+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16779 | |||||||||
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Title | Cryo-EM structure of CRaf dimer with 14:3:3 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Kinase / Complex / CYTOKINE | |||||||||
Function / homology | Function and homology information death-inducing signaling complex assembly / intermediate filament cytoskeleton organization / type B pancreatic cell proliferation / regulation of Rho protein signal transduction / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / regulation of cell motility / insulin secretion involved in cellular response to glucose stimulus / MAP kinase kinase kinase activity ...death-inducing signaling complex assembly / intermediate filament cytoskeleton organization / type B pancreatic cell proliferation / regulation of Rho protein signal transduction / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / regulation of cell motility / insulin secretion involved in cellular response to glucose stimulus / MAP kinase kinase kinase activity / Negative feedback regulation of MAPK pathway / GP1b-IX-V activation signalling / IFNG signaling activates MAPKs / ERBB2-ERBB3 signaling pathway / regulation of cell differentiation / face development / pseudopodium / somatic stem cell population maintenance / thyroid gland development / neurotrophin TRK receptor signaling pathway / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of protein-containing complex assembly / Schwann cell development / type II interferon-mediated signaling pathway / activation of adenylate cyclase activity / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / response to muscle stretch / myelination / CD209 (DC-SIGN) signaling / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / insulin-like growth factor receptor signaling pathway / thymus development / RAF activation / wound healing / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / Stimuli-sensing channels / Negative regulation of MAPK pathway / 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 / positive regulation of peptidyl-serine phosphorylation / MAPK cascade / Signaling by BRAF and RAF1 fusions / insulin receptor signaling pathway / regulation of apoptotic process / mitochondrial outer membrane / positive regulation of MAPK cascade / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / negative regulation of cell population proliferation / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of apoptotic process / apoptotic process / enzyme binding / Golgi apparatus / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / ATP binding / identical protein binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Spodoptera frugiperda (fall armyworm) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.46 Å | |||||||||
Authors | Dedden D / Graedler U / Schwarz D / Thomsen M / Leuthner B / Schneider E / Nitsche J | |||||||||
Funding support | 1 items
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Citation | Journal: J Mol Biol / Year: 2024 Title: Cryo-EM Structures of CRAF/14-3-3 and CRAF/14-3-3/MEK1 Complexes. Authors: Dirk Dedden / Julius Nitsche / Elisabeth V Schneider / Maren Thomsen / Daniel Schwarz / Birgitta Leuthner / Ulrich Grädler / 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) ...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/14-3-3 at 3.4 Å resolution and CRAF/14-3-3/MEK1 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/14-3-3 and CRAF/14-3-3/MEK1 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/14-3-3/MEK1 complex. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16779.map.gz | 59.6 MB | EMDB map data format | |
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Header (meta data) | emd-16779-v30.xml emd-16779.xml | 15.9 KB 15.9 KB | Display Display | EMDB header |
Images | emd_16779.png | 66.9 KB | ||
Filedesc metadata | emd-16779.cif.gz | 6.2 KB | ||
Others | emd_16779_half_map_1.map.gz emd_16779_half_map_2.map.gz | 59.1 MB 59.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16779 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16779 | HTTPS FTP |
-Validation report
Summary document | emd_16779_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_16779_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_16779_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | emd_16779_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16779 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16779 | HTTPS FTP |
-Related structure data
Related structure data | 8cpdMC 8chfC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_16779.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.731 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_16779_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16779_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Tetrameric complex of phosphorylated CRAF dimer with 14-3-3 isofo...
Entire | Name: Tetrameric complex of phosphorylated CRAF dimer with 14-3-3 isoform zeta |
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Components |
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-Supramolecule #1: Tetrameric complex of phosphorylated CRAF dimer with 14-3-3 isofo...
Supramolecule | Name: Tetrameric complex of phosphorylated CRAF dimer with 14-3-3 isoform zeta type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: RAF proto-oncogene serine/threonine-protein kinase
Macromolecule | Name: RAF proto-oncogene serine/threonine-protein kinase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 73.184477 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MEHIQGAWKT ISNGFGFKDA VFDGSSCISP TIVQQFGYQR RASDDGKLTD PSKTSNTIRV FLPNKQRTVV NVRNGMSLHD CLMKALKVR GLQPECCAVF RLLHEHKGKK ARLDWNTDAA SLIGEELQVD FLDHVPLTTH NFARKTFLKL AFCDICQKFL L NGFRCQTC ...String: MEHIQGAWKT ISNGFGFKDA VFDGSSCISP TIVQQFGYQR RASDDGKLTD PSKTSNTIRV FLPNKQRTVV NVRNGMSLHD CLMKALKVR GLQPECCAVF RLLHEHKGKK ARLDWNTDAA SLIGEELQVD FLDHVPLTTH NFARKTFLKL AFCDICQKFL L NGFRCQTC GYKFHEHCST KVPTMCVDWS NIRQLLLFPN STIGDSGVPA LPSLTMRRMR ESVSRMPVSS QHRYSTPHAF TF NTSSPSS EGSLSQRQRS TSTPNVHMVS TTLPVDSRMI EDAIRSHSES ASPSALSSSP NNLSPTGWSQ PKTPVPAQRE RAP VSGTQE KNKIRPRGQR DSSYDWEIEA SEVMLSTRIG SGSFGTVYKG KWHGDVAVKI LKVVDPTPEQ FQAFRNEVAV LRKT RHVNI LLFMGYMTKD NLAIVTQWCE GSSLYKHLHV QETKFQMFQL IDIARQTAQG MDYLHAKNII HRDMKSNNIF LHEGL TVKI GDFGLATVKS RWSGSQQVEQ PTGSVLWMAP EVIRMQDNNP FSFQSDVYSY GIVLYELMTG ELPYSHINNR DQIIFM VGR GYASPDLSKL YKNCPKAMKR LVADCVKKVK EERPLFPQIL SSIELLQHSL PKINRSA(SEP)EP SLHRAAHTED INA CTLTTS PRLPVF UniProtKB: RAF proto-oncogene serine/threonine-protein kinase |
-Macromolecule #2: 14-3-3 protein zeta isoform X1
Macromolecule | Name: 14-3-3 protein zeta isoform X1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Spodoptera frugiperda (fall armyworm) |
Molecular weight | Theoretical: 28.108514 KDa |
Sequence | String: 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 isoform X1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 65.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 653449 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |