+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20708 | |||||||||
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Title | B-Raf:14-3-3 complex | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information CD4-positive, alpha-beta T cell differentiation / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative regulation of synaptic vesicle exocytosis / Signalling to p38 via RIT and RIN / head morphogenesis / myeloid progenitor cell differentiation / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / endothelial cell apoptotic process ...CD4-positive, alpha-beta T cell differentiation / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative regulation of synaptic vesicle exocytosis / Signalling to p38 via RIT and RIN / head morphogenesis / myeloid progenitor cell differentiation / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / endothelial cell apoptotic process / negative regulation of fibroblast migration / positive regulation of glucose transmembrane transport / establishment of protein localization to membrane / MAP kinase kinase kinase activity / mitogen-activated protein kinase kinase binding / regulation of T cell differentiation / Negative feedback regulation of MAPK pathway / positive regulation of axonogenesis / Frs2-mediated activation / stress fiber assembly / positive regulation of axon regeneration / face development / synaptic vesicle exocytosis / somatic stem cell population maintenance / MAP kinase kinase activity / thyroid gland development / negative regulation of endothelial cell apoptotic process / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / response to cAMP / cellular response to calcium ion / ERK1 and ERK2 cascade / substrate adhesion-dependent cell spreading / cellular response to nerve growth factor stimulus / thymus development / epidermal growth factor receptor signaling pathway / long-term synaptic potentiation / animal organ morphogenesis / RAF activation / Spry regulation of FGF signaling / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / visual learning / response to peptide hormone / cellular response to xenobiotic stimulus / 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 / presynapse / T cell receptor signaling pathway / regulation of cell population proliferation / cell body / T cell differentiation in thymus / scaffold protein binding / negative regulation of neuron apoptotic process / positive regulation of ERK1 and ERK2 cascade / non-specific serine/threonine protein kinase / protein kinase activity / neuron projection / protein phosphorylation / intracellular membrane-bounded organelle / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / positive regulation of gene expression / negative regulation of apoptotic process / protein-containing complex binding / mitochondrion / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Asian cotton leafworm (butterflies/moths) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Kondo Y / Ognjenovic J / Banerjee S / Karandur D / Merk A / Kulhanek K / Wong K / Roose JP / Subramaniam S / Kuriyan J | |||||||||
Funding support | United States, Canada, 2 items
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Citation | Journal: Science / Year: 2019 Title: Cryo-EM structure of a dimeric B-Raf:14-3-3 complex reveals asymmetry in the active sites of B-Raf kinases. Authors: Yasushi Kondo / Jana Ognjenović / Saikat Banerjee / Deepti Karandur / Alan Merk / Kayla Kulhanek / Kathryn Wong / Jeroen P Roose / Sriram Subramaniam / John Kuriyan / Abstract: Raf kinases are important cancer drug targets. Paradoxically, many B-Raf inhibitors induce the activation of Raf kinases. Cryo-electron microscopy structural analysis of a phosphorylated B-Raf kinase ...Raf kinases are important cancer drug targets. Paradoxically, many B-Raf inhibitors induce the activation of Raf kinases. Cryo-electron microscopy structural analysis of a phosphorylated B-Raf kinase domain dimer in complex with dimeric 14-3-3, at a resolution of ~3.9 angstroms, shows an asymmetric arrangement in which one kinase is in a canonical "active" conformation. The distal segment of the C-terminal tail of this kinase interacts with, and blocks, the active site of the cognate kinase in this asymmetric arrangement. Deletion of the C-terminal segment reduces Raf activity. The unexpected asymmetric quaternary architecture illustrates how the paradoxical activation of Raf by kinase inhibitors reflects an innate mechanism, with 14-3-3 facilitating inhibition of one kinase while maintaining activity of the other. Conformational modulation of these contacts may provide new opportunities for Raf inhibitor development. #1: Journal: Science / Year: 2019 Title: Cryo-EM structure of a dimeric B-Raf:14-3-3 complex reveals asymmetry in the active sites of B-Raf kinases Authors: Kondo Y / Ognjenovic J / Banerjee S / Karandur D / Merk A / Kulhanek K / Wong K / Roose JP / Subramaniam S / Kuriyan J | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_20708.map.gz | 28.6 MB | EMDB map data format | |
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Header (meta data) | emd-20708-v30.xml emd-20708.xml | 14.5 KB 14.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_20708_fsc.xml | 7.2 KB | Display | FSC data file |
Images | emd_20708.png | 58.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20708 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20708 | HTTPS FTP |
-Validation report
Summary document | emd_20708_validation.pdf.gz | 488 KB | Display | EMDB validaton report |
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Full document | emd_20708_full_validation.pdf.gz | 487.6 KB | Display | |
Data in XML | emd_20708_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | emd_20708_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20708 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20708 | HTTPS FTP |
-Related structure data
Related structure data | 6uanMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10544 (Title: Cryo-EM structure of a dimeric B-Raf:14-3-3 complex reveals asymmetry in the active sites of B-Raf kinases Data size: 6.2 TB Data #1: Unaligned multi-frame micrographs of B-Raf:14-3-3 complex [micrographs - multiframe] Data #2: Unaligned multi-frame micrographs of B-Raf:14-3-3 complex [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_20708.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Ternary complex of B-Raf kinase domain dimer and 14-3-3 dimer
Entire | Name: Ternary complex of B-Raf kinase domain dimer and 14-3-3 dimer |
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Components |
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-Supramolecule #1: Ternary complex of B-Raf kinase domain dimer and 14-3-3 dimer
Supramolecule | Name: Ternary complex of B-Raf kinase domain dimer and 14-3-3 dimer type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) |
-Macromolecule #1: 14-3-3 zeta
Macromolecule | Name: 14-3-3 zeta / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Asian cotton leafworm (butterflies/moths) |
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 |
-Macromolecule #2: Serine/threonine-protein kinase B-raf
Macromolecule | Name: Serine/threonine-protein kinase B-raf / type: protein_or_peptide / ID: 2 / 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: 84.781922 KDa |
Recombinant expression | Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) |
Sequence | String: SGMAALSGGG GGGAEPGQAL FNGDMEPEAG AGAGAAASSA ADPAIPEEVW NIKQMIKLTQ EHIEALLDKF GGEHNPPSIY LEAYEEYTS KLDALQQREQ QLLESLGNGT DFSVSSSASM DTVTSSSSSS LSVLPSSLSV FQNPTDVARS NPKSPQKPIV R VFLPNKQR ...String: SGMAALSGGG GGGAEPGQAL FNGDMEPEAG AGAGAAASSA ADPAIPEEVW NIKQMIKLTQ EHIEALLDKF GGEHNPPSIY LEAYEEYTS KLDALQQREQ QLLESLGNGT DFSVSSSASM DTVTSSSSSS LSVLPSSLSV FQNPTDVARS NPKSPQKPIV R VFLPNKQR TVVPARCGVT VRDSLKKALM MRGLIPECCA VYRIQDGEKK PIGWDTDISW LTGEELHVEV LENVPLTTHN FV RKTFFTL AFCDFCRKLL FQGFRCQTCG YKFHQRCSTE VPLMCVNYDQ LDLLFVSKFF EHHPIPQEEA SLAETALTSG SSP SAPASD SIGPQILTSP SPSKSIPIPQ PFRPADEDHR NQFGQRDRSS SAPNVHINCM EPVNIDDLIR DQGFRGDGGS TTGL SATPP ASLPGSLTNV KALQKSPGPQ RERKSSSSSE DRNRMKTLGR RDSSDDWEIP DGQITVGQRI GSGSFGTVYK GKWHG DVAV KMLNVTAPTP QQLQAFKNEV GVLRKTRHVN ILLFMGYSTK PQLAIVTQWC EGSSLYHHLH IIETKFEMIK LIDIAR QTA QGMDYLHAKS IIHRDLKSNN IFLHEDLTVK IGDFGLATVK SRWSGSHQFE QLSGSILWMA PEVIRMQDKN PYSFQSD VY AFGIVLYELM TGQLPYSNIN NRDQIIFMVG RGYLSPDLSK VRSNCPKAMK RLMAECLKKK RDERPLFPQI LASIELLA R SLPKIHRSA(SEP) EPSLNRAGFQ TEDFSLYACA SPKTPIQAGG YGAFPVH |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL | ||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING | ||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 278 K / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |