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Yorodumi- EMDB-23814: Autoinhibited BRAF:(14-3-3)2 complex with the BRAF RBD resolved -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23814 | |||||||||
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Title | Autoinhibited BRAF:(14-3-3)2 complex with the BRAF RBD resolved | |||||||||
Map data | Autoinhibited B-Raf:(14-3-3)2 complex with resolved RBD | |||||||||
Sample |
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Function / homology | Function and homology information Golgi reassembly / synaptic target recognition / CD4-positive, alpha-beta T cell differentiation / NOTCH4 Activation and Transmission of Signal to the Nucleus / respiratory system process / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / myeloid progenitor cell differentiation / negative regulation of synaptic vesicle exocytosis / establishment of Golgi localization / tube formation ...Golgi reassembly / synaptic target recognition / CD4-positive, alpha-beta T cell differentiation / NOTCH4 Activation and Transmission of Signal to the Nucleus / respiratory system process / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / myeloid progenitor cell differentiation / negative regulation of synaptic vesicle exocytosis / establishment of Golgi localization / tube formation / Signalling to p38 via RIT and RIN / head morphogenesis / regulation of synapse maturation / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / endothelial cell apoptotic process / Rap1 signalling / negative regulation of fibroblast migration / positive regulation of D-glucose transmembrane transport / establishment of protein localization to membrane / negative regulation of protein localization to nucleus / mitogen-activated protein kinase kinase binding / regulation of T cell differentiation / Negative feedback regulation of MAPK pathway / KSRP (KHSRP) binds and destabilizes mRNA / positive regulation of axonogenesis / GP1b-IX-V activation signalling / Frs2-mediated activation / stress fiber assembly / positive regulation of axon regeneration / face development / somatic stem cell population maintenance / MAP kinase kinase activity / synaptic vesicle exocytosis / thyroid gland development / Regulation of localization of FOXO transcription factors / phosphoserine residue binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / MAP kinase kinase kinase activity / Activation of BAD and translocation to mitochondria / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of endothelial cell apoptotic process / cellular response to glucose starvation / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / positive regulation of substrate adhesion-dependent cell spreading / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / negative regulation of TORC1 signaling / negative regulation of innate immune response / response to cAMP / protein sequestering activity / cellular response to calcium ion / ERK1 and ERK2 cascade / regulation of ERK1 and ERK2 cascade / hippocampal mossy fiber to CA3 synapse / substrate adhesion-dependent cell spreading / thymus development / cellular response to nerve growth factor stimulus / Translocation of SLC2A4 (GLUT4) to the plasma membrane / long-term synaptic potentiation / animal organ morphogenesis / Deactivation of the beta-catenin transactivating complex / TP53 Regulates Metabolic Genes / lung development / RAF activation / Negative regulation of NOTCH4 signaling / Signaling by high-kinase activity BRAF mutants / Spry regulation of FGF signaling / MAP2K and MAPK activation / visual learning / epidermal growth factor receptor signaling pathway / regulation of protein stability / response to peptide hormone / 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 / Signaling by BRAF and RAF1 fusions / MAPK cascade / protein localization / melanosome / cellular response to xenobiotic stimulus / positive regulation of peptidyl-serine phosphorylation / presynapse / regulation of cell population proliferation / T cell receptor signaling pathway / T cell differentiation in thymus / cell body / scaffold protein binding / angiogenesis / DNA-binding transcription factor binding / vesicle / negative regulation of neuron apoptotic process / transmembrane transporter binding / blood microparticle / positive regulation of ERK1 and ERK2 cascade Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.07 Å | |||||||||
Authors | Martinez Fiesco JA / Ping Z / Durrant DE / Morrison DK | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural insights into the BRAF monomer-to-dimer transition mediated by RAS binding. Authors: Juliana A Martinez Fiesco / David E Durrant / Deborah K Morrison / Ping Zhang / Abstract: RAF kinases are essential effectors of RAS, but how RAS binding initiates the conformational changes needed for autoinhibited RAF monomers to form active dimers has remained unclear. Here, we present ...RAF kinases are essential effectors of RAS, but how RAS binding initiates the conformational changes needed for autoinhibited RAF monomers to form active dimers has remained unclear. Here, we present cryo-electron microscopy structures of full-length BRAF complexes derived from mammalian cells: autoinhibited, monomeric BRAF:14-3-3:MEK and BRAF:14-3-3 complexes, and an inhibitor-bound, dimeric BRAF:14-3-3 complex, at 3.7, 4.1, and 3.9 Å resolution, respectively. In both autoinhibited, monomeric structures, the RAS binding domain (RBD) of BRAF is resolved, revealing that the RBD forms an extensive contact interface with the 14-3-3 protomer bound to the BRAF C-terminal site and that key basic residues required for RBD-RAS binding are exposed. Moreover, through structure-guided mutational studies, our findings indicate that RAS-RAF binding is a dynamic process and that RBD residues at the center of the RBD:14-3-3 interface have a dual function, first contributing to RAF autoinhibition and then to the full spectrum of RAS-RBD interactions. | |||||||||
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_23814.map.gz | 1.3 MB | EMDB map data format | |
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Header (meta data) | emd-23814-v30.xml emd-23814.xml | 12.3 KB 12.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23814_fsc.xml | 4.7 KB | Display | FSC data file |
Images | emd_23814.png | 62.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23814 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23814 | HTTPS FTP |
-Validation report
Summary document | emd_23814_validation.pdf.gz | 375.8 KB | Display | EMDB validaton report |
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Full document | emd_23814_full_validation.pdf.gz | 375.4 KB | Display | |
Data in XML | emd_23814_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | emd_23814_validation.cif.gz | 9.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23814 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23814 | HTTPS FTP |
-Related structure data
Related structure data | 7mfeMC 7mfdC 7mffC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23814.map.gz / Format: CCP4 / Size: 8.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Autoinhibited B-Raf:(14-3-3)2 complex with resolved RBD | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.348 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 : Autoinhibited B-Raf:(14-3-3)2 complex with resolved RBD
Entire | Name: Autoinhibited B-Raf:(14-3-3)2 complex with resolved RBD |
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Components |
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-Supramolecule #1: Autoinhibited B-Raf:(14-3-3)2 complex with resolved RBD
Supramolecule | Name: Autoinhibited B-Raf:(14-3-3)2 complex with resolved RBD type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Serine/threonine-protein kinase B-raf
Macromolecule | Name: Serine/threonine-protein kinase B-raf / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 84.697695 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MAALSGGGGG GAEPGQALFN GDMEPEAGAG AGAAASSAAD PAIPEEVWNI KQMIKLTQEH IEALLDKFGG EHNPPSIYLE AYEEYTSKL DALQQREQQL LESLGNGTDF SVSSSASMDT VTSSSSSSLS VLPSSLSVFQ NPTDVARSNP KSPQKPIVRV F LPNKQRTV ...String: MAALSGGGGG GAEPGQALFN GDMEPEAGAG AGAAASSAAD PAIPEEVWNI KQMIKLTQEH IEALLDKFGG EHNPPSIYLE AYEEYTSKL DALQQREQQL LESLGNGTDF SVSSSASMDT VTSSSSSSLS VLPSSLSVFQ NPTDVARSNP KSPQKPIVRV F LPNKQRTV VPARCGVTVR DSLKKALMMR GLIPECCAVY RIQDGEKKPI GWDTDISWLT GEELHVEVLE NVPLTTHNFV RK TFFTLAF CDFCRKLLFQ GFRCQTCGYK FHQRCSTEVP LMCVNYDQLD LLFVSKFFEH HPIPQEEASL AETALTSGSS PSA PASDSI GPQILTSPSP SKSIPIPQPF RPADEDHRNQ FGQRDRSS(SEP)A PNVHINTIEP VNIDDLIRDQ GFRGDGGSTT GLSATPPAS LPGSLTNVKA LQKSPGPQRE RKSSSSSEDR NRMKTLGRRD SSDDWEIPDG QITVGQRIGS GSFGTVYKGK W HGDVAVKM LNVTAPTPQQ LQAFKNEVGV LRKTRHVNIL LFMGYSTKPQ LAIVTQWCEG SSLYHHLHII ETKFEMIKLI DI ARQTAQG MDYLHAKSII HRDLKSNNIF LHEDLTVKIG DFGLATVKSR WSGSHQFEQL SGSILWMAPE VIRMQDKNPY SFQ SDVYAF GIVLYELMTG QLPYSNINNR DQIIFMVGRG YLSPDLSKVR SNCPKAMKRL MAECLKKKRD ERPLFPQILA SIEL LARSL PKIHRSA(SEP)EP SLNRAGFQTE DFSLYACASP KTPIQAGGYG AFPVH |
-Macromolecule #2: 14-3-3 protein zeta/delta
Macromolecule | Name: 14-3-3 protein zeta/delta / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 27.777092 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MDKNELVQKA KLAEQAERYD DMAACMKSVT EQGAELSNEE RNLLSVAYKN VVGARRSSWR VVSSIEQKTE GAEKKQQMAR EYREKIETE LRDICNDVLS LLEKFLIPNA SQAESKVFYL KMKGDYYRYL AEVAAGDDKK GIVDQSQQAY QEAFEISKKE M QPTHPIRL ...String: MDKNELVQKA KLAEQAERYD DMAACMKSVT EQGAELSNEE RNLLSVAYKN VVGARRSSWR VVSSIEQKTE GAEKKQQMAR EYREKIETE LRDICNDVLS LLEKFLIPNA SQAESKVFYL KMKGDYYRYL AEVAAGDDKK GIVDQSQQAY QEAFEISKKE M QPTHPIRL GLALNFSVFY YEILNSPEKA CSLAKTAFDE AIAELDTLSE ESYKDSTLIM QLLRDNLTLW TSDTQGDEAE AG EGGEN |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-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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Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-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: 57.0 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 |