+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34906 | |||||||||
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Title | Cryo-EM structure of AdTx1-alpha1AAR-Nb6 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Toxin / alpha1AAR / GPCR / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information negative regulation of heart rate involved in baroreceptor response to increased systemic arterial blood pressure / alpha1-adrenergic receptor activity / positive regulation of the force of heart contraction by epinephrine-norepinephrine / norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure / pilomotor reflex / positive regulation of heart rate by epinephrine-norepinephrine / neuron-glial cell signaling / cell growth involved in cardiac muscle cell development / positive regulation of protein kinase C signaling / positive regulation of action potential ...negative regulation of heart rate involved in baroreceptor response to increased systemic arterial blood pressure / alpha1-adrenergic receptor activity / positive regulation of the force of heart contraction by epinephrine-norepinephrine / norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure / pilomotor reflex / positive regulation of heart rate by epinephrine-norepinephrine / neuron-glial cell signaling / cell growth involved in cardiac muscle cell development / positive regulation of protein kinase C signaling / positive regulation of action potential / : / positive regulation of smooth muscle contraction / adult heart development / Adrenoceptors / calcium ion transport into cytosol / positive regulation of cardiac muscle hypertrophy / adenylate cyclase-activating adrenergic receptor signaling pathway / smooth muscle contraction / positive regulation of vasoconstriction / positive regulation of cardiac muscle contraction / response to hormone / negative regulation of autophagy / positive regulation of synaptic transmission, GABAergic / caveola / MAPK cascade / G alpha (12/13) signalling events / cell-cell signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / toxin activity / positive regulation of cytosolic calcium ion concentration / G alpha (q) signalling events / nuclear membrane / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / intracellular signal transduction / response to xenobiotic stimulus / G protein-coupled receptor signaling pathway / protein heterodimerization activity / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / apoptotic process / signal transduction / extracellular region / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Dendroaspis angusticeps (eastern green mamba) / Lama glama (llama) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Liu X / Shi M | |||||||||
Funding support | China, 2 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of AdTx1-alpha1AAR-Nb6 Authors: Liu X / Shi M | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34906.map.gz | 25.4 MB | EMDB map data format | |
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Header (meta data) | emd-34906-v30.xml emd-34906.xml | 14.7 KB 14.7 KB | Display Display | EMDB header |
Images | emd_34906.png | 35.3 KB | ||
Filedesc metadata | emd-34906.cif.gz | 5.3 KB | ||
Others | emd_34906_half_map_1.map.gz emd_34906_half_map_2.map.gz | 25 MB 25 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34906 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34906 | HTTPS FTP |
-Validation report
Summary document | emd_34906_validation.pdf.gz | 717.1 KB | Display | EMDB validaton report |
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Full document | emd_34906_full_validation.pdf.gz | 716.7 KB | Display | |
Data in XML | emd_34906_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | emd_34906_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34906 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34906 | HTTPS FTP |
-Related structure data
Related structure data | 8hn1MC 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_34906.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0825 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_34906_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34906_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of AdTx1-alpha1AAR-Nb6
Entire | Name: Complex of AdTx1-alpha1AAR-Nb6 |
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Components |
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-Supramolecule #1: Complex of AdTx1-alpha1AAR-Nb6
Supramolecule | Name: Complex of AdTx1-alpha1AAR-Nb6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 100 KDa |
-Macromolecule #1: Toxin AdTx1
Macromolecule | Name: Toxin AdTx1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Dendroaspis angusticeps (eastern green mamba) |
Molecular weight | Theoretical: 7.743749 KDa |
Recombinant expression | Organism: Trichoplusia (butterflies/moths) |
Sequence | String: GPGSGSLTCV TSKSIFGITT EDCPDGQNLC FKRRHYVVPK IYDSTRGCAA TCPIPENYDS IHCCKTDKCN E UniProtKB: Toxin AdTx1 |
-Macromolecule #2: Alpha-1A adrenergic receptor
Macromolecule | Name: Alpha-1A adrenergic receptor / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 38.825605 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: DYKDDDDAMV FLSGQASDSS QCTQPPAPVQ ISKAILLGVI LGGLILFGVL GNILVILSVA CHRHLHSVTH YYIVNLAVAD LLLTSTVLP FSAIFEVLGY WAFGRVFCNI WAAVDVLCCT ARIWGLCIIS IDRYIGVSYP LRYPTIVTQR RGLMALLCVW A LSLVISIG ...String: DYKDDDDAMV FLSGQASDSS QCTQPPAPVQ ISKAILLGVI LGGLILFGVL GNILVILSVA CHRHLHSVTH YYIVNLAVAD LLLTSTVLP FSAIFEVLGY WAFGRVFCNI WAAVDVLCCT ARIWGLCIIS IDRYIGVSYP LRYPTIVTQR RGLMALLCVW A LSLVISIG PLFGWRQPAP EDETICQINE EPGYVLFSAL GSFYLPLAII LVMYCRVYVV AKRVRLLSGS REKDRNLRKA AK TLGIVVG CFVLCWLPFF LVMPIGSFFP DFKPSETVFK IVFWLGYLNS CINPIIYPCS SQEFKKAFQN VLRIQCLCRK QSS KHALGY TLHPPSQAVE GQHHHHHHHH UniProtKB: Alpha-1A adrenergic receptor |
-Macromolecule #3: Nb6
Macromolecule | Name: Nb6 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Lama glama (llama) |
Molecular weight | Theoretical: 14.730255 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MAQVQLQESG GGLVQAGESL RLSCAASGTI FRLYDMGWYR RVSGNQRELV ASITSGGSTK YGDSVKGRFT ISRDNAKNTV YLQMSSLKP EDTAVYYCNA EYRTGIWEEL LDGWGQGTQV TVSSHHHHHH EPEA |
-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 | 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: 1.8 µm / Nominal defocus min: 1.3 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 616710 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |