentType: OTHER / Details: Ab-initio reconstruction in CryoSPARC
Final angle assignmentType: OTHER / Details: NU-refinement in CryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-9mmr:
Cryo-EM structure of CRAF/MEK1/14-3-3 complex (open monomer conformation, CRAF Y340D/Y341D mutant)

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