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 13DV | pdb_000013dv

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 13DV

This is version 1.1 of the entry. See complete history. 

Literature

Cryo-EM and biochemical characterization of a BRAF/CRAF heterodimer shows that the NtA motif negative charge is dispensable for RAF activation.

Ha, B.H., Tkacik, E., Gazgalis, D., Kang, H., Jang, D.M., Chakraborty, S., Jeon, H., Eck, M.J.

(2026) Cell Rep 45: 118165-118165

  • DOI: https://doi.org/10.1016/j.celrep.2026.118165
  • Primary Citation Related Structures: 
    13DU, 13DV

  • PubMed Abstract: 

    Upon RAS-driven membrane recruitment, RAF kinases ARAF, BRAF, and CRAF are activated through homo- or heterodimerization to initiate MAP kinase signaling. Although RAF heterodimers drive physiologic and oncogenic signaling, they remain little studied structurally and biochemically. Here, we report the preparation, biochemical characterization, and cryo-EM structures of 14-3-3-bound BRAF/CRAF heterodimer complexes. The heterodimer exhibits kinetic parameters and RAF inhibitor sensitivities intermediate between, or closely matching, BRAF and CRAF homodimers. Cryo-EM structures reveal an organization identical to RAF homodimers, with an asymmetric interaction unique to the MEK1-bound structure in which the BRAF acidic NtA motif engages the CRAF RKTR motif. Mutagenesis reveals that replacing the acidic NtA sequence with basic RARA yields active dimers, showing that negative charge is dispensable for activity. Collectively, our findings suggest the NtA charge state influences RAF activity through effects on local backbone dynamics and inactive-state stability, rather than via stereospecific recognition across the dimer interface.


  • Organizational Affiliation: 
    • Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.

Macromolecule Content 

  • Total Structure Weight: 187.39 kDa 
  • Atom Count: 10,404 
  • Modeled Residue Count: 1,295 
  • Deposited Residue Count: 1,650 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase B-raf354Homo sapiensMutation(s): 0 
Gene Names: BRAF, BRAF1, RAFB1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P15056 (Homo sapiens)
Explore P15056 
Go to UniProtKB:  P15056
PHAROS:  P15056
GTEx:  ENSG00000157764 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15056
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
RAF proto-oncogene serine/threonine-protein kinase367Homo sapiensMutation(s): 4 
Gene Names: RAF1, RAF
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04049 (Homo sapiens)
Explore P04049 
Go to UniProtKB:  P04049
PHAROS:  P04049
GTEx:  ENSG00000132155 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04049
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Dual specificity mitogen-activated protein kinase kinase 1420Homo sapiensMutation(s): 2 
Gene Names: MAP2K1, MEK1, PRKMK1
EC: 2.7.12.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q02750 (Homo sapiens)
Explore Q02750 
Go to UniProtKB:  Q02750
PHAROS:  Q02750
GTEx:  ENSG00000169032 
Entity Groups
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UniProt GroupQ02750
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
14-3-3 protein epsilonD [auth X]262Spodoptera frugiperdaMutation(s): 0 
Gene Names: LOC118274546, SFRICE_002878
UniProt
Find proteins for A0A2H1VA22 (Spodoptera frugiperda)
Explore A0A2H1VA22 
Go to UniProtKB:  A0A2H1VA22
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UniProt GroupA0A2H1VA22
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
14-3-3 protein zetaE [auth Y]247Spodoptera frugiperdaMutation(s): 0 
Gene Names: LOC118271767
UniProt
Find proteins for A0A9R0D7T1 (Spodoptera frugiperda)
Explore A0A9R0D7T1 
Go to UniProtKB:  A0A9R0D7T1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A9R0D7T1
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LCJ
(Subject of Investigation/LOI)

Query on LCJ



Download:Ideal Coordinates CCD File
H [auth C]5-[(2-fluoro-4-iodophenyl)amino]-N-(2-hydroxyethoxy)imidazo[1,5-a]pyridine-6-carboxamide
C16 H14 F I N4 O3
RFWVETIZUQEJEF-UHFFFAOYSA-N
29L
(Subject of Investigation/LOI)

Query on 29L



Download:Ideal Coordinates CCD File
F [auth A],
G [auth B]
2-{4-[(1E)-1-(hydroxyimino)-2,3-dihydro-1H-inden-5-yl]-3-(pyridin-4-yl)-1H-pyrazol-1-yl}ethanol
C19 H18 N4 O2
DEZZLWQELQORIU-RELWKKBWSA-N
Modified Residues  1 Unique
IDChains Modified ResidueModification TypeFormula2D Diagram
SEP
Query on SEP
A, B
SERPhosphorylationC3 H8 N O6 P

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR35CA242461

Revision History  (Full details and data files)

  • Version 1.0: 2026-10-07
    Type: Initial release
  • Version 1.1: 2026-11-04
    Changes: Data collection, Database references