8CPD | pdb_00008cpd

Cryo-EM structure of CRaf dimer with 14:3:3

• PDB DOI: https://doi.org/10.2210/pdb8CPD/pdb
• EM Map EMD-16779: EMDB EMDataResource

• Classification: CYTOKINE
• Organism(s): Homo sapiens, Spodoptera frugiperda
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2023-03-02 Released: 2024-02-21 
• Deposition Author(s): Dedden, D., Graedler, U., Schwarz, D., Thomsen, M., Leuthner, B., Schneider, E., Nitsche, J.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.46 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM Structures of CRAF 2 /14-3-3 2 and CRAF 2 /14-3-3 2 /MEK1 2 Complexes.

Dedden, D., Nitsche, J., Schneider, E.V., Thomsen, M., Schwarz, D., Leuthner, B., Gradler, U.

(2024) J Mol Biology 436: 168483-168483

• PubMed: 38331211 
• DOI: https://doi.org/10.1016/j.jmb.2024.168483
• Primary Citation Related Structures: 
  8CHF, 8CPD


• PubMed Abstract: 
  

  RAF protein kinases are essential effectors in the MAPK pathway and are important cancer drug targets. Structural understanding of RAF activation is so far based on cryo-electron microscopy (cryo-EM) and X-ray structures of BRAF in different conformational states as inactive or active complexes with KRAS, 14-3-3 and MEK1. In this study, we have solved the first cryo-EM structures of CRAF ₂ /14-3-3 ₂ at 3.4 Å resolution and CRAF ₂ /14-3-3 ₂ /MEK1 ₂ at 4.2 Å resolution using CRAF kinase domain expressed as constitutively active Y340D/Y341D mutant in insect cells. The overall architecture of our CRAF ₂ /14-3-3 ₂ and CRAF ₂ /14-3-3 ₂ /MEK1 ₂ cryo-EM structures is highly similar to corresponding BRAF structures in complex with 14-3-3 or 14-3-3/MEK1 and represent the activated dimeric RAF conformation. Our CRAF cryo-EM structures provide additional insights into structural understanding of the activated CRAF ₂ /14-3-3 ₂ /MEK1 ₂ complex.

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Organizational Affiliation: 
• Proteros biostructures GmbH, Bunsenstraße 7a, D-82152 Planegg-Martinsried, Germany.
The Healthcare Business of Merck KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany.
The Healthcare Business of Merck KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 202.59 kDa 
• Atom Count: 8,030 
• Modeled Residue Count: 994 
• Deposited Residue Count: 1,790 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RAF proto-oncogene serine/threonine-protein kinase	A, C [auth B]	648	Homo sapiens	Mutation(s): 1  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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
14-3-3 protein zeta isoform X1	B [auth C], D	247	Spodoptera frugiperda	Mutation(s): 0
UniProt
Find proteins for A0A9R0D7T1 (Spodoptera frugiperda) Explore A0A9R0D7T1  Go to UniProtKB:  A0A9R0D7T1

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A, C [auth B]	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.46 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-02-21 
Deposition Author(s): Dedden, D., Graedler, U., Schwarz, D., Thomsen, M., Leuthner, B., Schneider, E., Nitsche, J.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2024-02-21
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Database references
• Version 1.2: 2024-11-20
  Changes: Data collection, Structure summary
• Version 1.3: 2025-07-09
  Changes: Data collection