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Yorodumi- PDB-8ps0: Cryo-EM structure of Sodium proton exchanger NhaA with bound card... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ps0 | ||||||
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Title | Cryo-EM structure of Sodium proton exchanger NhaA with bound cardiolipin | ||||||
Components | Na(+)/H(+) antiporter NhaA | ||||||
Keywords | TRANSPORT PROTEIN / Sodium proton exchanger / Cardiolipin / NhaA | ||||||
Function / homology | Na+/H+ antiporter NhaA / Na+/H+ antiporter domain superfamily / Na+/H+ antiporter 1 / sodium ion transmembrane transporter activity / regulation of pH / antiporter activity / plasma membrane / CARDIOLIPIN / Na(+)/H(+) antiporter NhaA Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.37 Å | ||||||
Authors | Gulati, A. / Meier, P. / Kokane, S. / Drew, D. | ||||||
Funding support | European Union, 1items
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Citation | Journal: To Be Published Title: Cryo-EM structure of Sodium proton exchanger NhaA with bound cardiolipin Authors: Kokane, S. / Meier, P. / Gulati, A. / Matsuoka, R. / Pipatpolkai, T. / Delemotte, L. / Drew, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ps0.cif.gz | 185.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ps0.ent.gz | 117.9 KB | Display | PDB format |
PDBx/mmJSON format | 8ps0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ps0_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8ps0_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8ps0_validation.xml.gz | 41.4 KB | Display | |
Data in CIF | 8ps0_validation.cif.gz | 57.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ps/8ps0 ftp://data.pdbj.org/pub/pdb/validation_reports/ps/8ps0 | HTTPS FTP |
-Related structure data
Related structure data | 17841MC 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
#1: Protein | Mass: 42304.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: nhaA, nahA, BLM69_005044, BvCmsKKP061_01067, EL79_3853, JNP96_04275, WR15_27505 Production host: Escherichia coli (E. coli) / References: UniProt: Q53YW7 #2: Chemical | 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 | Name: NhaA dimer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | 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: 600 nm |
Image recording | Electron dose: 68.11 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 78917 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 95.47 Å2 | ||||||||||||||||||||||||
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