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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 / labyrinthine layer development / MAP-kinase scaffold activity / type B pancreatic cell proliferation ...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 / labyrinthine layer development / MAP-kinase scaffold activity / type B pancreatic cell proliferation / cerebellar cortex formation / regulation of Rho protein signal transduction / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / Signaling by MAP2K mutants / regulation of cell motility / insulin secretion involved in cellular response to glucose stimulus / regulation of Golgi inheritance / spindle pole body / MAP kinase kinase kinase activity / trachea formation / Negative feedback regulation of MAPK pathway / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / positive regulation of axonogenesis / GP1b-IX-V activation signalling / IFNG signaling activates MAPKs / Frs2-mediated activation / regulation of epidermal cell division / protein kinase C inhibitor activity / ERBB2-ERBB3 signaling pathway / regulation of cell differentiation / positive regulation of epidermal cell differentiation / protein kinase activator activity / keratinocyte development / keratinization / endodermal cell differentiation / MAPK3 (ERK1) activation / face development / pseudopodium / somatic stem cell population maintenance / MAP kinase kinase activity / Bergmann glial cell differentiation / thyroid gland development / neurotrophin TRK receptor signaling pathway / Uptake and function of anthrax toxins / glutathione transferase / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / glutathione transferase activity / phosphoserine residue binding / extrinsic apoptotic signaling pathway via death domain receptors / 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 / activation of adenylate cyclase activity / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of stem cell proliferation / RHO GTPases activate PKNs / keratinocyte differentiation / Signal transduction by L1 / protein sequestering activity / protein kinase A signaling / response to muscle stretch / ERK1 and ERK2 cascade / negative regulation of innate immune response / protein serine/threonine/tyrosine kinase activity / myelination / protein export from nucleus / glutathione metabolic process / CD209 (DC-SIGN) signaling / protein serine/threonine kinase activator activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / insulin-like growth factor receptor signaling pathway / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / thymus development / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cell motility / TP53 Regulates Metabolic Genes / RAF activation / negative regulation of protein kinase activity / wound healing / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / positive regulation of protein serine/threonine kinase activity / Stimuli-sensing channels / cellular senescence / neuron differentiation / Negative regulation of MAPK pathway 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 Nondegrading 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 / Ayşegül Özen / 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 / Ayşegül Özen / 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 are a driver for many cancers. NST-628 is a potent pan-RAF-MEK molecular glue that prevents the ...Alterations in the RAS-MAPK signaling cascade are common across multiple solid tumor types and are a driver for many cancers. NST-628 is a potent pan-RAF-MEK molecular glue that prevents the 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 analyses of RAF-MEK complexes show that NST-628 engages all isoforms of RAF and 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 areas of unmet patient need. Significance: This study introduces NST-628, a molecular glue having differentiated mechanism and drug-like properties. NST-628 treatment leads to broad efficacy with high tolerability and central nervous system activity across multiple RAS- and RAF-driven tumor models. NST-628 has the potential to provide transformative clinical benefits as both monotherapy and vertical combination anchor. | |||||||||
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 | 17.6 KB 17.6 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 |
-Validation report
Summary document | emd_43931_validation.pdf.gz | 594.3 KB | Display | EMDB validaton report |
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Full document | emd_43931_full_validation.pdf.gz | 593.9 KB | Display | |
Data in XML | emd_43931_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | emd_43931_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43931 ftp://ftp.pdbj.org/pub/emdb/validation_reports/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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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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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.36 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 83248 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |