+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41883 | ||||||||||||
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Title | Structure of the HER4/NRG1b Homodimer Extracellular Domain | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | Receptor Tyrosine Kinase / MEMBRANE PROTEIN / TRANSFERASE | ||||||||||||
Function / homology | Function and homology information ERBB3 signaling pathway / positive regulation of peptidyl-tyrosine autophosphorylation / sequestering of metal ion / establishment of planar polarity involved in nephron morphogenesis / ERBB4 signaling pathway / epidermal growth factor receptor activity / ERBB4-ERBB4 signaling pathway / olfactory bulb interneuron differentiation / central nervous system morphogenesis / ventricular cardiac muscle cell differentiation ...ERBB3 signaling pathway / positive regulation of peptidyl-tyrosine autophosphorylation / sequestering of metal ion / establishment of planar polarity involved in nephron morphogenesis / ERBB4 signaling pathway / epidermal growth factor receptor activity / ERBB4-ERBB4 signaling pathway / olfactory bulb interneuron differentiation / central nervous system morphogenesis / ventricular cardiac muscle cell differentiation / positive regulation of striated muscle cell differentiation / neuregulin receptor activity / negative regulation of secretion / cardiac muscle tissue regeneration / endocardial cell differentiation / animal organ development / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / mitochondrial fragmentation involved in apoptotic process / neural crest cell development / ERBB2 Activates PTK6 Signaling / cardiac muscle cell myoblast differentiation / cell communication / protein tyrosine kinase activator activity / GABA receptor binding / transmembrane receptor protein tyrosine kinase activator activity / PI3K events in ERBB4 signaling / mammary gland epithelial cell differentiation / cardiac muscle cell differentiation / embryonic pattern specification / Signaling by ERBB4 / mammary gland development / chemorepellent activity / ventricular trabecula myocardium morphogenesis / positive regulation of protein localization to cell surface / ErbB-3 class receptor binding / ERBB2 Regulates Cell Motility / regulation of postsynaptic neurotransmitter receptor internalization / PI3K events in ERBB2 signaling / activation of transmembrane receptor protein tyrosine kinase activity / neural crest cell migration / ERBB signaling pathway / neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of cardiac muscle cell apoptotic process / epidermal growth factor receptor binding / cell fate commitment / ERBB2-ERBB3 signaling pathway / cell surface receptor signaling pathway via JAK-STAT / Long-term potentiation / cellular response to epidermal growth factor stimulus / Signaling by ERBB2 / positive regulation of cell adhesion / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / SHC1 events in ERBB4 signaling / GABA-ergic synapse / mammary gland alveolus development / GRB2 events in ERBB2 signaling / transmembrane receptor protein tyrosine kinase activity / neurogenesis / SHC1 events in ERBB2 signaling / basal plasma membrane / Nuclear signaling by ERBB4 / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of cardiac muscle cell proliferation / transcription coregulator activity / cell surface receptor protein tyrosine kinase signaling pathway / synapse assembly / Downregulation of ERBB4 signaling / lactation / regulation of cell migration / activation of protein kinase B activity / Downregulation of ERBB2:ERBB3 signaling / Signaling by ERBB2 TMD/JMD mutants / cytokine activity / Signaling by ERBB2 KD Mutants / receptor protein-tyrosine kinase / Downregulation of ERBB2 signaling / positive regulation of receptor signaling pathway via JAK-STAT / postsynaptic density membrane / growth factor activity / wound healing / positive regulation of protein-containing complex assembly / neuromuscular junction / peptidyl-tyrosine phosphorylation / receptor tyrosine kinase binding / Constitutive Signaling by Aberrant PI3K in Cancer / integrin binding / PIP3 activates AKT signaling / cell migration / nervous system development / presynaptic membrane / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / heart development / RAF/MAP kinase cascade / positive regulation of cell growth / basolateral plasma membrane / protein tyrosine kinase activity / postsynaptic membrane / Estrogen-dependent gene expression / protein autophosphorylation Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.38 Å | ||||||||||||
Authors | Trenker R / Diwanji D / Bingham T / Verba KA / Jura N | ||||||||||||
Funding support | Germany, United States, 3 items
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Citation | Journal: To Be Published Title: Structure of the HER2/HER4/NRG1b Heterodimer Extracellular Domain Authors: Trenker R / Diwanji D / Bingham T / Verba KA / Jura N | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41883.map.gz | 204.1 MB | EMDB map data format | |
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Header (meta data) | emd-41883-v30.xml emd-41883.xml | 18.2 KB 18.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41883_fsc.xml | 13.4 KB | Display | FSC data file |
Images | emd_41883.png | 49.2 KB | ||
Masks | emd_41883_msk_1.map | 216 MB | Mask map | |
Filedesc metadata | emd-41883.cif.gz | 6.6 KB | ||
Others | emd_41883_half_map_1.map.gz emd_41883_half_map_2.map.gz | 200.4 MB 200.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41883 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41883 | HTTPS FTP |
-Validation report
Summary document | emd_41883_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_41883_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_41883_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | emd_41883_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41883 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41883 | HTTPS FTP |
-Related structure data
Related structure data | 8u4iMC 8u4lC C: citing same article (ref.) M: atomic model generated by this map |
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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_41883.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.835 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_41883_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_41883_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41883_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : HER4/NRG1b homodimer
Entire | Name: HER4/NRG1b homodimer |
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Components |
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-Supramolecule #1: HER4/NRG1b homodimer
Supramolecule | Name: HER4/NRG1b homodimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Receptor tyrosine-protein kinase erbB-4
Macromolecule | Name: Receptor tyrosine-protein kinase erbB-4 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: receptor protein-tyrosine kinase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 68.07282 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QSVCAGTENK LSSLSDLEQQ YRALRKYYEN CEVVMGNLEI TSIEHNRDLS FLRSVREVTG YVLVALNQFR YLPLENLRII RGTKLYEDR YALAIFLNYR KDGNFGLQEL GLKNLTEILN GGVYVDQNKF LCYADTIHWQ DIVRNPWPSN LTLVSTNGSS G CGRCHKSC ...String: QSVCAGTENK LSSLSDLEQQ YRALRKYYEN CEVVMGNLEI TSIEHNRDLS FLRSVREVTG YVLVALNQFR YLPLENLRII RGTKLYEDR YALAIFLNYR KDGNFGLQEL GLKNLTEILN GGVYVDQNKF LCYADTIHWQ DIVRNPWPSN LTLVSTNGSS G CGRCHKSC TGRCWGPTEN HCQTLTRTVC AEQCDGRCYG PYVSDCCHRE CAGGCSGPKD TDCFACMNFN DSGACVTQCP QT FVYNPTT FQLEHNFNAK YTYGAFCVKK CPHNFVVDSS SCVRACPSSK MEVEENGIKM CKPCTDICPK ACDGIGTGSL MSA QTVDSS NIDKFINCTK INGNLIFLVT GIHGDPYNAI EAIDPEKLNV FRTVREITGF LNIQSWPPNM TDFSVFSNLV TIGG RVLYS GLSLLILKQQ GITSLQFQSL KEISAGNIYI TDNSNLCYYH TINWTTLFST INQRIVIRDN RKAENCTAEG MVCNH LCSS DGCWGPGPDQ CLSCRRFSRG RICIESCNLY DGEFREFENG SICVECDPQC EKMEDGLLTC HGPGPDNCTK CSHFKD GPN CVEKCPDGLQ GANSFIFKYA DPDRECHPCH PNCTQGCNGP TSHDCIY UniProtKB: Receptor tyrosine-protein kinase erbB-4 |
-Macromolecule #2: Isoform 6 of Pro-neuregulin-1, membrane-bound isoform
Macromolecule | Name: Isoform 6 of Pro-neuregulin-1, membrane-bound isoform / 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: 5.890792 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SHLVKCAEKE KTFCVNGGEC FMVKDLSNPS RYLCKCPNEF TGDRCQNYVM AS UniProtKB: Pro-neuregulin-1, membrane-bound isoform |
-Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / 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: 7.4 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Support film - Material: GRAPHENE OXIDE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average electron dose: 68.7 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: 2.0 µm / Nominal defocus min: 0.9 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |