+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18743 | |||||||||||||||
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Title | Structure of interleukin 6 (gp130 P496L mutant). | |||||||||||||||
Map data | Sharpened map. | |||||||||||||||
Sample |
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Keywords | interleukin / gp130 / IMMUNE SYSTEM | |||||||||||||||
Function / homology | Function and homology information oncostatin-M receptor activity / ciliary neurotrophic factor binding / positive regulation of interleukin-21 production / regulation of astrocyte activation / IL-6-type cytokine receptor ligand interactions / glucagon secretion / leukemia inhibitory factor receptor activity / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / Interleukin-27 signaling ...oncostatin-M receptor activity / ciliary neurotrophic factor binding / positive regulation of interleukin-21 production / regulation of astrocyte activation / IL-6-type cytokine receptor ligand interactions / glucagon secretion / leukemia inhibitory factor receptor activity / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / Interleukin-27 signaling / triglyceride mobilization / interleukin-6 receptor activity / interleukin-6 binding / regulation of glucagon secretion / Interleukin-6 signaling / hepatic immune response / negative regulation of interleukin-1-mediated signaling pathway / Interleukin-35 Signalling / regulation of vascular endothelial growth factor production / oncostatin-M receptor complex / negative regulation of primary miRNA processing / ciliary neurotrophic factor receptor binding / interleukin-11 receptor activity / interleukin-11 binding / T follicular helper cell differentiation / ciliary neurotrophic factor-mediated signaling pathway / germinal center B cell differentiation / ciliary neurotrophic factor receptor complex / interleukin-27-mediated signaling pathway / interleukin-6 receptor complex / positive regulation of extracellular matrix disassembly / positive regulation of receptor signaling pathway via STAT / positive regulation of apoptotic DNA fragmentation / response to peptidoglycan / positive regulation of type B pancreatic cell apoptotic process / regulation of microglial cell activation / hepatocyte proliferation / neutrophil apoptotic process / regulation of Notch signaling pathway / interleukin-6 receptor binding / negative regulation of collagen biosynthetic process / : / interleukin-11-mediated signaling pathway / inflammatory response to wounding / T-helper 17 cell lineage commitment / positive regulation of T-helper 2 cell cytokine production / positive regulation of B cell activation / endocrine pancreas development / positive regulation of glomerular mesangial cell proliferation / negative regulation of interleukin-8 production / positive regulation of acute inflammatory response / protein tyrosine kinase activator activity / regulation of neuroinflammatory response / vascular endothelial growth factor production / positive regulation of astrocyte differentiation / negative regulation of chemokine production / positive regulation of neuroinflammatory response / positive regulation of leukocyte chemotaxis / intestinal epithelial cell development / positive regulation of platelet aggregation / positive regulation of cytokine production involved in inflammatory response / neutrophil mediated immunity / negative regulation of lipid storage / cytokine receptor activity / negative regulation of bone resorption / positive regulation of leukocyte adhesion to vascular endothelial cell / CD163 mediating an anti-inflammatory response / positive regulation of immunoglobulin production / glycogen metabolic process / interleukin-6-mediated signaling pathway / maintenance of blood-brain barrier / Interleukin-6 signaling / positive regulation of Notch signaling pathway / negative regulation of fat cell differentiation / negative regulation of cytosolic calcium ion concentration / neuronal cell body membrane / positive regulation of smooth muscle cell migration / MAPK3 (ERK1) activation / monocyte chemotaxis / positive regulation of interleukin-17 production / Interleukin-10 signaling / cytokine binding / MAPK1 (ERK2) activation / regulation of insulin secretion / positive regulation of glial cell proliferation / positive regulation of interleukin-10 production / humoral immune response / Transcriptional Regulation by VENTX / positive regulation of vascular endothelial growth factor production / regulation of angiogenesis / positive regulation of osteoblast differentiation / coreceptor activity / positive regulation of epithelial to mesenchymal transition / positive regulation of chemokine production / extrinsic apoptotic signaling pathway / positive regulation of T cell proliferation / response to glucocorticoid / positive regulation of tyrosine phosphorylation of STAT protein / liver regeneration / positive regulation of smooth muscle cell proliferation Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) / Mus musculus (house mouse) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.16 Å | |||||||||||||||
Authors | Gardner S / Bubeck D / Jin Y | |||||||||||||||
Funding support | United Kingdom, European Union, 4 items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams / Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18743.map.gz | 323.7 MB | EMDB map data format | |
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Header (meta data) | emd-18743-v30.xml emd-18743.xml | 24.1 KB 24.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18743_fsc.xml | 14.8 KB | Display | FSC data file |
Images | emd_18743.png | 101.4 KB | ||
Masks | emd_18743_msk_1.map | 343 MB | Mask map | |
Filedesc metadata | emd-18743.cif.gz | 7.2 KB | ||
Others | emd_18743_additional_1.map.gz emd_18743_additional_2.map.gz emd_18743_half_map_1.map.gz emd_18743_half_map_2.map.gz | 170.8 MB 3.6 MB 317.7 MB 317.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18743 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18743 | HTTPS FTP |
-Related structure data
Related structure data | 8qy6MC 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_18743.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Sharpened map. | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_18743_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map.
File | emd_18743_additional_1.map | ||||||||||||
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Annotation | Unsharpened map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Locally filtered map.
File | emd_18743_additional_2.map | ||||||||||||
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Annotation | Locally filtered map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2.
File | emd_18743_half_map_1.map | ||||||||||||
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Annotation | Half map 2. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1.
File | emd_18743_half_map_2.map | ||||||||||||
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Annotation | Half map 1. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : IL-6 signalling complex
Entire | Name: IL-6 signalling complex |
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Components |
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-Supramolecule #1: IL-6 signalling complex
Supramolecule | Name: IL-6 signalling complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Interleukin-6 receptor subunit beta
Macromolecule | Name: Interleukin-6 receptor subunit beta / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 102.568906 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MSAPRIWLAQ ALLFFLTTES IGQLLEPCGY IYPEFPVVQR GSNFTAICVL KEACLQHYYV NASYIVWKTN HAAVPREQVT VINRTTSSV TFTDVVLPSV QLTCNILSFG QIEQNVYGVT MLSGFPPDKP TNLTCIVNEG KNMLCQWDPG RETYLETNYT L KSEWATEK ...String: MSAPRIWLAQ ALLFFLTTES IGQLLEPCGY IYPEFPVVQR GSNFTAICVL KEACLQHYYV NASYIVWKTN HAAVPREQVT VINRTTSSV TFTDVVLPSV QLTCNILSFG QIEQNVYGVT MLSGFPPDKP TNLTCIVNEG KNMLCQWDPG RETYLETNYT L KSEWATEK FPDCQSKHGT SCMVSYMPTY YVNIEVWVEA ENALGKVSSE SINFDPVDKV KPTPPYNLSV TNSEELSSIL KL SWVSSGL GGLLDLKSDI QYRTKDASTW IQVPLEDTMS PRTSFTVQDL KPFTEYVFRI RSIKDSGKGY WSDWSEEASG TTY EDRPSR PPSFWYKTNP SHGQEYRSVR LIWKALPLSE ANGKILDYEV ILTQSKSVSQ TYTVTGTELT VNLTNDRYVA SLAA RNKVG KSAAAVLTIP SPHVTAAYSV VNLKAFPKDN LLWVEWTPPP KPVSKYILEW CVLSENAPCV EDWQQEDATV NRTHL RGRL LESKCYQITV TLVFATGPGG SESLKAYLKQ AAPARGPTVR TKKVGKNEAV LAWDQIPVDD QNGFIRNYSI SYRTSV GKE MVVHVDSSHT EYTLSSLSSD TLYMVRMAAY TDEGGKDGPE FTFTTPKFAQ GEIEAIVVPV CLAFLLTTLL GVLFCFN KR DLIKKHIWPN VPDPSKSHIA QWSPHTPPRH NFNSKDQMYS DGNFTDVSVV EIEANNKKPC PDDLKSVDLF KKEKVSTE G HSSGIGGSSC MSSSRPSISS NEENESAQST ASTVQYSTVV HSGYRHQVPS VQVFSRSEST QPLLDSEERP EDLQLVDSV DGGDEILPRQ PYFKQNCSQP EACPEISHFE RSNQVLSGNE EDFVRLKQQQ VSDHISQPYG SEQRRLFQEG STADALGTGA DGQMERFES VGMETTIDEE IPKSYLPQTV RQGGYMPQ UniProtKB: Interleukin-6 receptor subunit beta |
-Macromolecule #2: Interleukin-6
Macromolecule | Name: Interleukin-6 / 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: 23.743189 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MNSFSTSAFG PVAFSLGLLL VLPAAFPAPV PPGEDSKDVA APHRQPLTSS ERIDKQIRYI LDGISALRKE TCNKSNMCES SKEALAENN LNLPKMAEKD GCFQSGFNEE TCLVKIITGL LEFEVYLEYL QNRFESSEEQ ARAVQMSTKV LIQFLQKKAK N LDAITTPD ...String: MNSFSTSAFG PVAFSLGLLL VLPAAFPAPV PPGEDSKDVA APHRQPLTSS ERIDKQIRYI LDGISALRKE TCNKSNMCES SKEALAENN LNLPKMAEKD GCFQSGFNEE TCLVKIITGL LEFEVYLEYL QNRFESSEEQ ARAVQMSTKV LIQFLQKKAK N LDAITTPD PTTNASLLTK LQAQNQWLQD MTTHLILRSF KEFLQSSLRA LRQM UniProtKB: Interleukin-6 |
-Macromolecule #3: Interleukin-6 receptor subunit alpha
Macromolecule | Name: Interleukin-6 receptor subunit alpha / 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: 51.605348 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MLAVGCALLA ALLAAPGAAL APRRCPAQEV ARGVLTSLPG DSVTLTCPGV EPEDNATVHW VLRKPAAGSH PSRWAGMGRR LLLRSVQLH DSGNYSCYRA GRPAGTVHLL VDVPPEEPQL SCFRKSPLSN VVCEWGPRST PSLTTKAVLL VRKFQNSPAE D FQEPCQYS ...String: MLAVGCALLA ALLAAPGAAL APRRCPAQEV ARGVLTSLPG DSVTLTCPGV EPEDNATVHW VLRKPAAGSH PSRWAGMGRR LLLRSVQLH DSGNYSCYRA GRPAGTVHLL VDVPPEEPQL SCFRKSPLSN VVCEWGPRST PSLTTKAVLL VRKFQNSPAE D FQEPCQYS QESQKFSCQL AVPEGDSSFY IVSMCVASSV GSKFSKTQTF QGCGILQPDP PANITVTAVA RNPRWLSVTW QD PHSWNSS FYRLRFELRY RAERSKTFTT WMVKDLQHHC VIHDAWSGLR HVVQLRAQEE FGQGEWSEWS PEAMGTPWTE SRS PPAENE VSTPMQALTT NKDDDNILFR DSANATSLPV QDSSSVPLPT FLVAGGSLAF GTLLCIAIVL RFKKTWKLRA LKEG KTSMH PPYSLGQLVP ERPRPTPVLV PLISPPVSPS SLGSDNTSSH NRPDARDPRS PYDISNTDYF FPR UniProtKB: Interleukin-6 receptor subunit alpha |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 2 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / 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 / Nominal defocus max: 2.25 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |