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- PDB-9veb: Cryo-EM structure of the aspartate:alanine antiporter AspT mutant L60C -
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Open data
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Basic information
Entry | Database: PDB / ID: 9veb | |||||||||||||||||||||
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Title | Cryo-EM structure of the aspartate:alanine antiporter AspT mutant L60C | |||||||||||||||||||||
![]() | Aspartate/alanine antiporter | |||||||||||||||||||||
![]() | TRANSPORT PROTEIN / amino acid / antiporter / elevator mechanism | |||||||||||||||||||||
Function / homology | YidE/YbjL duplication / Aspartate-alanine antiporter / Predicted Permease Membrane Region / : / antiporter activity / identical protein binding / plasma membrane / Aspartate/alanine antiporter![]() | |||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.56 Å | |||||||||||||||||||||
![]() | Nanatani, K. / Kanno, R. / Kawabata, T. / Watanabe, S. / Hidaka, M. / Yamanaka, T. / Toda, K. / Fujiki, T. / Kunii, K. / Miyamoto, A. ...Nanatani, K. / Kanno, R. / Kawabata, T. / Watanabe, S. / Hidaka, M. / Yamanaka, T. / Toda, K. / Fujiki, T. / Kunii, K. / Miyamoto, A. / Chiba, F. / Ogasawara, S. / Murata, T. / Humbel, B.M. / Inaba, K. / Mitsuoka, K. / Guan, L. / Abe, K. / Yamamoto, M. / Koshiba, S. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure and molecular mechanism of the aspartate:alanine antiporter AspT from Tetragenococcus halophilus Authors: Nanatani, K. / Kanno, R. / Kawabata, T. / Watanabe, S. / Hidaka, M. / Yamanaka, T. / Toda, K. / Fujiki, T. / Kunii, K. / Miyamoto, A. / Chiba, F. / Ogasawara, S. / Murata, T. / Humbel, B.M. ...Authors: Nanatani, K. / Kanno, R. / Kawabata, T. / Watanabe, S. / Hidaka, M. / Yamanaka, T. / Toda, K. / Fujiki, T. / Kunii, K. / Miyamoto, A. / Chiba, F. / Ogasawara, S. / Murata, T. / Humbel, B.M. / Inaba, K. / Mitsuoka, K. / Guan, L. / Abe, K. / Yamamoto, M. / Koshiba, S. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 205.8 KB | Display | ![]() |
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PDB format | ![]() | 162.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 37.6 KB | Display | |
Data in CIF | ![]() | 55.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 64996MC ![]() 8xw5C ![]() 8y1xC ![]() 9vdcC C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 57977.789 Da / Num. of mol.: 2 / Mutation: L60C Source method: isolated from a genetically manipulated source Details: A purification His-tag (Hisx6) was inserted between L331 and K332; however, this His-tag was not observed in the current map and is not included in the model. Source: (gene. exp.) ![]() ![]() ![]() Has protein modification | 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 |
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Sample preparation
Component | Name: aspartate:alanine antiporter AspT mutant - L60C / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.0579 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: ![]() | ||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||||||
Buffer solution | pH: 6 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 6.14 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 300 |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 6000 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||
Particle selection | Num. of particles selected: 1634276 | |||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | |||||||||||||||||||||
3D reconstruction | Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 250605 / Algorithm: FOURIER SPACE / Symmetry type: POINT | |||||||||||||||||||||
Atomic model building | Protocol: BACKBONE TRACE / Space: REAL | |||||||||||||||||||||
Atomic model building | Source name: AlphaFold / Type: in silico model | |||||||||||||||||||||
Refinement | Highest resolution: 3.56 Å |