+Open data
-Basic information
Entry | Database: PDB / ID: 8sgi | ||||||||||||
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Title | Cryo-EM structure of human NCX1 in complex with SEA0400 | ||||||||||||
Components |
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Keywords | TRANSPORT PROTEIN / Na/Ca exchanger / sodium calcium exchanger | ||||||||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||||||||
Authors | Xue, J. / Jiang, Y. | ||||||||||||
Funding support | United States, 3items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8sgi.cif.gz | 196.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8sgi.ent.gz | 146.3 KB | Display | PDB format |
PDBx/mmJSON format | 8sgi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8sgi_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8sgi_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8sgi_validation.xml.gz | 45 KB | Display | |
Data in CIF | 8sgi_validation.cif.gz | 65.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sg/8sgi ftp://data.pdbj.org/pub/pdb/validation_reports/sg/8sgi | HTTPS FTP |
-Related structure data
Related structure data | 40456MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 109181.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SLC8A1, CNC, NCX1 / Production host: Homo sapiens (human) / References: UniProt: P32418 |
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-Antibody , 2 types, 2 molecules LH
#2: Antibody | Mass: 21740.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
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#3: Antibody | Mass: 26435.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
-Non-polymers , 4 types, 11 molecules
#4: Chemical | ChemComp-EKY / | ||||
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#5: Chemical | ChemComp-CA / #6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Source (natural) |
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Source (recombinant) | Organism: Homo sapiens (human) | ||||||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 368227 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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