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Yorodumi- EMDB-43931: CryoEM structure of activated CRAF/MEK/14-3-3 complex with NST-628 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43931 | |||||||||
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Title | CryoEM structure of activated CRAF/MEK/14-3-3 complex with NST-628 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Inhibitor / complex / SIGNALING PROTEIN / TRANSFERASE | |||||||||
Function / homology | Function and homology information death-inducing signaling complex assembly / epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / intermediate filament cytoskeleton organization / placenta blood vessel development / regulation of axon regeneration / mitogen-activated protein kinase kinase / type B pancreatic cell proliferation / labyrinthine layer development / MAP-kinase scaffold activity ...death-inducing signaling complex assembly / epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / intermediate filament cytoskeleton organization / placenta blood vessel development / regulation of axon regeneration / mitogen-activated protein kinase kinase / type B pancreatic cell proliferation / labyrinthine layer development / MAP-kinase scaffold activity / cerebellar cortex formation / regulation of Rho protein signal transduction / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Signaling by MAP2K mutants / Rap1 signalling / regulation of cell motility / insulin secretion involved in cellular response to glucose stimulus / regulation of Golgi inheritance / trachea formation / Negative feedback regulation of MAPK pathway / regulation of early endosome to late endosome transport / GP1b-IX-V activation signalling / positive regulation of axonogenesis / regulation of stress-activated MAPK cascade / IFNG signaling activates MAPKs / Frs2-mediated activation / protein kinase activator activity / regulation of epidermal cell division / ERBB2-ERBB3 signaling pathway / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell differentiation / face development / endodermal cell differentiation / MAPK3 (ERK1) activation / pseudopodium / somatic stem cell population maintenance / neurotrophin TRK receptor signaling pathway / Bergmann glial cell differentiation / MAP kinase kinase activity / thyroid gland development / glutathione transferase / Uptake and function of anthrax toxins / Regulation of localization of FOXO transcription factors / glutathione transferase activity / keratinocyte proliferation / extrinsic apoptotic signaling pathway via death domain receptors / MAP kinase kinase kinase activity / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / negative regulation of protein-containing complex assembly / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Schwann cell development / type II interferon-mediated signaling pathway / protein kinase A signaling / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / RHO GTPases activate PKNs / keratinocyte differentiation / ERK1 and ERK2 cascade / response to muscle stretch / activation of adenylate cyclase activity / myelination / protein export from nucleus / negative regulation of innate immune response / protein serine/threonine/tyrosine kinase activity / CD209 (DC-SIGN) signaling / protein serine/threonine kinase activator activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / protein sequestering activity / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / insulin-like growth factor receptor signaling pathway / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / thymus development / Signal transduction by L1 / stem cell proliferation / cell motility / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / RAF activation / Signaling by high-kinase activity BRAF mutants / wound healing / MAP2K and MAPK activation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of protein serine/threonine kinase activity / Stimuli-sensing channels / neuron differentiation / 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 Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.36 Å | |||||||||
Authors | Quade B / Cohen SE / Huang X | |||||||||
Funding support | 1 items
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Citation | Journal: Cancer Discov / Year: 2024 Title: The pan-RAF-MEK non degrading molecular glue NST-628 is a potent and brain penetrant inhibitor of the RAS-MAPK pathway with activity across diverse RAS- and RAF-driven cancers. Authors: Meagan B Ryan / Bradley Quade / Natasha Schenk / Zhong Fang / Marshall Zingg / Steven E Cohen / Brooke M Swalm / Chun Li / Aysegul Ozen / Chaoyang Ye / Maria Stella Ritorto / Xin Huang / ...Authors: Meagan B Ryan / Bradley Quade / Natasha Schenk / Zhong Fang / Marshall Zingg / Steven E Cohen / Brooke M Swalm / Chun Li / Aysegul Ozen / Chaoyang Ye / Maria Stella Ritorto / Xin Huang / Arvin C Dar / Yongxin Han / Klaus P Hoeflich / Michael Hale / Margit Hagel / Abstract: Alterations in the RAS-MAPK signaling cascade are common across multiple solid tumor types and is a driver for many cancers. NST-628 is a potent pan-RAF-MEK molecular glue that prevents ...Alterations in the RAS-MAPK signaling cascade are common across multiple solid tumor types and is a driver for many cancers. NST-628 is a potent pan-RAF-MEK molecular glue that prevents phosphorylation and activation of MEK by RAF, overcoming the limitations of traditional RAS-MAPK inhibitors and leading to deep durable inhibition of the pathway. Cellular, biochemical, and structural analysis of RAF-MEK complexes show that NST-628 engages all isoforms of RAFand prevents the formation of BRAF-CRAF heterodimers, a differentiated mechanism from all current RAF inhibitors. With a potent and durable inhibition of the RAF-MEK signaling complex as well as high intrinsic permeability into the brain, NST-628 demonstrates broad efficacy in cellular and patient-derived tumor models harboring diverse MAPK pathway alterations, including orthotopic intracranial models. Given its functional and pharmacokinetic mechanisms that are differentiated from previous therapies , NST-628 is positioned to make an impact clinically in an areas of unmet patient need. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_43931.map.gz | 2.3 MB | EMDB map data format | |
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Header (meta data) | emd-43931-v30.xml emd-43931.xml | 17.5 KB 17.5 KB | Display Display | EMDB header |
Images | emd_43931.png | 48.2 KB | ||
Filedesc metadata | emd-43931.cif.gz | 6.6 KB | ||
Others | emd_43931_half_map_1.map.gz emd_43931_half_map_2.map.gz | 23.4 MB 23.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43931 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43931 | HTTPS FTP |
-Related structure data
Related structure data | 9axaMC 9axcC 9axhC 9axmC 9axxC 9axyC 9ay7C 9ayaC 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_43931.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.8105 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_43931_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_43931_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : CRAF/MEK/14-3-3 complex with NST-628
Entire | Name: CRAF/MEK/14-3-3 complex with NST-628 |
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Components |
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-Supramolecule #1: CRAF/MEK/14-3-3 complex with NST-628
Supramolecule | Name: CRAF/MEK/14-3-3 complex with NST-628 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: GST26/CRAF chimera
Macromolecule | Name: GST26/CRAF chimera / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: glutathione transferase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 64.798465 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MSPILGYWKI KGLVQPTRLL LEYLEEKYEE HLYERDEGDK WRNKKFELGL EFPNLPYYID GDVKLTQSMA IIRYIADKHN MLGGCPKER AEISMLEGAV LDIRYGVSRI AYSKDFETLK VDFLSKLPEM LKMFEDRLCH KTYLNGDHVT HPDFMLYDAL D VVLYMDPM ...String: MSPILGYWKI KGLVQPTRLL LEYLEEKYEE HLYERDEGDK WRNKKFELGL EFPNLPYYID GDVKLTQSMA IIRYIADKHN MLGGCPKER AEISMLEGAV LDIRYGVSRI AYSKDFETLK VDFLSKLPEM LKMFEDRLCH KTYLNGDHVT HPDFMLYDAL D VVLYMDPM CLDAFPKLVC FKKRIEAIPQ IDKYLKSSKY IAWPLQGWQA TFGGGDHPPK SDSQPKTPVP AQRERAPVSG TQ EKNKIRP RGQRDSSDDW EIEASEVMLS TRIGSGSFGT VYKGKWHGDV AVKILKVVDP TPEQFQAFRN EVAVLRKTRH VNI LLFMGY MTKDNLAIVT QWCEGSSLYK HLHVQETKFQ MFQLIDIARQ TAQGMDYLHA KNIIHRDMKS NNIFLHEGLT VKIG DFGLA TVKSRWSGSQ QVEQPTGSVL WMAPEVIRMQ DNNPFSFQSD VYSYGIVLYE LMTGELPYSH INNRDQIIFM VGRGY ASPD LSKLYKNCPK AMKRLVADCV KKVKEERPLF PQILSSIELL QHSLPKINRS A(SEP)EPSLHRAA HTEDINACTL TT SPRLPVF UniProtKB: Glutathione S-transferase class-mu 26 kDa isozyme, RAF proto-oncogene serine/threonine-protein kinase |
-Macromolecule #2: Dual specificity mitogen-activated protein kinase kinase 1
Macromolecule | Name: Dual specificity mitogen-activated protein kinase kinase 1 type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: mitogen-activated protein kinase kinase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 43.518988 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GMPKKKPTPI QLNPAPDGSA VNGTSSAETN LEALQKKLEE LELDEQQRKR LEAFLTQKQK VGELKDDDFE KISELGAGNG GVVFKVSHK PSGLVMARKL IHLEIKPAIR NQIIRELQVL HECNSPYIVG FYGAFYSDGE ISICMEHMDG GSLDQVLKKA G RIPEQILG ...String: GMPKKKPTPI QLNPAPDGSA VNGTSSAETN LEALQKKLEE LELDEQQRKR LEAFLTQKQK VGELKDDDFE KISELGAGNG GVVFKVSHK PSGLVMARKL IHLEIKPAIR NQIIRELQVL HECNSPYIVG FYGAFYSDGE ISICMEHMDG GSLDQVLKKA G RIPEQILG KVSIAVIKGL TYLREKHKIM HRDVKPSNIL VNSRGEIKLC DFGVSGQLID AMANAFVGTR SYMSPERLQG TH YSVQSDI WSMGLSLVEM AVGRYPIPPP DAKELELMFG CQVEGDAAET PPRPRTPGRP LSSYGMDSRP PMAIFELLDY IVN EPPPKL PSGVFSLEFQ DFVNKCLIKN PAERADLKQL MVHAFIKRSD AEEVDFAGWL CSTIGLNQPS TPTHAAGV UniProtKB: Dual specificity mitogen-activated protein kinase kinase 1 |
-Macromolecule #3: 14-3-3 protein sigma
Macromolecule | Name: 14-3-3 protein sigma / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 27.807064 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MERASLIQKA KLAEQAERYE DMAAFMKGAV EKGEELSCEE RNLLSVAYKN VVGGQRAAWR VLSSIEQKSN EEGSEEKGPE VREYREKVE TELQGVCDTV LGLLDSHLIK EAGDAESRVF YLKMKGDYYR YLAEVATGDD KKRIIDSARS AYQEAMDISK K EMPPTNPI ...String: MERASLIQKA KLAEQAERYE DMAAFMKGAV EKGEELSCEE RNLLSVAYKN VVGGQRAAWR VLSSIEQKSN EEGSEEKGPE VREYREKVE TELQGVCDTV LGLLDSHLIK EAGDAESRVF YLKMKGDYYR YLAEVATGDD KKRIIDSARS AYQEAMDISK K EMPPTNPI RLGLALNFSV FHYEIANSPE EAISLAKTTF DEAMADLHTL SEDSYKDSTL IMQLLRDNLT LWTADNAGEE GG EAPQEPQ S UniProtKB: 14-3-3 protein sigma |
-Macromolecule #4: N-[3-fluoro-4-({7-[(3-fluoropyridin-2-yl)oxy]-4-methyl-2-oxo-2H-1...
Macromolecule | Name: N-[3-fluoro-4-({7-[(3-fluoropyridin-2-yl)oxy]-4-methyl-2-oxo-2H-1-benzopyran-3-yl}methyl)pyridin-2-yl]-N'-methylsulfuric diamide type: ligand / ID: 4 / Number of copies: 2 / Formula: A1AHE |
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Molecular weight | Theoretical: 488.464 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS GLACIOS |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.36 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 83248 |