+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40456 | ||||||||||||
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Title | Cryo-EM structure of human NCX1 in complex with SEA0400 | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | Na/Ca exchanger / sodium calcium exchanger / TRANSPORT PROTEIN | ||||||||||||
Function / homology | Function and homology information relaxation of smooth muscle / vascular associated smooth muscle contraction / calcium ion export / regulation of cell communication by electrical coupling / calcium:sodium antiporter activity / regulation of the force of heart contraction / membrane depolarization during cardiac muscle cell action potential / sodium ion export across plasma membrane / cell communication by electrical coupling involved in cardiac conduction / negative regulation of protein serine/threonine kinase activity ...relaxation of smooth muscle / vascular associated smooth muscle contraction / calcium ion export / regulation of cell communication by electrical coupling / calcium:sodium antiporter activity / regulation of the force of heart contraction / membrane depolarization during cardiac muscle cell action potential / sodium ion export across plasma membrane / cell communication by electrical coupling involved in cardiac conduction / negative regulation of protein serine/threonine kinase activity / sodium ion import across plasma membrane / intracellular sodium ion homeostasis / regulation of cardiac muscle contraction by calcium ion signaling / calcium ion transport into cytosol / calcium ion import / cardiac muscle cell development / relaxation of cardiac muscle / Sodium/Calcium exchangers / Reduction of cytosolic Ca++ levels / calcium ion transmembrane import into cytosol / ankyrin binding / negative regulation of cytosolic calcium ion concentration / calcium ion import across plasma membrane / cellular response to caffeine / positive regulation of the force of heart contraction / intercalated disc / regulation of cardiac conduction / sodium ion transmembrane transport / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / positive regulation of bone mineralization / calcium ion homeostasis / cardiac muscle contraction / Ion homeostasis / monoatomic ion transport / muscle contraction / axon terminus / T-tubule / cytoskeletal protein binding / response to muscle stretch / regulation of heart rate / cell periphery / calcium ion transmembrane transport / sarcolemma / Z disc / intracellular calcium ion homeostasis / cellular response to reactive oxygen species / regulation of gene expression / transmembrane transporter binding / postsynapse / postsynaptic density / calmodulin binding / axon / neuronal cell body / dendrite / calcium ion binding / synapse / nucleoplasm / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) / Mus musculus (house mouse) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||||||||
Authors | Xue J / Jiang Y | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: To Be Published Title: Structural mechanisms of human cardiac sodium calcium exchanger NCX1 Authors: Xue J / Han Y / Zeng W / Jiang Y | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40456.map.gz | 167.8 MB | EMDB map data format | |
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Header (meta data) | emd-40456-v30.xml emd-40456.xml | 24.5 KB 24.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40456_fsc.xml | 11.9 KB | Display | FSC data file |
Images | emd_40456.png | 96.6 KB | ||
Filedesc metadata | emd-40456.cif.gz | 6.9 KB | ||
Others | emd_40456_additional_1.map.gz emd_40456_additional_2.map.gz emd_40456_additional_3.map.gz emd_40456_half_map_1.map.gz emd_40456_half_map_2.map.gz | 167.9 MB 167.8 MB 167.9 MB 165 MB 165 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40456 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40456 | HTTPS FTP |
-Validation report
Summary document | emd_40456_validation.pdf.gz | 920.5 KB | Display | EMDB validaton report |
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Full document | emd_40456_full_validation.pdf.gz | 920.1 KB | Display | |
Data in XML | emd_40456_validation.xml.gz | 20.2 KB | Display | |
Data in CIF | emd_40456_validation.cif.gz | 25.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40456 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40456 | HTTPS FTP |
-Related structure data
Related structure data | 8sgiMC 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_40456.map.gz / Format: CCP4 / Size: 178 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: 0.83 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: focused TM map2 of NCX1 in complex with SEA0400
File | emd_40456_additional_1.map | ||||||||||||
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Annotation | focused TM map2 of NCX1 in complex with SEA0400 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: focused TM map1 of NCX1 in complex with SEA0400
File | emd_40456_additional_2.map | ||||||||||||
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Annotation | focused TM map1 of NCX1 in complex with SEA0400 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: focused CBD map of NCX1 in complex with SEA0400
File | emd_40456_additional_3.map | ||||||||||||
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Annotation | focused CBD map of NCX1 in complex with SEA0400 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_40456_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_40456_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : human NCX1-SEA0400 in complex with antibody Fab fragment
+Supramolecule #1: human NCX1-SEA0400 in complex with antibody Fab fragment
+Supramolecule #2: human cardiac sodium calcium exchanger NCX1 in complex with SEA0400
+Supramolecule #3: antibody Fab fragment
+Macromolecule #1: Sodium/calcium exchanger 1
+Macromolecule #2: Fab light chain
+Macromolecule #3: Fab heavy chain
+Macromolecule #4: 2-{4-[(2,5-difluorophenyl)methoxy]phenoxy}-5-ethoxyaniline
+Macromolecule #5: CALCIUM ION
+Macromolecule #6: SODIUM ION
+Macromolecule #7: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 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: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |