+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18741 | |||||||||||||||
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Title | Structure of interleukin 11 (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 / interleukin-11 receptor binding / IL-6-type cytokine receptor ligand interactions / leukemia inhibitory factor receptor activity / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / Interleukin-27 signaling / triglyceride mobilization / Interleukin-6 signaling / Interleukin-35 Signalling ...oncostatin-M receptor activity / interleukin-11 receptor binding / IL-6-type cytokine receptor ligand interactions / leukemia inhibitory factor receptor activity / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / Interleukin-27 signaling / triglyceride mobilization / Interleukin-6 signaling / Interleukin-35 Signalling / oncostatin-M receptor complex / ciliary neurotrophic factor receptor binding / interleukin-11 receptor activity / interleukin-11 binding / interleukin-6 receptor activity / interleukin-6 binding / ciliary neurotrophic factor receptor complex / interleukin-27-mediated signaling pathway / interleukin-6 receptor complex / head development / megakaryocyte differentiation / negative regulation of hormone secretion / regulation of Notch signaling pathway / interleukin-6 receptor binding / interleukin-11-mediated signaling pathway / developmental process / positive regulation of astrocyte differentiation / intestinal epithelial cell development / IL-6-type cytokine receptor ligand interactions / cytokine receptor activity / glycogen metabolic process / interleukin-6-mediated signaling pathway / neuronal cell body membrane / positive regulation of Notch signaling pathway / negative regulation of cytosolic calcium ion concentration / protein tyrosine kinase activator activity / positive regulation of smooth muscle cell migration / fat cell differentiation / cytokine binding / positive regulation of osteoblast differentiation / coreceptor activity / positive regulation of T cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / B cell differentiation / cytokine activity / growth factor activity / cytokine-mediated signaling pathway / transmembrane signaling receptor activity / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of peptidyl-serine phosphorylation / cell body / scaffold protein binding / negative regulation of neuron apoptotic process / cell population proliferation / positive regulation of MAPK cascade / receptor complex / membrane raft / external side of plasma membrane / neuronal cell body / dendrite / positive regulation of cell population proliferation / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) / Mus musculus (house mouse) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.06 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_18741.map.gz | 323.9 MB | EMDB map data format | |
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Header (meta data) | emd-18741-v30.xml emd-18741.xml | 24.1 KB 24.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18741_fsc.xml | 14.8 KB | Display | FSC data file |
Images | emd_18741.png | 130.4 KB | ||
Masks | emd_18741_msk_1.map | 343 MB | Mask map | |
Filedesc metadata | emd-18741.cif.gz | 7.3 KB | ||
Others | emd_18741_additional_1.map.gz emd_18741_additional_2.map.gz emd_18741_half_map_1.map.gz emd_18741_half_map_2.map.gz | 171.6 MB 3.8 MB 317.8 MB 317.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18741 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18741 | HTTPS FTP |
-Validation report
Summary document | emd_18741_validation.pdf.gz | 748.5 KB | Display | EMDB validaton report |
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Full document | emd_18741_full_validation.pdf.gz | 748.1 KB | Display | |
Data in XML | emd_18741_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | emd_18741_validation.cif.gz | 30.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18741 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18741 | HTTPS FTP |
-Related structure data
Related structure data | 8qy4MC 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_18741.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_18741_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map.
File | emd_18741_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_18741_additional_2.map | ||||||||||||
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Annotation | Locally filtered map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1.
File | emd_18741_half_map_1.map | ||||||||||||
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Annotation | Half map 1. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2.
File | emd_18741_half_map_2.map | ||||||||||||
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Annotation | Half map 2. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : IL-11 signalling complex
Entire | Name: IL-11 signalling complex |
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Components |
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-Supramolecule #1: IL-11 signalling complex
Supramolecule | Name: IL-11 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-11
Macromolecule | Name: Interleukin-11 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 21.455186 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MNCVCRLVLV VLSLWPDTAV APGPPPGPPR VSPDPRAELD STVLLTRSLL ADTRQLAAQL RDKFPADGDH NLDSLPTLAM SAGALGALQ LPGVLTRLRA DLLSYLRHVQ WLRRAGGSSL KTLEPELGTL QARLDRLLRR LQLLMSRLAL PQPPPDPPAP P LAPPSSAW ...String: MNCVCRLVLV VLSLWPDTAV APGPPPGPPR VSPDPRAELD STVLLTRSLL ADTRQLAAQL RDKFPADGDH NLDSLPTLAM SAGALGALQ LPGVLTRLRA DLLSYLRHVQ WLRRAGGSSL KTLEPELGTL QARLDRLLRR LQLLMSRLAL PQPPPDPPAP P LAPPSSAW GGIRAAHAIL GGLHLTLDWA VRGLLLLKTR L UniProtKB: Interleukin-11 |
-Macromolecule #2: Interleukin-6 receptor subunit beta
Macromolecule | Name: Interleukin-6 receptor subunit beta / 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: 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 #3: Interleukin-11 receptor subunit alpha
Macromolecule | Name: Interleukin-11 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: 45.266156 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MSSSCSGLSR VLVAVATALV SASSPCPQAW GPPGVQYGQP GRSVKLCCPG VTAGDPVSWF RDGEPKLLQG PDSGLGHELV LAQADSTDE GTYICQTLDG ALGGTVTLQL GYPPARPVVS CQAADYENFS CTWSPSQISG LPTRYLTSYR KKTVLGADSQ R RSPSTGPW ...String: MSSSCSGLSR VLVAVATALV SASSPCPQAW GPPGVQYGQP GRSVKLCCPG VTAGDPVSWF RDGEPKLLQG PDSGLGHELV LAQADSTDE GTYICQTLDG ALGGTVTLQL GYPPARPVVS CQAADYENFS CTWSPSQISG LPTRYLTSYR KKTVLGADSQ R RSPSTGPW PCPQDPLGAA RCVVHGAEFW SQYRINVTEV NPLGASTRLL DVSLQSILRP DPPQGLRVES VPGYPRRLRA SW TYPASWP CQPHFLLKFR LQYRPAQHPA WSTVEPAGLE EVITDAVAGL PHAVRVSARD FLDAGTWSTW SPEAWGTPST GTI PKEIPA WGQLHTQPEV EPQVDSPAPP RPSLQPHPRL LDHRDSVEQV AVLASLGILS FLGLVAGALA LGLWLRLRRG GKDG SPKPG FLASVIPVDR RPGAPNL UniProtKB: Interleukin-11 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: 10 / 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 |