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Yorodumi- EMDB-25715: Structure of active Janus Kinase (JAK) dimer complexed with cytok... -
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-Basic information
Entry | Database: EMDB / ID: EMD-25715 | ||||||||||||
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Title | Structure of active Janus Kinase (JAK) dimer complexed with cytokine receptor intracellular domain | ||||||||||||
Map data | Phenix local anisotropic sharpened map based on half maps, cropped. An uncropped map was used for Phenix real-space refinement. | ||||||||||||
Sample |
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Keywords | signaling complex / Janus Kinase / JAK / oncogenic mutation / gain-of-function mutation / cytokine receptor / SIGNALING PROTEIN | ||||||||||||
Function / homology | Function and homology information response to type III interferon / interleukin-28 receptor complex / Interleukin-20 family signaling / mucosal immune response / positive regulation of cellular respiration / protein localization to cell-cell junction / interleukin-11-mediated signaling pathway / CCR5 chemokine receptor binding / positive regulation of homotypic cell-cell adhesion / interleukin-9-mediated signaling pathway ...response to type III interferon / interleukin-28 receptor complex / Interleukin-20 family signaling / mucosal immune response / positive regulation of cellular respiration / protein localization to cell-cell junction / interleukin-11-mediated signaling pathway / CCR5 chemokine receptor binding / positive regulation of homotypic cell-cell adhesion / interleukin-9-mediated signaling pathway / interleukin-4-mediated signaling pathway / interleukin-2-mediated signaling pathway / regulation of defense response to virus by host / interleukin-15-mediated signaling pathway / cytokine receptor activity / growth hormone receptor binding / type I interferon-mediated signaling pathway / interleukin-6-mediated signaling pathway / positive regulation of sprouting angiogenesis / extrinsic component of cytoplasmic side of plasma membrane / cell surface receptor signaling pathway via JAK-STAT / endomembrane system / type II interferon-mediated signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / cytokine-mediated signaling pathway / positive regulation of protein localization to nucleus / protein phosphatase binding / defense response to virus / cytoskeleton / intracellular signal transduction / response to antibiotic / ubiquitin protein ligase binding / ATP binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||
Authors | Glassman CR / Tsutsumi N / Jude KM / Garcia KC | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Science / Year: 2022 Title: Structure of a Janus kinase cytokine receptor complex reveals the basis for dimeric activation. Authors: Caleb R Glassman / Naotaka Tsutsumi / Robert A Saxton / Patrick J Lupardus / Kevin M Jude / K Christopher Garcia / Abstract: Cytokines signal through cell surface receptor dimers to initiate activation of intracellular Janus kinases (JAKs). We report the 3.6-angstrom-resolution cryo-electron microscopy structure of full- ...Cytokines signal through cell surface receptor dimers to initiate activation of intracellular Janus kinases (JAKs). We report the 3.6-angstrom-resolution cryo-electron microscopy structure of full-length JAK1 complexed with a cytokine receptor intracellular domain Box1 and Box2 regions captured as an activated homodimer bearing the valine→phenylalanine (VF) mutation prevalent in myeloproliferative neoplasms. The seven domains of JAK1 form an extended structural unit, the dimerization of which is mediated by close-packing of the pseudokinase (PK) domains from the monomeric subunits. The oncogenic VF mutation lies within the core of the JAK1 PK interdimer interface, enhancing packing complementarity to facilitate ligand-independent activation. The carboxy-terminal tyrosine kinase domains are poised for transactivation and to phosphorylate the receptor STAT (signal transducer and activator of transcription)-recruiting motifs projecting from the overhanging FERM (four-point-one, ezrin, radixin, moesin)-SH2 (Src homology 2)-domains. Mapping of constitutively active JAK mutants supports a two-step allosteric activation mechanism and reveals opportunities for selective therapeutic targeting of oncogenic JAK signaling. | ||||||||||||
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_25715.map.gz | 13.2 MB | EMDB map data format | |
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Header (meta data) | emd-25715-v30.xml emd-25715.xml | 26.4 KB 26.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_25715_fsc.xml | 15 KB | Display | FSC data file |
Images | emd_25715.png | 176.4 KB | ||
Masks | emd_25715_msk_1.map emd_25715_msk_2.map | 244.1 MB 244.1 MB | Mask map | |
Filedesc metadata | emd-25715.cif.gz | 7.6 KB | ||
Others | emd_25715_additional_1.map.gz emd_25715_additional_2.map.gz emd_25715_half_map_1.map.gz emd_25715_half_map_2.map.gz | 13.2 MB 121.3 MB 226 MB 226 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25715 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25715 | HTTPS FTP |
-Validation report
Summary document | emd_25715_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_25715_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_25715_validation.xml.gz | 20 KB | Display | |
Data in CIF | emd_25715_validation.cif.gz | 25.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25715 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25715 | HTTPS FTP |
-Related structure data
Related structure data | 7t6fMC 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_25715.map.gz / Format: CCP4 / Size: 14.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Phenix local anisotropic sharpened map based on half maps, cropped. An uncropped map was used for Phenix real-space refinement. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8521 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_25715_msk_1.map | ||||||||||||
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-Mask #2
File | emd_25715_msk_2.map | ||||||||||||
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-Additional map: DeepEMhancer sharpened map with masking, cropped, for overall...
File | emd_25715_additional_1.map | ||||||||||||
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Annotation | DeepEMhancer sharpened map with masking, cropped, for overall map representation. | ||||||||||||
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-Additional map: Unsharpen full map.
File | emd_25715_additional_2.map | ||||||||||||
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Annotation | Unsharpen full map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A.
File | emd_25715_half_map_1.map | ||||||||||||
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Annotation | Half map A. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B.
File | emd_25715_half_map_2.map | ||||||||||||
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Annotation | Half map B. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : GCN4-zippered dimeric IFN-lambda intracellular domain bound to tw...
Entire | Name: GCN4-zippered dimeric IFN-lambda intracellular domain bound to two Jak1s |
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Components |
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-Supramolecule #1: GCN4-zippered dimeric IFN-lambda intracellular domain bound to tw...
Supramolecule | Name: GCN4-zippered dimeric IFN-lambda intracellular domain bound to two Jak1s type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 Details: Co-expressed GST-fused GCN4-IFN-lambda and full-length Jak1 in T. ni. GST tagged was removed by 3C protease digestion. |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 290 KDa |
-Macromolecule #1: Tyrosine-protein kinase
Macromolecule | Name: Tyrosine-protein kinase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: non-specific protein-tyrosine kinase |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 136.026844 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MQYLNIKEDC NAMAFCAKMR SFKKTEVKQV VPEPGVEVTF YLLDREPLRL GSGEYTAEEL CIRAAQECSI SPLCHNLFAL YDESTKLWY APNRIITVDD KTSLRLHYRM RFYFTNWHGT NDNEQSVWRH SPKKQKNGYE KKRVPEATPL LDASSLEYLF A QGQYDLIK ...String: MQYLNIKEDC NAMAFCAKMR SFKKTEVKQV VPEPGVEVTF YLLDREPLRL GSGEYTAEEL CIRAAQECSI SPLCHNLFAL YDESTKLWY APNRIITVDD KTSLRLHYRM RFYFTNWHGT NDNEQSVWRH SPKKQKNGYE KKRVPEATPL LDASSLEYLF A QGQYDLIK CLAPIRDPKT EQDGHDIENE CLGMAVLAIS HYAMMKKMQL PELPKDISYK RYIPETLNKS IRQRNLLTRM RI NNVFKDF LKEFNNKTIC DSSVSTHDLK VKYLATLETL TKHYGAEIFE TSMLLISSEN ELSRCHSNDS GNVLYEVMVT GNL GIQWRQ KPNVVPVEKE KNKLKRKKLE YNKHKKDDER NKLREEWNNF SYFPEITHIV IKESVVSINK QDNKNMELKL SSRE EALSF VSLVDGYFRL TADAHHYLCT DVAPPLIVHN IQNGCHGPIC TEYAINKLRQ EGSEEGMYVL RWSCTDFDNI LMTVT CFEK SEVLGGQKQF KNFQIEVQKG RYSLHGSMDH FPSLRDLMNH LKKQILRTDN ISFVLKRCCQ PKPREISNLL VATKKA QEW QPVYSMSQLS FDRILKKDII QGEHLGRGTR THIYSGTLLD YKDEEGIAEE KKIKVILKVL DPSHRDISLA FFEAASM MR QVSHKHIVYL YGVCFRDVEN IMVEEFVEGG PLDLFMHRKS DALTTPWKFK VAKQLASALS YLEDKDLVHG NVCTKNLL L AREGIDSDIG PFIKLSDPGI PVSVLTRQEC IERIPWIAPE CVEDSKNLSV AADKWSFGTT LWEICYNGEI PLKDKTLIE KERFYESRCR PVTPSCKELA DLMTRCMNYD PNQRPFFRAI MRDINKLEEQ NPDIVSEKQP TTEVDPTHFE KRFLKRIRDL GEGHFGKVE LCRYDPEGDN TGEQVAVKSL KPESGGNHIA DLKKEIEILR NLYHENIVKY KGICMEDGGN GIKLIMEFLP S GSLKEYLP KNKNKINLKQ QLKYAIQICK GMDYLGSRQY VHRDLAARNV LVESEHQVKI GDFGLTKAIE TDKEYYTVKD DR DSPVFWY APECLIQCKF YIASDVWSFG VTLHELLTYC DSDFSPMALF LKMIGPTHGQ MTVTRLVNTL KEGKRLPCPP NCP DEVYQL MRKCWEFQPS NRTTFQNLIE GFEALLKGSD RKAAVSHWQH HHHHHHH UniProtKB: Tyrosine-protein kinase |
-Macromolecule #2: Interferon lambda receptor 1
Macromolecule | Name: Interferon lambda receptor 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 9.895373 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: GPRMKQLEDK VEELLSKNYH LENEVARLKK LVGERKIMKG NPWFQGVKTP RALDFSEYRY PVATFQPSGP EFSDDLILCP QKELT UniProtKB: Interferon lambda receptor 1 |
-Macromolecule #3: ADENOSINE
Macromolecule | Name: ADENOSINE / type: ligand / ID: 3 / Number of copies: 2 / Formula: ADN |
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Molecular weight | Theoretical: 267.241 Da |
Chemical component information | ChemComp-ADN: |
-Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 6 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
Details: additive: 0.01% w/v DDM | ||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: LEICA EM GP / Details: 3 s blotting before plunging. | ||||||||||||
Details | GCN4-mIFN-lambda-box1box2-mJak1 V657F |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 2 / Number real images: 29467 / Average electron dose: 55.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated magnification: 58680 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 29000 |
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
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-7t6f: |