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- EMDB-64982: Cryo-EM structure of the aspartate:alanine antiporter AspT WT -

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Basic information

Entry
Database: EMDB / ID: EMD-64982
TitleCryo-EM structure of the aspartate:alanine antiporter AspT WT
Map datacomposite map
Sample
  • Organelle or cellular component: aspartate:alanine antiporter AspT
    • Protein or peptide: Aspartate/alanine antiporter
  • Ligand: ASPARTIC ACID
Keywordsamino acid / antiporter / elevator mechanism / TRANSPORT PROTEIN
Function / homologyYidE/YbjL duplication / Aspartate-alanine antiporter / Predicted Permease Membrane Region / : / antiporter activity / identical protein binding / plasma membrane / Aspartate/alanine antiporter
Function and homology information
Biological speciesTetragenococcus halophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsNanatani 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 BM / Inaba K / Mitsuoka K / Guan L / Abe K / Yamamoto M / Koshiba S
Funding support Japan, 5 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16K07653 Japan
Japan Society for the Promotion of Science (JSPS)20K05779 Japan
Japan Society for the Promotion of Science (JSPS)23K05004 Japan
Japan Agency for Medical Research and Development (AMED)JP23ama121019 Japan
Japan Agency for Medical Research and Development (AMED)JP23ama121038 Japan
CitationJournal: To Be Published
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 BM / Inaba K / Mitsuoka K / Guan ...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 BM / Inaba K / Mitsuoka K / Guan L / Abe K / Yamamoto M / Koshiba S
History
DepositionJun 8, 2025-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64982.png

Downloads & links

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Map

FileDownload / File: emd_64982.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 256 pix.
= 216.32 Å		0.85 Å/pix.
x 256 pix.
= 216.32 Å		0.85 Å/pix.
x 256 pix.
= 216.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.845 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.621
Minimum - Maximum-1.0844994 - 3.0795913
Average (Standard dev.)0.019693773 (±0.07984242)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 216.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : aspartate:alanine antiporter AspT

EntireName: aspartate:alanine antiporter AspT
Components
  • Organelle or cellular component: aspartate:alanine antiporter AspT
    • Protein or peptide: Aspartate/alanine antiporter
  • Ligand: ASPARTIC ACID

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Supramolecule #1: aspartate:alanine antiporter AspT

SupramoleculeName: aspartate:alanine antiporter AspT / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Tetragenococcus halophilus (bacteria) / Strain: D10
Molecular weightTheoretical: 58 KDa

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Macromolecule #1: Aspartate/alanine antiporter

MacromoleculeName: Aspartate/alanine antiporter / type: protein_or_peptide / ID: 1
Details: The purification His-tag (Hisx6) is inserted at L331 and K332; however, this His-tag is not visible in the current map and is therefore not included in the model.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Tetragenococcus halophilus (bacteria) / Strain: D10
Molecular weightTheoretical: 58.084 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MNAIGNFLVG TPVFTIFICL ALGYLLGKLK IGSFTLGATV GVLIVALLIG QLGVFPRDTL LGDIFFDFFM FAIGYRVGPS FISSMKKFG AKIVYATLIF LVSAFIVAYA CFKMFHIGPG IAAGIIAGGL TQSAVIGSSL ETISKLPISD HLKTLYSNQI P IVYTLTYV ...String:
MNAIGNFLVG TPVFTIFICL ALGYLLGKLK IGSFTLGATV GVLIVALLIG QLGVFPRDTL LGDIFFDFFM FAIGYRVGPS FISSMKKFG AKIVYATLIF LVSAFIVAYA CFKMFHIGPG IAAGIIAGGL TQSAVIGSSL ETISKLPISD HLKTLYSNQI P IVYTLTYV FGTIGVLIFL RDIMPKLMHI DLKKQAVKTA KELDMIPVPV IVASTHFYTI NDGSSLIGQT LGTVNTKFAK GL VAAGLND SADMASVINA GDVLAISGGI DEIGRAVQEF NLLEVTGKTK AYVSKQVVLK KNFSADVLKN AQDKGVLVAT LAG DVMDPA QFSTLHHHHH HKPAESVTLV GQKDAVSEVQ SQLGRLRAAE NIINYSWFAL GIALSAALGI VGTKVSGVPI ALGG GTASL IVGLVQSIYR DKHAHMDTIP DSLLEFFQSI GLNLFIATVG LSAAKTFISA IQSMGISVLL IGAVISILPH IITFV ICYY LMKMEPISII GAQTGADTLS AALNDVSERV GSDASPFFAA AVAPAYAIGN IFLTLMGPIF IVLLS

UniProtKB: Aspartate/alanine antiporter

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Macromolecule #2: ASPARTIC ACID

MacromoleculeName: ASPARTIC ACID / type: ligand / ID: 2 / Number of copies: 2 / Formula: ASP
Molecular weightTheoretical: 133.103 Da
Chemical component information

ChemComp-ASP:
ASPARTIC ACID

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.83 mg/mL
BufferpH: 6
Component:
ConcentrationFormulaName
20.0 mMC6H13NO4S2-(N-morpholino)ethanesulfonic acid
100.0 mMNaClsodium chloride
0.003 %C47H88O22Lauryl maltose neopentyl glycol
100.0 mMC4H7NO4L-aspartic acid
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 8 / Number real images: 12357 / Average exposure time: 30.6 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 96000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1636712
CTF correctionSoftware - Name: RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 125465
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: BACKBONE TRACE
Output model

PDB-9vdc:
Cryo-EM structure of the aspartate:alanine antiporter AspT WT

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